IMPROVED GENE EDITING SYSTEMS UTILIZING TRANS RECRUITING COMPONENTS

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No. 63/417,119, filed October 18, 2022, U.S. Provisional Application No. 63/478,861, filed January’ 6, 2023, and U.S. Provisional Application No. 63/530,644, filed August 3, 2023. The contents of the aforementioned applications are hereby incorporated by reference in their entirety.

BACKGROUND

Integration of a nucleic acid of interest into a genome occurs at low frequency and with little site specificity, in the absence of a specialized protein to promote the insertion event. Some existing approaches, like CRISPR/Cas9, are more suited for small edits that rely on host repair pathways, and are less effective at integrating longer sequences. Other existing approaches, like Cre/loxP, require a first step of inserting a loxP site into the genome and then a second step of inserting a sequence of interest into the loxP site. There is a need in the art for improved compositions (c.g., proteins and nucleic acids) and methods for inserting, altering, or deleting sequences of interest in a genome.

SUMMARY OF THE INVENTION

This disclosure relates to novel compositions, systems and methods for altering a genome at one or more locations in a host cell, tissue or subject, in vivo or in vitro. In particular, the invention features compositions, systems and methods for inserting, altering, or deleting sequences of interest in a host genome.

As demonstrated in this disclosure, Applicants have discovered compositions and mechanisms for enabling editing sequences of interest in a host genome by delivering gene modifying polypeptide, or a polynucleotide encoding such polypeptide, in conjunction with separate RNA template elements, including a trans template RNA element. The present disclosure relates, in part, to association of a trans template RNA to a gene modifying poly peptide :sgRNA:target genomic DNA complex by two or more interactions. Without wishing to be bound by theory , it is has been found that such association by way of two or more interactions or points of anchoring can achieve high rewriting activity, e.g., for achieving single or several nucleotide long edits. As described herein, examples of two of more interactions include, for example. 1) an RRS (RBD recruitment site):RBD (RNA-binding domain) interaction, typically between the gene modifying polypeptide and the 3’ end of the trans template, and 2) a 5’ end block Cas9 scaffold and spacer to target DNA interaction (mediated via an additional gene modifying polypeptide). This configuration exemplifies exemplary interactions that together anchor a trans template RNA to a gene modifying polypeptide: sgRNA:target genomic DNA complex to enable rewriting. It is further contemplated that the presence of both an RRS:RBD interaction and a 5’ end block spacer can provide high rewriting activity and the presence of tire 5’ end block spacer rescues rewriting activity observed with a trans template having a weaker RRS:RBD interaction.

The present disclosure further relates, in part, to gene modifying systems designed to facilitate long edits (e.g., long insertions, e.g., insertions of greater than or equal to 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 225, 250, 275, or 300 nucleotides) in the genome of a host cell, tissue, or subject, in vivo or in vitro. The present disclosure relates, in part, to trans template RNA elements comprising a 5’ end block gRNA spacer, where the gRNA spacer has a length sufficient to support nicking of a target sequence in genomic DNA. Without wishing to be bound by theory, it has been found that a 5’ end block gRNA spacer that supports nicking enables a trans template RNA-containing gene modifying system to achieve long edits (e.g., long insertions). The present disclosure further relates, in part, to trans template RNA elements comprising long post-edit homology regions (e.g., comprising at least 30, 35, 40, 45, 50, 55, or 60 nucleotides). Without wishing to be bound by theory , it has been found that a long post-edit homology region enables a trans template RNA-containing gene modifying system to achieve long edits (e.g., long insertions). The present disclosure also provides various gene modified polypeptides suitable for use with trans templates.

Features of the compositions or methods can include one or more of the following enumerated embodiments.

1. A template RNA comprising: a) a heterologous object sequence comprising, from 5’ to 3': i) a post-edit homology region having a length of at least 30 nucleotides, ii) a mutation region having a length of at least 20 nucleotides, to introduce a mutation into a target nucleic acid sequence wherein the mutation region, and iii) optionally, a pre-edit homology region, and b) a primer binding site sequence (PBS sequence) that binds a first portion of tire target nucleic acid sequence, wherein first portion is in the first strand of the target nucleic acid sequence, and wherein the PBS sequence is 3’ of the heterologous object sequence. c) an RBD recruitment site (RRS), wherein the RRS is 5 ’ of the heterologous object sequence or 3’ of the PBS sequence; and d) an end block sequence which is 5’ of the heterologous object sequence (e.g., wherein the end block sequence is 5’ of both of the heterologous object sequence and tire RRS). wherein the end block sequence comprises: i) a gRNA spacer (optionally, having a length of at least 18 nt), wherein the gRNA spacer is complementary to a second portion of the target nucleic acid sequence wherein the second portion is on the first strand of the target nucleic acid sequence; and ii) a gRNA scaffold.

2. A template RNA comprising: a) a heterologous object sequence comprising, from 5’ to 3': i) a post-edit homology region having a length of at least 7. 10, 13, 15, 17, 20, 25, or 30 nucleotides, ii) a mutation region having a length of at least 20 nucleotides, to introduce a mutation into a target nucleic acid sequence wherein the mutation region, and iii) optionally, a pre-edit homology region, and b) a primer binding site sequence (PBS sequence) that binds a first portion of the target nucleic acid sequence, wherein first portion is in the first strand of the target nucleic acid sequence, and wherein the PBS sequence is 3 ' of the heterologous object sequence, c) an RBD recruitment site (RRS), wherein the RRS is 5 ’ of the heterologous object sequence or 3’ of the PBS sequence; and d) an end block sequence which is 5’ of the heterologous object sequence (e.g., wherein the end block sequence is 5’ of both of tire heterologous object sequence and tire RRS). wherein the end block sequence comprises: i) a gRNA spacer (optionally having a length of at least 18 nt), wherein the gRNA spacer is complementary to a second portion of the target nucleic acid sequence wherein tire second portion is on the first strand of the target nucleic acid sequence; and ii) a gRNA scaffold.

3. A template RNA comprising: a) a heterologous object sequence comprising a mutation region to introduce a mutation into a target nucleic acid sequence (wherein optionally the heterologous object sequence comprises, from 5’ to 3’, a post-edit homology region, the mutation region, and a pre-edit homology region), and b) a primer binding site sequence (PBS sequence) that binds a first portion of the target nucleic acid sequence, wherein first portion is in the first strand of the target nucleic acid sequence, and wherein the PBS sequence is 3’ of the heterologous object sequence, and c) an RBD recruitment site (RRS), wherein the RRS is 3’ of the PBS sequence or 5’ of the heterologous object sequence.

4. A template RNA comprising: a) a heterologous object sequence comprising a mutation region to introduce a mutation into a target nucleic acid sequence (wherein optionally the heterologous object sequence comprises, from 5’ to 3’, a post-edit homology region, the mutation region, and a pre-edit homology region), and b) a primer binding site sequence (PBS sequence) that binds a first portion of the target nucleic acid sequence, wherein first portion is in the first strand of the target nucleic acid sequence, and wherein the PBS sequence is 3’ of the heterologous object sequence, and c) an RBD recruitment site (RRS), wherein optionally the RRS is situated between the PBS sequence and the heterologous object sequence, or within the heterologous object sequence (e.g., between the pre-edit homology region and the mutation region).

5. The template RNA of any of tire preceding embodiments, wherein the post-edit homology region comprises, in 5' to 3’ order: i) a primer homology region, and ii) optionally, an extension homology region.

6. The template RNA of embodiment 5, wherein the primer homology region has a length of at least 7, 10, 13, 15, 17, 20, 25, 30, or 31 nucleotides.

7. The template RNA of embodiment 5, wherein tire primer homology region has a length of 5-50, 5-10, 7-10, 10-15, 15-20, 20-25. 25-30, 30-35, or 35-50 nucleotides.

8. The template RNA of any of any of the preceding embodiments, which lacks an extension homology region.

9. The template RNA of any of embodiments 5-7, wherein the extension homology region has a length of at least 8, 15, 23, or 31 nucleotides.

10. The template RNA of any of embodiments 5-7, wherein the extension homology region has a length of at least 15 nucleotides.

11. The template RNA of any of embodiments 5-7, wherein the extension homology region has a length of 1-5, 5-10, 10-15, 15-20, 20-25, 25-30, or 30-35 nucleotides.

12. The template RNA of any of embodiments 5-11, wherein the extension homology region and the primer homology region together have a length of at least 17 or 20 nucleotides.

13. The template RNA of any of the preceding embodiments, wherein tire region of the target nucleic acid corresponding to the PBS is 0-10 nt, e g., 6 nt from the region of the target nucleic acid corresponding to the post-edit homology region.

14. The template RNA of any of the preceding embodiments, wherein the post-edit homology region has a length of at least 44, 45, 46, 47, 48, 49, or 50 nucleotides.

15. The template RNA of any of the preceding embodiments, wherein the post-edit homology region has a length of at least 30. 35, 40, or 45 nucleotides.

16. The template RNA of any of the preceding embodiments, wherein tire post-edit homology region has a length of 30-35, 35-40, 40-45 or 45-50 nucleotides.

17. The template RNA of any of the preceding embodiments, wherein the post-edit homology region has a length of 46 nucleotides. 18. The template RNA of any of the preceding embodiments, wherein the heterologous object sequence (e.g., between the post-edit homology region and the mutation region) comprises a deletion relative to a portion of the target nucleic acid sequence, the portion comprising at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 100, 200, 300, or 400 contiguous nucleotides, or 2-10. 10-20, 20-50, 50-100, 100-200, or 200-500 contiguous nucleotides of the target nucleic acid sequence.

19. The template RNA of embodiment 18, which results in a deletion in the target DNA that is between the first stand nick and second strand nick.

20. The template RNA of embodiment 19, wherein a first end of the deletion is 6 bp away from the first strand nick.

21. The template RNA of embodiment 19, wherein a second end of the deletion is 15-20, 20-25, 20- 30, 30-35, 35-50, 50-100, 100-200, or 200-500 bp away from the second strand nick.

22. The template RNA of any of embodiments 18-21, wherein the deletion in the target DNA is immediately adjacent to the region of the target nucleic acid corresponding to the post-edit homology region.

23. The template RNA of any of the preceding embodiments, wherein the editing does not increase the length of the target nucleic acid sequence.

24. The template RNA of any of the preceding embodiments, wherein the mutation region has a length of at least 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 125, 130, 140, 150, 175, or 200 nucleotides.

25. The template RNA of any of the preceding embodiments, wherein tire mutation region has a length of about 20-300, 30-250, 50-200, 125-175, 100-150, or 150-200 nucleotides.

26. The template RNA of any of the preceding embodiments, wherein the post-edit homology region has a length of at least 35, 40, 45, 46, 50, 55, 60, 70, 80, 90, 100, 102, or 150 nucleotides.

27. The template RNA of any of the preceding embodiments, wherein the post-edit homology region has a length of about 35-55 or 40-50 nucleotides. 28. The template RNA of any of the preceding embodiments, wherein the pre-edit homology region has a length of about 5-10, 10-15, or 15-20 nucleotides.

29. The template RNA of any of the preceding embodiments, wherein the PBS sequence has a length of 8-20, 10-15, or 13 nucleotides.

30. The template RNA of any of the preceding embodiments, wherein the RRS comprises an MS2 sequence.

31 . The template RNA of any of the preceding embodiments, which comprises a plurality (e g., 2, 3, or 4) of RRS sequences in tandem.

32. The template RNA of embodiment 31, wherein the plurality of RRS sequences are MS2 sequences.

33. The template RNA of any of the preceding embodiments, which comprises a linker sequence between the RRS and PBS, wherein optionally the linker sequence has a length of 4-20 nucleotides, e.g., 8 or 16 nucleotides.

34. The template RNA of any of the preceding embodiments, wherein the end block sequence comprises a sequence of Table 41 or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity thereto.

35. The template RNA of any of the preceding embodiments, wherein the RRS is 3’ of the PBS sequence.

36. The template RNA of any of embodiments any of embodiments 1-32, wherein the RRS is 5’ of the heterologous object sequence. 37. The template RNA of any of the preceding embodiments, wherein the RRS has a sequence according to Table 40 or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity thereto.

38. The template RNA of any of the preceding embodiments, which comprises a plurality of RRSs, e.g., a tandem array of 2, 3, 4, 5, or 10 RRSs.

39. The template RNA of any of the preceding embodiments, wherein tire PBS sequence comprises 8-17 nucleotides, e.g.. 8-17 nucleotides of 100% identity to the target nucleic acid sequence.

40. The template RNA of any of the preceding emdobiments, wherein tire pre-edit homology region comprises up to 20 nucleotides, e.g., up to 20 nucleotides of 100% identity to the target nucleic acid sequence.

41. The template RNA of any of the preceding embodiments, wherein the post-edit homology region comprises 30-500 nucleotides, e.g., 30-500 nucleotides of 100% identity to the target nucleic acid sequence.

42. The template RNA of any of the preceding embodiments, wherein the mutation region is configured to produce an insertion in the target nucleic acid.

43. The template RNA of any of the preceding embodiments, wherein the gRNA scaffold is situated between the gRNA spacer and the heterologous object sequence.

44. The template RNA of any of the preceding embodiments, which comprises an end block sequence, e.g., an end block sequence of Table 41 or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity thereto.

45. The template RNA of any of the preceding embodiments, which comprises an end block sequence 5’ of the heterologous object sequence.

46. The template RNA of any of the preceding embodiments, which comprises an end block sequence 3’ of tire PBS sequence, and optionally wherein the RRS is situated between the end block sequence and the PBS sequence. 47. The template RNA of any of the preceding embodiments, which comprises a first end block sequence 3’ of tire PBS sequence and a second end block sequence 5’ of tire heterologous object sequence.

48. The template RNA of any of the preceding embodiments, wherein the end block sequence is 5’ of the heterologous object sequence and the RRS is 3’ of the PBS sequence.

49. The template RNA of any of embodiments 1-47, wherein the end block sequence is 3' of the PBS sequence and the RRS is 5’ of the heterologous object sequence.

50. The template RNA of any of the preceding embodiments, wherein the RRS has a sequence according to Table 40 or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity thereto, or the reverse complement thereof.

51. The template RNA of any of the preceding embodiments, which comprises a plurality of RRSs, e.g.. a tandem array of 2, 3, 4, 5. or 10 RRSs.

52. The template RNA of any if the preceding embodiments, wherein the PBS sequence is 5 - 1000 nt in length.

53. The template RNA of any if the preceding embodiments, wherein the PBS sequence comprises 8- 17 nucleotides, e.g., 8-17 nucleotides of 100% identity to the target nucleic acid sequence.

54. The template RNA of any of the preceding embodiments wherein the pre-edit homology region comprises up to 30 nucleotides, e.g.. up to 20 nucleotides, e.g., up to 20 nucleotides of 100% identity to the target nucleic acid sequence. 55. The template RNA of any of the preceding embodiments, which does not comprise a post-edit homology region.

56. The template RNA of any of embodiments 1-54, wherein the post-edit homology region comprises 5-1000, 5-500 nucleotides, e.g., 5-500 nucleotides of 100% identity to the target nucleic acid sequence.

57. The template RNA of any of the preceding embodiments, which does not comprise a post-edit homology region.

58. The template RNA of any of the preceding embodiments, wherein the mutation region is configured to produce an insertion, a deletion, or a substitution in the target nucleic acid.

59. The template RNA of any of the preceding embodiments, wherein the mutation region comprises a first region (e.g.. a first nucleotide) designed to insert a first sequence alteration into the target nucleic acid and a second region (e.g.. a second nucleotide) designed to inactivate a PAM sequence in the target nucleic acid (e.g., a ‘'PAM-kill” mutation as described herein).

60. The template RNA of any of the preceding embodiments, which further comprises: a gRNA spacer that is complementary to a different portion (e.g., a second portion) of the target nucleic acid sequence, e g., wherein the different portion (e.g., second portion) is on the first strand of the target nucleic acid sequence; and a gRNA scaffold.

61. The template RNA of embodiment 60, wherein the gRNA spacer is 5 ’ of the heterologous object sequence. 62. The template RNA of embodiment 60 or 61, wherein the gRNA scaffold is situated between the gRNA spacer and the heterologous object sequence.

63. The template RNA of any of embodiments 60-62 wherein the gRNA spacer and the PBS sequence bind the same strand of the target nucleic acid sequence.

64. The template RNA of any of embodiments 60-63 wherein the gRNA spacer, the heterologous object sequence, and the PBS sequence bind the same strand of the target nucleic acid sequence.

65. The template RNA of any of the preceding embodiments, which does not comprise a gRNA spacer or a gRNA scaffold.

66. The template RNA of any of the preceding embodiments, w hich comprises a linker of up to 20 nucleotides between the RRS and the PBS sequence.

67. A gene modifying polypeptide comprising: a reverse transcriptase (RT) domain; and a DNA binding domain (DBD) that binds to a target nucleic acid sequence and is heterologous to the RT domain (e.g., a Cas domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase domain); and a RNA-binding domain (RBD) that is heterologous to tire DBD and the RT domain.

68. A gene modifying polypeptide comprising: a reverse transcriptase (RT) domain; and a DNA binding domain (DBD) that binds to a target nucleic acid sequence and is heterologous to the RT domain (e.g., a Cas domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase domain); and a RNA-binding domain (RBD) that is heterologous to the DBD and the RT domain, wherein the domains are arranged, in an N-terminal to C -terminal direction: a) DBD, RT domain, RBD; b) RT domain, DBD, RBD; c) RBD, DBD, RT domain; d) RBD, RT domain, DBD; e) DBD, RBD, RT domain; or f) RT domain, RBD, DBD.

69. A gene modifying polypeptide comprising: a reverse transcriptase (RT) domain; and a DNA binding domain (DBD) that binds to a target nucleic acid sequence and is heterologous to the RT domain (e.g., a Cas nickase domain, e.g., a Cas9 nickase domain); and a plurality (e.g., 2, 3, 4, or 5) RNA-binding domains (RBD) that are heterologous to the DBD and the RT domain.

70. The gene modify ing polypeptide of embodiment 69, wherein the RBD has an amino acid sequence according to Table 31. or at least 75%, 80%. 85%. 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

71. The gene modifying polypeptide of any of embodiments 67-70, wherein the plurality of RBDs have the same amino acid sequence as each other.

72. The gene modifying polypeptide of any of embodiments 67-70, wherein tire plurality of RBDs have different amino acid sequences from each other.

73. The gene modifying polypeptide of any of embodiments 67-72, wherein the DBD has an amino acid sequence according to Table 7 or 8, or at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

74. The gene modifying polypeptide of any of embodiments 67-73, wherein the RT domain is from a retrovirus, or a polypeptide domain having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% amino acids sequence identity thereto.

75. The gene modifying polypeptide of any of embodiments 67-74, wherein the RT domain has an amino acid sequence according to Table 6, or at least 75%, 80%, 85%, 90%, 95%, 96%. 97%. 98%, or 99% identity thereto.

76. The gene modifying polypeptide of any of embodiments 67-75, wherein the gene modifying polypeptide comprises a linker. 77. The gene modifying polypeptide of any of embodiment 76, wherein the linker comprises a sequence according to Table 10, or a sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

78. The gene modifying polypeptide of embodiment 76 or 77. wherein the linker is disposed between the DBD and the RT domain, the RT domain and the RBD, or between the RBD and the DBD.

79. The gene modifying polypeptide of any of embodiments 67-78, wherein the gene modifying polypeptide comprises, in an N-terminal to C-terminal direction: a) the DBD, a first linker, the RT domain, a second linker, the RBD; b) the RT domain, a first linker, the DBD, a second linker, the RBD: c) the RBD, a first linker, the DBD, a second linker, the RT domain: d) RBD, a first linker, RT domain, a second linker, DBD: e) the DBD, a first linker, the RBD, a second linker, the RT domain; or f) the RT domain, a first linker, the RBD, a second linker, the DBD.

80. The gene modifying polypeptide of any of embodiments 67-79, which was produced by intein- mediated fusion of an N-terminal portion comprising an intein-N domain and a C-terminal portion comprising an intein-C domain.

81. A polypeptide system (e.g., a polypeptide complex) comprising: a) a reverse transcriptase (RT) domain; and b) a DNA binding domain (DBD) that binds to a target nucleic acid sequence and is heterologous to the RT domain (e.g., a Cas domain, e.g., a Cas9 domain, e.g., a Cas9 nickase domain); and c) a RNA-binding domain (RBD) that is heterologous to the DBD and the RT domain, wherein at least 2 of (e.g., all of) (a), (b), and (c) are in separate polypeptides, e.g., separate polypeptides that noncovalently fonn a complex.

82. The polypeptide system of embodiment 81, wherein complex formation is mediated by a first dimerization domain that binds a second, compatible dimerization domain.

83. The polypeptide system of embodiment 82, wherein complex formation is mediated by a third dimerization domain that binds a fourth, compatible dimerization domain. 84. The polypeptide system of any of embodiments 81-83, wherein: the RBD is operably linked (e.g., via a linker) to a first dimerization domain; the DBD is operably linked (e.g., via a linker) to a second dimerization domain that binds the first dimerization domain; the DBD is operably linked (e.g., via a linker) to a third dimerization domain; and the RT domain is operably linked (e.g., via a linker) to a fourth dimerization domain that binds the third dimerization domain.

85. The polypeptide system of any of embodiments 81-84, wherein the first and second dimerization domains are: chemical- induced dimerization domains, light-induced dimerization domains, antibody- peptide dimerization domains, or coiled coil dimerization domains.

86. The polypeptide system of any of embodiments 81-85, wherein the third and fourth dimerization domains are: chemical- induced dimerization domains, light-induced dimerization domains, antibody- peptide dimerization domains, or coiled coil dimerization domains.

87. The polypeptide system of any of embodiments 81-86, wherein the first dimerization domain and the second dimerization domain are each present in a plurality of copies, e.g., 2, 3, 4, 5, 10, 15, 20, or 30 copies.

88. The polypeptide system of any of embodiments 81-87, wherein the third dimerization domain and the fourth dimerization domain are each present in a plurality of copies, e.g., 2, 3, 4, 5, 10, 15, 20, or 30 copies.

89. The polypeptide system of any of embodiments 81-88, wherein the first dimerization domain and the second dimerization domain have the same sequence (e.g., wherein the first dimerization domain and the second dimerization domain form a homodimer).

90. The polypeptide system of any of embodiments 81-89, wherein the third dimerization domain and the fourth dimerization domain have the same sequence (e.g., wherein the third dimerization domain and the fourth dimerization domain form a homodimer). 91. The polypeptide system of any of embodiments 81-90, wherein the first dimerization domain and the second dimerization domain have different sequences (e.g., wherein the first dimerization domain and the second dimerization domain form a heterodimer).

92. The polypeptide system of any of embodiments 81-91, wherein the third dimerization domain and the fourth dimerization domain have different sequences (e.g.. wherein the third dimerization domain and the fourth dimerization domain form a hetero dimer).

93. The polypeptide system of any of embodiments 81-92, wherein the DBD is operably linked to one or more additional DBDs, wherein optionally the additional DBDs have the same sequence as the DBD.

94. The polypeptide system of any of embodiments 81-93, wherein the RBD has an amino acid sequence according to Table 31, or at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

95. The polypeptide system of any of embodiments 81-94, wherein the plurality of RBDs have the same amino acid sequence as each other.

96. The polypeptide system of any of embodiments 81-94, wherein the plurality of RBDs have different amino acid sequences from each other.

97. The polypeptide system of any of embodiments 81-96, wherein the DBD has an amino acid sequence according to Table 7 or 8, or at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

98. The polypeptide system of any of embodiments 81-97, wherein the RT domain is from a retrovirus, or a polypeptide domain having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% amino acids sequence identity thereto.

99. The polypeptide system of any of embodiments 81-98, wherein the RT domain has an amino acid sequence according to Table 6, or at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. 100. The polypeptide system of any of embodiments 81-99, wherein each linker independently comprises a sequence according to Table 10, or a sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

101. A nucleic acid or a plurality of nucleic acids encoding the polypeptides of any of the systems of embodiment 81-100.

102. A gene modifying system comprising the template RNA of any of embodiments 1-66 and a gene modifying polypeptide, or a nucleic acid encoding the gene modifying polypeptide.

103. A system comprising: a template RNA (e.g.. the template RNA of any of embodiments 1-66); a gene modifying polypeptide of any of embodiments 67-80 or the polypeptide system of any of embodiments 81-100; and a first gRNA comprising: a gRNA spacer that binds a third portion of tire target nucleic acid sequence, wherein tire third portion is on the second strand of the target nucleic acid sequence: and a gRNA scaffold that binds the DBD of the gene modifying polypeptide or the polypeptide system.

104. The system of embodiment 103, wherein the template RNA does not comprise a gRNA spacer or a gRNA scaffold.

105. The gene modify ing polypeptide or system of any of embodiments 67-80 or 102-104, wherein the gene modifying polypeptide comprises a reverse transcriptase (RT) domain; a DNA binding domain (DBD) that binds to a target nucleic acid sequence and is heterologous to the RT domain (e.g., a Cas domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase domain); and a RNA-binding domain (RBD) that is heterologous to tire DBD and the RT domain.

106. The gene modifying polypeptide or system of any of embodiments 67-80 or 102-105 wherein the domains are arranged, in an N-terminal to C-terminal direction: a) DBD, RT domain, RBD; b) RT domain, DBD, RBD; c) RBD, DBD, RT domain; d) RBD, RT domain, DBD; e) DBD, RBD, RT domain; or f) RT domain, RBD, DBD.

107. The gene modifying polypeptide or system of any of embodiments 67-80 or 102-106. which comprises a plurality (e.g., 2, 3, 4, or 5) RNA-binding domains (RBD) that are heterologous to the DBD and the RT domain.

108. The gene modifying polypeptide or system of any of embodiments 67-80 or 102-107, wherein the RBD has an amino acid sequence according to Table 31, or at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

109. The gene modifying polypeptide or system of any of embodiments 67-80 or 102-108, wherein the plurality of RBDs have the same amino acid sequence as each other.

110. The gene modifying polypeptide or system of any of embodiments 67-80 or 102-108, wherein the plurality of RBDs have different amino acid sequences from each other.

111. The gene modifying polypeptide or system of any of embodiments 67-80 or 102-110, wherein the DBD has an amino acid sequence according to Table 7 or 8, or at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identify thereto.

112. The gene modifying polypeptide or system of any of any of embodiments 67-80 or 102-111, wherein the RT domain has an amino acid sequence according to Table 6, or at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identify thereto.

113. The gene modifying polypeptide or system of any of embodiments 67-80 or 102-112, wherein the gene modifying polypeptide comprises a linker.

1 14. The gene modifying polypeptide or system of embodiment 1 13, wherein the linker of the gene modifying polypeptide comprises a sequence according to Table 10, or a sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. 115. The gene modifying polypeptide or system of embodiments 113 or 114, wherein the linker of the gene modifying polypeptide is disposed between the DBD and the RT domain, the RT domain and the RBD, or between the RBD and the DBD.

116. The gene modifying polypeptide or system of any of embodiments 67-80 or 102-115, wherein the gene modifying polypeptide comprises, in an N-terminal to C-terminal direction: a) the DBD, a first linker, the RT domain, a second linker, the RBD; b) the RT domain, a first linker, the DBD, a second linker, the RBD; c) the RBD, a first linker, the DBD, a second linker, the RT domain; d) RBD, a first linker, RT domain, a second linker, DBD; e) the DBD, a first linker, the RBD, a second linker, the RT domain: or f) the RT domain, a first linker, the RBD, a second linker, the DBD.

117. The gene modifying polypeptide or system of any of embodiments 67-80 or 102-116, wherein the gene modifying polypeptide was produced by intein-mediated fusion of an N-terminal portion comprising an intein-N domain and a C-terminal portion comprising an intein-C domain.

118. The gene modifying polypeptide or system of any of embodiments 67-80 or 102-117, wherein the gene modifying polypeptide binds the gRNA scaffold.

119. The gene modifying polypeptide or system of any of embodiments 67-80 or 102-117, wherein the gene modifying polypeptide does not substantially bind the gRNA scaffold.

120. The system of any of embodiments 102 or 105-119, which further comprises a gRNA, wherein the gRNA comprises: a second gRNA spacer that binds a third portion of the target nucleic acid sequence, wherein the third portion is on the second strand of the target nucleic acid sequence; and a second gRNA scaffold that binds the DBD of the gene modify ing polypeptide.

121. The system of embodiment 120. wherein the second gRNA scaffold has a different sequence from the sequence of the gRNA scaffold in the template RNA. 122. The system of embodiment 120 or 121, wherein the gRNA directs a first strand nick to a first site of a first strand of a target nucleic acid molecule, and/or the end block sequence directs a second strand nick to a second site of a second strand of the target nucleic acid molecule.

123. The system of embodiment 122. wherein the first strand nick and the second strand nick are about 18, 19, 20, 21. 22. 23. 24, 25-50, 50-100, 100-200, or 200-500 nucleotides apart in the target nucleic acid molecule.

124. The system of embodiment 122, wherein the first strand nick and the second strand nick are about 15-20 or 20-25 nucleotides apart in the target nucleic acid molecule.

125. The system of any of embodiments 102-124, wherein the post-edit homology region comprises the same nucleic acid sequence as a region in the second strand of the target nucleic acid molecule comprising the second site.

126. The system of any of embodiments 102-125, wherein the post-edit homology region comprises the nucleic acid sequence of at least a portion of (e.g., all of) the gRNA spacer of the end block sequence, wherein optionally: a) the post-edit homology region comprises the nucleic acid sequence of the gRNA spacer of the end block sequence; b) tire post-edit homology region comprises tire nucleic acid sequence of a portion of, but not all of, the gRNA spacer of the end block sequence.

127. The system of any of embodiments 102-126, wherein the post-edit homology region comprises a first subregion and the gRNA spacer of the end block sequence comprises a second subregion, wherein the first subregion and the second subregion have the same nucleic acid sequence.

128. The system of any of embodiments 102-127, wherein the distance between (i) the second portion of the target nucleic acid sequence and (ii) the third portion of the target nucleic acid sequence is about 12, 13, 14, 15, 16. 17, 18, or 19 nucleotides.

129. The system of any of embodiments 102-128, which further comprises a second Cas protein or a nucleic acid encoding the second Cas protein. 130. The system of embodiment 129, wherein the second Cas protein is a Cas nickase protein (e.g., a Cas9 nickase protein) or a dead Cas protein (e.g., a dead Cas9 protein).

131. The system of embodiment 129 or 130, wherein tire second Cas protein binds the gRNA scaffold of the template RNA.

132. The system of any of embodiments 129-131, wherein the gene modifying polypeptide does not substantially bind the gRNA scaffold of the template RNA.

133. The system of any of embodiments 129-132, wherein the second Cas protein does not substantially bind the second gRNA scaffold.

134. The system of any of embodiments 102-133, wherein the gRNA spacer of the template RNA induces nicking of the target nucleic acid, e.g., at the second strand of the target nucleic acid sequence.

135. The system of any of embodiments 102-134, wherein the gRNA spacer binds to a region of the target nucleic acid sequence that is within about 5, 10. 15. 20, 25, 30, or 40 nucleotides of the region of the target nucleic acid sequence bound by the PBS sequence.

136. The system of any of embodiments 102-135, which further comprises: a second Cas protein (e.g., a dead Cas protein), or a nucleic acid encoding tire second Cas protein and a second gRNA comprising: a gRNA spacer that binds the first strand of the target nucleic acid at a location 3 ’ of the location bound by the PBS sequence, and a gRNA scaffold that binds the second Cas protein.

137 The system of embodiment 136. wherein the second Cas protein is a dead Cas protein (e.g., a dead Cas9 protein) or a Cas nickase protein (e.g., a Cas9 nickase protein) 138. The system of embodiment 136, wherein the gRNA spacer of the second gRNA has a length of at least 18 nucleotides (e.g., 18-28 nucleotides, e.g., 18-21 nucleotides) and the second Cas protein is a dead Cas protein.

139. The system of embodiment 136. wherein the gRNA spacer of the second gRNA has a length of 17 nucleotides or less (e.g., 14-17 nucleotides), wherein optionally the second Cas protein is a Cas nickase protein.

140. The system of any of embodiments 102-139, wherein the template RNA comprises: a gRNA spacer that is complementary to a second portion of the target nucleic acid sequence wherein the second portion is on the first strand of the target nucleic acid sequence; and a gRNA scaffold.

141. The system of embodiment 140. wherein the gRNA scaffold binds the DBD of the gene modifying polypeptide or the polypeptide system.

142. The system of any of embodiments 102-141, wherein the gRNA spacer has a length of 17 nucleotides or less.

143. The system of any of embodiments 102-142, wherein the gRNA spacer of tire template RNA induces nicking of the template nucleic acid, e.g., at the second strand of the target nucleic acid sequence.

144. The system of any of embodiments 102-143, wherein the gRNA spacer of the template RNA does not induce nicking of the template nucleic acid.

145. A system comprising: i) a template RNA of any of embodiments 1-66 (e.g., a template RNA of embodiment 65); ii) a first polypeptide comprising: a DNA binding domain (DBD) (e.g., a Cas domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase domain); and a RNA-binding domain (RBD) that is heterologous to the DBD, wherein the RBD binds the RRS of the template RNA; iii) a first gRNA comprising: a gRNA spacer that directs the DBD of the first polypeptide to a second portion of the target nucleic acid sequence, wherein the second portion of the target nucleic acid sequence is on the second strand of the nucleic acid sequence; and a gRNA scaffold that binds the DBD of the first polypeptide; iv) a second polypeptide comprising: an RT domain, and a DNA binding domain (DBD) (e.g., a Cas domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase domain), that is heterologous to the RT domain, and wherein the DBD of the second polypeptide has a different sequence from the DBD of the first polypeptide; and v) a second gRNA comprising: a gRNA spacer that directs the DBD of the second polypeptide to a third portion of the target nucleic acid sequence, wherein the third portion is on tire first strand of tire target nucleic acid, and a gRNA scaffold that binds the DBD of the second polypeptide.

146. The system of embodiment 145, wherein tire DBD of the second polypeptide comprises a Cas nickase domain or a dead Cas domain.

147. The system of embodiment 145, wherein the gRNA spacer of the second RNA induces nicking of the template nucleic acid, e.g., at the second strand of the target nucleic acid sequence.

148. The system of embodiment 145, wherein the gRNA spacer of the second RNA does not induce nicking of tire template nucleic acid.

149. The system of embodiment 145. wherein the first gRNA does not detectably bind to the DBD of the second polypeptide. 150. The system of embodiment 145, wherein the second gRNA does not detectably bind to the DBD of the first polypeptide.

151. A system comprising : i) a template RNA of any of embodiments 1-66, wherein tire template RNA comprises: a gRNA spacer that is complementary to a second portion of the target nucleic acid sequence wherein the second portion is on the first strand of the target nucleic acid sequence; and a gRNA scaffold; ii) a first polypeptide comprising: a DNA binding domain (DBD) (e.g., a Cas domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase domain); and a RNA-binding domain (RBD) that is heterologous to the DBD, wherein the RBD binds the RRS of the template RNA; iii) a first gRNA comprising: a gRNA spacer that directs the DBD of the first polypeptide to a third portion of the target nucleic acid sequence, wherein the third portion of the target nucleic acid sequence is on the second strand of the nucleic acid sequence; and a gRNA scaffold that binds the DBD of the first polypeptide; and iv) a second polypeptide comprising: an RT domain, and a DNA binding domain (DBD) (e.g., a Cas domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase domain), that is heterologous to the RT domain, and wherein the DBD of the second polypeptide has a different sequence from the DBD of the first polypeptide, and wherein the gRNA scaffold of the template RNA binds the DBD of the second polypeptide.

152. The system of embodiment 151, wherein the DBD of the second polypeptide comprises a Cas nickase domain or a dead Cas domain. 153. The system of embodiment 151, wherein the gRNA spacer of the template RNA induces nicking of the template nucleic acid, e.g., at the second strand of the target nucleic acid sequence.

154. The system of embodiment 151, wherein the gRNA spacer of the template RNA does not induce nicking of tire template nucleic acid.

155. The system of any of embodiments 151-154, wherein the first gRNA does not detectably bind to the DBD of the second polypeptide.

156. The system of any of embodiments 151-155, wherein the gRNA of the template RNA does not detectably bind to the DBD of the first polypeptide.

157. A polypeptide system comprising: a first polypeptide comprising: a DNA binding domain (DBD) (e.g.. a Cas domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase domain); a RNA-binding domain (RBD) that is heterologous to the DBD; and optionally, a linker disposed between the DBD and the RBD; and a second polypeptide comprising: an RT domain, and a DNA binding domain (DBD) (e.g., a Cas domain, e.g., a Cas nickase domain. e.g., a Cas9 nickase domain), that is heterologous to the RT domain: and optionally, a linker disposed between the RT domain and the DBD.

158. The template RNA or system of any of embodiments 1-66 or 102-157, wherein the target nucleic acid sequence is a target gene, enhancer, or promoter.

159. The template RNA of system of any of embodiments 1-66 or 102-158, wherein the target nucleic acid sequence is a human target gene, human enhancer, or human promoter. 160. The system or polypeptide system of any of embodiments 67-159, wherein the RBD has a sequence of Table 31, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity thereto.

161. A method for modifying a target nucleic acid in a cell (e.g., a human cell), the method comprising contacting the cell with the system of any one of embodiments 102-160. or nucleic acid encoding the same, thereby modifying the target nucleic acid.

162. The method of embodiment 161, wherein presence of the second polypeptide, compared to an otherwise similar system lacking the second polypeptide, results in one or more of: increased unwinding of the target nucleic acid; increased number of target nucleic acids that are modified; increased length of insertion into the target nucleic acid; or reduced MMR activity at the target nucleic acid.

163. The method of embodiment 161 or 162, wherein the cell is in vivo or ex vivo.

164. The method of any of embodiments 161-163, which results in an insertion into the target nucleic acid.

165. The method of embodiment 164, wherein the insertion has a length of at least 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 125, 130, 140, 150, 175, or 200 nucleotides.

166. The method of embodiment 164 or 165, wherein the insertion has a length of about 20-300, 30- 250, 50-200, 125-175, 100-150, or 150-200 nucleotides.

167. A template RNA comprising: a) a heterologous object sequence comprising a mutation region to introduce a mutation into a target nucleic acid sequence (wherein optionally the heterologous object sequence comprises, from 5‘ to 3’. a post-edit homology region, the mutation region, and a pre-edit homology region), and b) a primer binding site sequence (PBS sequence) that binds a first portion of the target nucleic acid sequence, wherein first portion is in the first strand of the target nucleic acid sequence, and wherein the PBS sequence is 3’ of the heterologous object sequence, and c) an RBD recruitment site (RRS), wherein the RRS is 3’ of the PBS sequence or 5’ of the heterologous object sequence.

168. The template RNA of any of embodiments 1-66 or 167, wherein the RRS comprises the RRS of a template sequence as listed in Table S4, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%,

98%, or 99% identity thereto.

169. The template RNA of any of embodiments 1-66, 167, or 168, which comprises an end block sequence, e.g., an end block sequence of Table 41, or comprising a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity thereto.

170. The template RNA of any of embodiments 1-66 or 167-169, wherein the end block sequence is 5’ of the heterologous object sequence (e.g., located at the 5’ end of the template RNA), optionally wherein the RRS is 3’ of the PBS sequence.

171. The template RNA of any of embodiments 1-66 or 167-170, wherein the end block sequence comprises a gRNA scaffold.

172. The template RNA of any of embodiments 1-66 or 167-171, wherein the gRNA scaffold is chosen from Table 41 .

173. The template RNA of any of embodiments 1-66 or 167-172, wherein the gRNA scaffold is a Cas9 scaffold.

174. The template RNA of any of embodiments 1-66 or 167-173, wherein the end block sequence comprises a gRNA spacer, e.g., positioned at the 5’ end of the end block sequence (e.g., 5’ of the gRNA scaffold and/or positioned at the 5' end of the template RNA).

175. The template RNA of any of embodiments 1-66 or 167-174, wherein the gRNA spacer induces nicking of the target nucleic acid.

176. The template RNA of any of embodiments 1-66 or 167-175, wherein the end block sequence binds to a DNA binding domain, e.g., of a gene modify ing polypeptide (e.g., as described herein). 177. The template RNA of any of embodiments 1-66 or 167-176, wherein the gene modifying polypeptide bound to the end block sequence does not create a nick in the second strand of the target nucleic acid sequence.

178. The template RNA of any of embodiments 1-66 or 167-177, wherein the gRNA spacer binds to a second portion of the first strand of the target nucleic acid sequence located 3 ’ relative to the first portion of the target nucleic acid sequence.

179. The template RNA of embodiment 178, wherein the 5’ end of tire portion of the first strand bound by tire gRNA spacer is between 10-20, 20-30, 30-40, 40-50, 50-100, 100-150, or 150-200 nucleotides from the 3’ end of the first portion.

180. The template RNA of any of embodiments 1-66 or 167-179, wherein:

(i) the gRNA spacer has a length of less than or equal to 17 nucleotides, e.g., about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or 17 nucleotides;

(ii) the gRNA spacer has 100% complementarity to the second portion on the first strand of the target nucleic acid sequence; and/or

(iii) the gRNA spacer directs nicking activity by a Cas domain.

181. The template RNA of embodiment 180, wherein:

(i) tire gRNA spacer has a length of less than or equal to 17 nucleotides, e.g., about 5, 6, 7, 8, 9,

10, 11, 12. 13, 14, 15, 16, or 17 nucleotides; and

(ii) the gRNA spacer has 100% complementarity to the second portion on the first strand of the target nucleic acid sequence.

182. The template RNA of embodiment 180, wherein:

(ii) the gRNA spacer has 100% complementarity to the second portion on the first strand of tire target nucleic acid sequence; and

(iii) the gRNA spacer directs nicking activity by a Cas domain.

183. The template RNA of any of embodiments 1-66 or 167-182, wherein the end block sequence is 3’ of the PBS sequence and/or the RRS (e.g., located at the 3’ end of the template RNA), optionally wherein the RRS is 5’ of the heterologous object sequence. 184. The template RNA of embodiment 183, wherein the end block sequence comprises GGGTCAGGAGCCCCCCCCTGAACCCAGGATAACCCTCAAAGTCGGGGGGC (SEQ ID NO: 18,101), an end block sequence of Table 41, or comprising a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity to any thereof.

185. The template RNA of any of embodiments 1-66 or 167-184, wherein the end block sequence comprises an aptamer.

186. The template RNA of any of embodiments 1-66 or 167-185, wherein the end block sequence is capable of binding to an RNA aptamer-binding protein (e.g., an RNA aptamer-binding protein attached to a gene modifying polypeptide, e.g., at the DBD).

187. The template RNA of any of embodiments 1-66 or 167-186, wherein the end block sequence comprises one or more hairpins (e g., 1, 2, 3, 4, or 5 hairpins).

188. The template RNA of any of embodiments 1-66 or 167-187, wherein the end block comprises an ePEG end block.

189. The template RNA of any of embodiments 1-66 or 167-188, further comprising: a 5’ end block sequence, e.g., an end block sequence of Table 41, or comprising a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity thereto, wherein the 5’ end block sequence is 5 ' of tire heterologous object sequence (e.g.. located at tire 5’ end of the template RNA), optionally wherein the RRS is 3' of the PBS sequence; and a 3' end block sequence, e.g., an end block sequence of Table 41 or the sequence GGGTCAGGAGCCCCCCCCTGAACCCAGGATAACCCTCAAAGTCGGGGGGC (SEQ ID NO: 18,101), or comprising a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity to any thereof, wherein the 3’ end block sequence is 3’ of the PBS sequence and/or the RRS (e.g., located at the 3’ end of the template RNA), optionally wherein the RRS is 5’ of the heterologous object sequence.

190. The template RNA of any of embodiments 1-66 or 167-189, wherein the RRS comprises an MS2 sequence.

191. The template RNA of any of embodiments 1-66 or 167-190, wherein the RRS binds to an MCP polypeptide.

192. The template RNA of any of embodiments 1-66 or 167-191, wherein the RRS comprises a PP7 sequence. 193. The template RNA of any of embodiments 1-66 or 167-192, wherein the RRS and the PBS are separated by a region having of length of about 5-10, 10-15, or 15-20 nucleotides (e.g., about 8 nucleotides or about 16 nucleotides).

194. The template RNA of any of embodiments 1-66 or 167-193, wherein the RRS has a sequence according to Table 40 or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%. 98%, or 99% identity thereto.

195. The template RNA of any of embodiments 1-66 or 167-194, which comprises a plurality of RRSes (e.g., identical or different RRSes), e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 RRSes, e.g., a tandem array of 2, 3, 4, 5, or 10 RRSs.

196. The template RNA of embodiment 195, wherein the plurality of RRSes each comprises an MS2 sequence.

197. The template RNA of embodiment 195 or 196, wherein the plurality of RRSes comprises 4 repeats of the MS2 sequence.

198. The template RNA of any of embodiments 1-66 or 167-197, wherein the PBS sequence comprises 8-17 nucleotides, e.g., 8-17 nucleotides of 100% identity to the target nucleic acid sequence.

199. The template RNA of embodiment 198, wherein the PBS sequence has a length of about 8, 13, or 17 nucleotides.

200. The template RNA of embodiment 198, wherein the PBS sequence has a length of about 13 nucleotides.

201. The template RNA of any of embodiments 1-66 or 167-200, wherein the pre-edit homology region comprises up to 20 nucleotides, e.g., up to 20 nucleotides of 100% identity to the target nucleic acid sequence.

202. The template RNA of any of embodiments 1-66 or 167-201, wherein the post-edit homology region comprises 5-500 nucleotides, e.g, 5-500 nucleotides of 100% identity to the target nucleic acid sequence.

203. The template RNA of any of embodiments 1-66 or 167-202, wherein the post-edit homology region comprises 10-20, 20-30, 30-40, 40-50, 50-60, or 60-70 nucleotides, e.g., about 12 nucleotides or about 63 nucleotides. 204. The template RNA of embodiment 203, wherein the post-edit homology region comprises one or more (e.g., 1, 2, 3, 4, or 5) single nucleotide substitutions, e.g., at approximately regular intervals (e.g., spaced about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides apart).

205. The template RNA of any of embodiments 1-66 or 167-204, wherein the mutation region is configured to produce an insertion, a deletion, or a substitution in the target nucleic acid.

206. The template RNA of any of embodiments 1-64, 66, or 167-205, wherein the gRNA spacer is complementary to a different portion (e.g., a second portion) of the target nucleic acid sequence, e.g., wherein the different portion (e.g., second portion) is on the first strand of the target nucleic acid sequence.

207. The template RNA of embodiment 206, wherein the gRNA spacer is 5' of the heterologous object sequence.

208. The template RNA of embodiment 206 or 207, wherein the gRNA scaffold is situated between the gRNA spacer and the heterologous object sequence.

209. The template RNA of any of embodiments 1-64, 66, or 167-208, wherein the gRNA spacer and the PBS sequence bind the same strand of the target nucleic acid sequence.

210. The template RNA of any of embodiments 1-64, 66, or 167-209, wherein the gRNA spacer, the heterologous object sequence, and the PBS sequence bind the same strand of the target nucleic acid sequence.

211. The template RNA of any of embodiments 3, 4, 66, or 167-173, which does not comprise a gRNA spacer or a gRNA scaffold.

212. The template RNA of any of embodiments 1-66 or 167-211, which comprises a linker of up to 20 nucleotides between the RRS and the PBS sequence.

213. The template RNA of any of embodiments 1-66 or 167-212, wherein the template RNA is linear. 214. The template RNA of any of embodiments 1-66 or 167-212, wherein the template RNA is circular.

215. A gene modifying polypeptide comprising : a reverse transcriptase (RT) domain; and a DNA binding domain (DBD) that binds to a target nucleic acid sequence and is heterologous to the RT domain (e.g., a Cas domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase domain); and a RNA-binding domain (RBD) that is heterologous to the DBD and the RT domain, wherein the domains are arranged, in an N-terminal to C-terminal direction:

(a) DBD, RT domain, RBD;

(b) RT domain, DBD, RBD;

(c) RBD. DBD, RT domain;

(d) RBD, RT domain, DBD:

(e) DBD, RBD, RT domain; or

(f) RT domain, RBD, DBD.

216. The gene modifying polypeptide of embodiment 215, further comprising one or more (e.g., 1. 2, 3, or 4) additional RBDs (e.g., one or more additional copies of the RBD, e.g., adjacent to the RBD).

217. A gene modifying polypeptide comprising: a reverse transcriptase (RT) domain; and a DNA binding domain (DBD) that binds to a target nucleic acid sequence and is heterologous to the RT domain (e.g., a Cas nickase domain, e.g., a Cas9 nickase domain); and a plurality (e.g., 2, 3, 4, or 5) RNA-binding domains (RBD) that are heterologous to the DBD and the RT domain.

218. The gene modifying polypeptide of any of embodiments 215-217, wherein the RBD comprises an amino acid sequence according to Table 31 or the amino acid sequence of the RBD of a gene modifying polypeptide as listed in any of Tables S1-S3, or an amino acid sequence having at least 75%. 80%, 85%, 90%, 95%, 96%. 97%. 98%. or 99% identity thereto.

219. The gene modifying polypeptide of any of embodiments 215-218, wherein the plurality of RBDs have the same amino acid sequence as each other. 220. The gene modifying polypeptide of any of embodiments 215-218, wherein the plurality of RBDs have different amino acid sequences from each other.

221. The gene modifying polypeptide of any of embodiments 215-220, wherein the DBD comprises an amino acid sequence according to Table 7 or 8 or the amino acid sequence of the DBD of a gene modifying polypeptide as listed in any of Tables S1-S3, or an amino acid sequence having at least 75%. 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

222. The gene modifying polypeptide of any of embodiments 215-221, wherein the RT domain is from a retrovirus, or a polypeptide domain having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% amino acids sequence identity thereto.

223. The gene modifying polypeptide of any of embodiments 215-222, wherein the RT domain comprises an amino acid sequence according to Table 6 or the amino acid sequence of the RT domain of a gene modifying polypeptide as listed in any of Tables SI -S3, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

224. The gene modifying polypeptide of any of embodiments 215-223, wherein:

(a) the RBD comprises an amino acid sequence of the RBD of a gene modifying polypeptide as listed in any of Tables S1-S3, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto;

(b) the DBD comprises an amino acid sequence of the DBD of said gene modify ing polypeptide listed in any of Tables S1-S3, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto; and

(c) the RT domain comprises an amino acid sequence of the RT domain of said gene modifying polypeptide listed in any of Tables S1-S3, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identify thereto.

225. The gene modifying polypeptide of any of embodiments 215-224, wherein the gene modify ing polypeptide comprises a linker.

226. The gene modifying polypeptide of embodiment 225, wherein the linker is 2-5 amino acids in length (e.g., 4 amino acids in length). 227. The gene modifying polypeptide of embodiment 225, wherein tire linker is 5-10 amino acids in length (e.g., 8 amino acids in length).

228. The gene modifying polypeptide of embodiment 225, wherein the linker is 10-20 amino acids in length (e.g., 16 amino acids in length).

229. The gene modifying polypeptide of any of embodiments 225-228, wherein the linker comprises a sequence according to Table 10, or a sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

230. The gene modifying polypeptide of any of embodiments 225-229. wherein the linker is disposed between the DBD and the RT domain, the RT domain and the RBD, or betw een the RBD and the DBD.

231. The gene modifying polypeptide of any of embodiments 215-230, which comprises a first linker and a second linker, wherein:

(i) the first linker is disposed between tire DBD and the RT domain and the second linker is disposed between the RT domain and the RBD;

(ii) the first linker is disposed between tire DBD and tire RBD and the second linker is disposed between the RBD and RT domain; or

(iii) the first linker is disposed between the RT domain and the DBD and the second linker is disposed between the DBD and RBD.

232. The gene modifying polypeptide of any of embodiments 215-231. wherein the gene modifying polypeptide comprises, in an N-terminal to C-terminal direction: g) the DBD, a first linker, the RT domain, a second linker, the RBD; h) the RT domain, a first linker, the DBD, a second linker, the RBD; i) the RBD, a first linker, the DBD, a second linker, the RT domain; j) RBD, a first linker, RT domain, a second linker, DBD; k) the DBD, a first linker, the RBD, a second linker, the RT domain: or l) the RT domain, a first linker, the RBD, a second linker, the DBD.

233. The gene modifying polypeptide of any of embodiments 215-232, which was produced by intein- mediated fusion of an N-terminal portion comprising an intein-N domain and a C-terminal portion comprising an intein-C domain. 234. The gene modifying polypeptide of any of embodiments 215-233, wherein the DBD comprises a

Cas domain, e.g., a Cas9 domain, e.g., a Cas9 nickase domain (e.g., as described herein).

235. The gene modifying polypeptide embodiment 234, wherein the Cas domain is a dCas9 domain.

236. The gene modifying polypeptide embodiment 234, wherein the Cas domain is an nCas9 domain.

237. The gene modifying polypeptide of any of embodiments 215-236, wherein the RT domain comprises an AVIRE domain (e g., as described herein), or an amino acid sequence have at least 70%, 75%, 80%, 85%, 90%, 95%. 96%. 97%, 98%, or 99% sequence identity thereto.

238. The gene modifying polypeptide of embodiment 237, wherein the AVIRE domain comprises an AVIRE amino acid sequence listed in Table 6 or an amino acid sequence have at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity thereto.

239. The gene modifying polypeptide of any of embodiments 215-237, wherein the RT domain comprises an ML VMS domain (e.g., as described herein, e.g., an MLVMS RT domain as listed in Table 6), or an amino acid sequence have at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity thereto.

240. The gene modify ing polypeptide of embodiment 239, wherein the MLVMS domain comprises an MLVMS amino acid sequence listed in Table 6 or an amino acid sequence have at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%. 98%, or 99% sequence identity thereto

241. The gene modifying polypeptide of any of embodiments 215-240, wherein the domains are arranged, in an N -terminal to C -terminal direction: a) DBD, RT domain, RBD; b) RT domain, DBD, RBD; c) RBD, DBD. RT domain; d) RBD, RT domain, DBD; e) DBD, RBD, RT domain; or f) RT domain, RBD, DBD. 242. The gene modifying polypeptide of embodiment 241, further comprising one or more (e.g., 1, 2, 3, or 4) additional RBDs (e.g., one or more additional copies of the RED, e.g., adjacent to the RBD).

243. The gene modifying polypeptide of any of embodiments 215-242, further comprising one or more additional RT domains (e.g., one or more additional copies of the RT domain, e g., adjacent to tire RT domain).

244. The gene modifying polypeptide of embodiment 243, wherein one or more of the additional RT domains comprises an AVIRE domain (e.g., as described herein).

245. The gene modifying polypeptide of any of embodiments 215-244. wherein one or more of the additional RT domains comprises an MLVMS domain (e.g.. as described herein).

246. The gene modifying polypeptide of any of embodiments 215-245, comprising an RNA aptamerbinding domain.

247. The gene modifying polypeptide of embodiment 246, wherein the DBD is attached to the RNA aptamer-binding domain, e.g., via a linker.

248. A polypeptide system (e.g., a polypeptide complex) comprising: a) a reverse transcriptase (RT) domain; and b) a DNA binding domain (DBD) that binds to a target nucleic acid sequence and is heterologous to the RT domain (e g., a Cas domain, e g., a Cas9 domain, e.g., a Cas9 nickase domain); and c) a RNA-binding domain (RBD) that is heterologous to the DBD and the RT domain, wherein at least 2 of (e.g., all of) (a), (b), and (c) are in separate polypeptides, e.g., separate polypeptides that noncovalently form a complex.

249. The polypeptide system of embodiment 248, wherein the RT domain and the DBD are in separate polypeptides.

250. The polypeptide system of embodiment 248-249, wherein the RT domain and the RBD are in separate polypeptides. 251. The polypeptide system of embodiment 248-250, wherein complex formation is mediated by a first dimerization domain that binds a second, compatible dimerization domain.

252. The polypeptide system of embodiment 248-250, wherein complex formation is mediated by a third dimerization domain that binds a fourth, compatible dimerization domain.

253. The polypeptide system of any of embodiments 248-252, wherein: the RBD is operably linked (e.g., via a linker) to a first dimerization domain; the DBD is operably linked (e.g., via a linker) to a second dimerization domain that binds the first dimerization domain; the DBD is operably linked (e.g., via a linker) to a third dimerization domain; and the RT domain is operably linked (e.g., via a linker) to a fourth dimerization domain that binds the third dimerization domain.

254. The polypeptide system of any of embodiment 251, wherein the first and second dimerization domains are: chemical- induced dimerization domains, light-induced dimerization domains, antibody- peptide dimerization domains, or coiled coil dimerization domains.

255. The polypeptide system of any of embodiment 252, wherein the third and fourth dimerization domains are: chemical- induced dimerization domains, light-induced dimerization domains, antibody- peptide dimerization domains, or coiled coil dimerization domains.

256. The polypeptide system of any of embodiment 251 or 254, wherein the first dimerization domain and the second dimerization domain are each present in a plurality of copies, e.g., 2, 3, 4, 5, 10, 15, 20, or 30 copies.

257. The polypeptide system of any of embodiment 252 or 255, wherein the third dimerization domain and tire fourth dimerization domain are each present in a plurality of copies, e.g., 2, 3, 4, 5, 10, 15, 20, or 30 copies.

258. The polypeptide system of any of embodiments 251 , 254, or 256, wherein the first dimerization domain and the second dimerization domain have the same sequence (e.g., wherein the first dimerization domain and the second dimerization domain form a homodimer). 259. The polypeptide system of any of embodiments 252, 255, or 257, wherein the third dimerization domain and the fourth dimerization domain have the same sequence (e.g., wherein the third dimerization domain and the fourth dimerization domain form a homodimer).

260. The polypeptide system of any of embodiments 251, 254, 256, or 258, wherein the first dimerization domain and the second dimerization domain have different sequences (e.g., wherein the first dimerization domain and the second dimerization domain form a heterodimer).

261. The polypeptide system of any of embodiments 252, 255, 257, or 259, wherein the third dimerization domain and the fourth dimerization domain have different sequences (e.g., wherein the third dimerization domain and tire fourth dimerization domain fonn a hetero dimer).

262. The polypeptide system of any of embodiments 248-261, wherein the DBD is operably linked to one or more additional DBDs, wherein optionally the additional DBDs have the same sequence as the DBD.

263. The polypeptide system of any of embodiments 248-262, wherein the RBD has an amino acid sequence according to Table 31, or at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

264. The polypeptide system of any of embodiments 248-263, wherein the plurality of RBDs have the same amino acid sequence as each other.

265. The polypeptide system of any of embodiments 248-263, wherein the plurality of RBDs have different amino acid sequences from each other.

266. The polypeptide system of any of embodiments 248-265, wherein the DBD has an amino acid sequence according to Table 31, or at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

267. The polypeptide system of any of embodiments 248-266, wherein the RT domain is from a retrovirus, or a polypeptide domain having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% amino acids sequence identity thereto. 268. The polypeptide system of any of embodiments 248-267, wherein the RT domain has an amino acid sequence according to Table 6, or at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

269. The polypeptide system of any of embodiments 248-268, wherein each linker independently comprises a sequence according to Table 10, or a sequence having at least 75%. 80%. 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

270. A nucleic acid or a plurality of nucleic acids encoding the polypeptides of any of embodiments 67-100, 102-156, or 215-269.

271. A system comprising: a template RNA of any of embodiments 1-66 or 167-214; a gene modifying polypeptide, e.g., a gene modifying polypeptide of any of embodiments 67-80, or 215-269, or a polypeptide system, e.g., a polypeptide system of any of embodiments 81-100, or 248- 269; and a first gRNA comprising: a gRNA spacer that binds a third portion of the target nucleic acid sequence, wherein the third portion is one the second strand of the target nucleic acid sequence; and a gRNA scaffold that binds the DBD of the gene modifying polypeptide or the polypeptide system.

272. The system of embodiment 271, wherein the gRNA scaffold of the first gRNA has the same protein binding specificity as the gRNA sequence of the template RNA.

273. The system of embodiment 272. wherein the gRNA sequence of the template RNA binds to a first copy of a gene modifying polypeptide (e.g., at the DBD of the gene modifying polypeptide), and the gRNA scaffold of the first gRNA binds to a second copy of the gene modifying polypeptide (e.g., at tire DBD of the gene modifying polypeptide).

274. The system of embodiment 271. wherein the template RNA does not comprise a gRNA spacer or a gRNA scaffold. 275. The system of embodiment 271-273, wherein the gRNA spacer binds to a region of the target nucleic acid sequence that is within about 5, 10, 15, 20, 25, 30, or 40 nucleotides of the region of the target nucleic acid sequence bound by the PBS sequence.

276. The system of any of embodiments 271-273, or 275, which further comprises: a second Cas protein (e.g., a dead Cas protein) or a nucleic acid encoding the second Cas protein and a second gRNA comprising: a gRNA spacer that binds the first strand of the target nucleic acid at a location 3 ’ of the location bound by the PBS sequence, and a gRNA scaffold that binds the second Cas protein.

277. The system of embodiment 276, wherein the second Cas protein is a dead Cas protein (e.g., a dead Cas9 protein) or a Cas nickase protein (e.g., a Cas9 nickase protein)

278. The system of embodiment 276 or 277, wherein the gRNA spacer of tire second gRNA has a length of at least 18 nucleotides (e.g., 18-28 nucleotides, e.g., 18-21 nucleotides) and the second Cas protein is a dead Cas protein.

279. The system of embodiment 276 or 277, wherein the gRNA spacer of the second gRNA has a length of 17 nucleotides or less (e.g., 14-17 nucleotides), wherein optionally tire second Cas protein is a Cas nickase protein.

280. The system of any of embodiments 271-273, or 275-279, wherein the template RNA further comprises: a gRNA spacer that is complementary to a second portion of the target nucleic acid sequence wherein the second portion is on the first strand of tire target nucleic acid sequence; and a gRNA scaffold.

281. The system of embodiment 271-273, or 275-280, wherein the gRNA scaffold binds the DBD of the gene modifying polypeptide or the polypeptide system.

282. The system of embodiment 271-273, or 275-281, wherein the gRNA spacer has a length of 17 nucleotides or less. 283. The system of any of embodiments 271-273, or 275-282, wherein the gRNA spacer of the template RNA induces nicking of the template nucleic acid, e.g., at the second strand of the target nucleic acid sequence.

284. The system of any of embodiments 271-273, or 275-282, wherein the gRNA spacer of the template RNA does not induce nicking of the template nucleic acid.

285. A system comprising: i) atemplate RNA of any of embodiments 1-66, or 167-214 (e.g., a template RNA of embodiment 18); ii) a first polypeptide comprising: a DNA binding domain (DBD) (e.g., a Cas domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase domain); and a RNA-binding domain (RBD) that is heterologous to the DBD, wherein the RBD binds the RRS of the template RNA; iii) a first gRNA comprising: a gRNA spacer that directs the DBD of the first polypeptide to a second portion of the target nucleic acid sequence, wherein the second portion of the target nucleic acid sequence is on the second strand of the nucleic acid sequence; and a gRNA scaffold that binds the DBD of the first polypeptide; iv) a second polypeptide comprising: an RT domain, and a DNA binding domain (DBD) (e.g., a Cas domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase domain), that is heterologous to the RT domain, and wherein the DBD of the second polypeptide has a different sequence from the DBD of the first polypeptide; and v) a second gRNA comprising: a gRNA spacer that directs the DBD of the second polypeptide to a third portion of the target nucleic acid sequence, wherein the third portion is on tire first strand of tire target nucleic acid, and a gRNA scaffold that binds the DBD of the second polypeptide. 286. The system of embodiment 285, wherein the DBD of the second polypeptide comprises a Cas nickase domain or a dead Cas domain.

287. The system of embodiment 285 or 286, wherein the gRNA spacer of the second RNA induces nicking of the template nucleic acid, e.g., at the second strand of the target nucleic acid sequence.

288. The system of embodiment 285 or 286, wherein the gRNA spacer of the second RNA does not induce nicking of the template nucleic acid.

289. The system of any of embodiments 285-288, wherein the first gRNA does not detectably bind to the DBD of the second polypeptide.

290. The system of any of embodiments 285-289, wherein the second gRNA does not detectably bind to the DBD of the first polypeptide.

291. A system comprising : i) atemplate RNA of any of embodiments 1-66. or 167-214, wherein the template RNA comprises: a gRNA spacer that is complementary to a second portion of the target nucleic acid sequence wherein the second portion is on the first strand of the target nucleic acid sequence; and a gRNA scaffold; ii) a first polypeptide comprising: a DNA binding domain (DBD) (e.g., a Cas domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase domain); and a RNA-binding domain (RBD) that is heterologous to the DBD, wherein the RBD binds the RRS of the template RNA; iii) a first gRNA comprising: a gRNA spacer that directs the DBD of the first polypeptide to a third portion of the target nucleic acid sequence, wherein the third portion of the target nucleic acid sequence is on the second strand of the nucleic acid sequence; and a gRNA scaffold that binds the DBD of tire first polypeptide; and iv) a second polypeptide comprising: an RT domain, and a DNA binding domain (DBD) (e.g., a Cas domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase domain), that is heterologous to the RT domain, and wherein the DBD of the second polypeptide has a different sequence from the DBD of the first polypeptide, and wherein the gRNA scaffold of the template RNA binds the DBD of the second polypeptide.

292. The system of embodiment 291, wherein the DBD of the second polypeptide comprises a Cas nickase domain or a dead Cas domain.

293. The system of embodiment 291 or 292, wherein tire gRNA spacer of the template RNA induces nicking of the template nucleic acid, e.g., at the second strand of the target nucleic acid sequence.

294. The system of embodiments 291-293, wherein the gRNA spacer of the template RNA does not induce nicking of the template nucleic acid.

295. The system of any of embodiments 291-293, wherein the first gRNA does not detectably bind to the DBD of the second polypeptide.

296. The system of any of embodiments 291-295, wherein the gRNA of the template RNA does not detectably bind to the DBD of the first polypeptide.

297. A polypeptide system comprising: a first polypeptide comprising: a DNA binding domain (DBD) (e.g., a Cas domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase domain): a RNA-binding domain (RBD) that is heterologous to the DBD; and optionally, a linker disposed between the DBD and the RBD; and a second polypeptide comprising: an RT domain, and a DNA binding domain (DBD) (e.g., a Cas domain, e.g., a Cas nickase domain, e.g., a Cas9 nickase domain), that is heterologous to the RT domain; and optionally, a linker disposed between the RT domain and the DBD. 298. The template RNA or system of any of embodiments 1-66, 102-156, 167-214, or 271-297, wherein the target nucleic acid sequence is a target gene, enhancer, or promoter.

299. The template RNA of system any of embodiments 1-66, 102-156, 167-214, or 271-298, wherein the target nucleic acid sequence is a human target gene, human enhancer, or human promoter.

300. The system or polypeptide system of any of embodiments 81-100, 102-156, or 248-299, wherein the RED has a sequence of Table 31, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity thereto.

301. The system or polypeptide system of any of embodiments 81-100, 102-156, or 248-300, wherein the domains are arranged, in an N-terminal to C-terminal direction, the RT domain, a first linker, the DBD, a second linker, and the RBD.

302. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-301, wherein the domains are arranged, in an N-terminal to C-terminal direction, the RBD, a first linker, the RT domain, a second linker, and the DBD.

303. The system or polypeptide system of embodiment 301 or 302, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein:

(i) tire DBD comprises a Cas9 domain (e.g., as described herein);

(ii) tire first linker comprises the amino acid sequence of SEQ ID NO: 217, and/or the second linker comprises the amino acid sequence of SEQ ID NO: 217; and/or

(iii) the RBD comprises one or more (e.g., 1, 2, or 4) MCPs (e.g., as listed in Table 31).

304. The system, polypeptide system, or gene modifying polypeptide of embodiment 303, wherein the MCP comprises an N55K mutation.

305. The system or polypeptide system of embodiment 303 or 304. or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the RBD comprises, in N-terminal to C-direction, a first amino acid sequence according to SEQ ID NO: 18003, an alanine residue, and a second amino acid sequence according to SEQ ID NO: 18003. 306. The system or polypeptide system of embodiment 303 or 304, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the RED comprises, in N-terminal to C-direction, a first amino acid sequence according to SEQ ID NO: 18002, an alanine residue, and a second amino acid sequence according to SEQ ID NO: 18003.

307. The system or polypeptide system of embodiment 303 or 304. or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the RBD comprises, in N-terminal to C-terminal direction, a first amino acid sequence according to SEQ ID NO: 18003, an alanine residue, a second amino acid sequence according to SEQ ID NO: 18003, optionally a linker sequence, a third amino acid sequence according to SEQ ID NO: 18003, an alanine residue, and a fourth amino acid sequence according to SEQ ID NO: 18003.

308. The system or polypeptide system of embodiment 303 or 304, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the RBD comprises, in N-terminal to C-terminal direction, a first amino acid sequence according to SEQ ID NO: 18002, an alanine residue, a second amino acid sequence according to SEQ ID NO: 18003, optionally a linker sequence, a third amino acid sequence according to SEQ ID NO: 18002, an alanine residue, and a fourth amino acid sequence according to SEQ ID NO: 18003.

309. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-308, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the domains are arranged, in an N-terminal to C-terminal direction, the RT domain, a first linker comprising the amino acid sequence of SEQ ID NO: 217, a Cas9 domain, a second linker comprising the amino acid sequence of SEQ ID NO: 217, and an MCP.

310. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-309, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein tire domains are arranged, in an N-terminal to C-terminal direction, the RT domain, a first linker comprising the amino acid sequence of SEQ ID NO: 217, a Cas9 domain, a second linker comprising the amino acid sequence of SEQ ID NO: 217, and two MCPs.

311. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-310, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the domains are arranged, in an N-terminal to C-terminal direction, the RT domain, a first linker comprising the amino acid sequence of SEQ ID NO: 217, a Cas9 domain, a second linker comprising the amino acid sequence of SEQ ID NO: 217, a first amino acid sequence according to SEQ ID NO: 18003, an alanine residue, and a second amino acid sequence according to SEQ ID NO: 18003.

312. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-311, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the domains are arranged, in an N-terminal to C-terminal direction, the RT domain, a first linker comprising the amino acid sequence of SEQ ID NO: 217, a Cas9 domain, a second linker comprising the amino acid sequence of SEQ ID NO: 217, a first amino acid sequence according to SEQ ID NO: 18002, an alanine residue, and a second amino acid sequence according to SEQ ID NO: 18003.

313. The system or polypeptide system of any of embodiments 67-100, 102-156. or 248-312, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the domains are arranged, in an N-terminal to C-terminal direction, the RT domain, a first linker comprising the amino acid sequence of SEQ ID NO: 217, a Cas9 domain, a second linker comprising the amino acid sequence of SEQ ID NO: 217, and four MCPs.

314. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-313, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the domains are arranged, in an N-terminal to C-terminal direction, the RT domain, a first linker comprising the amino acid sequence of SEQ ID NO: 217, a Cas9 domain, a second linker comprising the amino acid sequence of SEQ ID NO: 217, and a first amino acid sequence according to SEQ ID NO: 18003, an alanine residue, a second amino acid sequence according to SEQ ID NO: 18003. optionally a linker sequence, a third amino acid sequence according to SEQ ID NO: 18003, an alanine residue, and a fourth amino acid sequence according to SEQ ID NO: 18003.

315. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-314, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the domains are arranged, in an N-terminal to C-terminal direction, the RT domain, a first linker comprising the amino acid sequence of SEQ ID NO: 217, a Cas9 domain, a second linker comprising the amino acid sequence of SEQ ID NO: 217, a first amino acid sequence according to SEQ ID NO: 18002, an alanine residue, a second amino acid sequence according to SEQ ID NO: 18003, optionally a linker sequence, a third amino acid sequence according to SEQ ID NO: 18002, an alanine residue, and a fourth amino acid sequence according to SEQ ID NO: 18003. 316. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-315, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the domains are arranged, in an N-terminal to C-terminal direction, an MCP, a first linker comprising the amino acid sequence of SEQ ID NO: 217. the RT domain, a second linker comprising the amino acid sequence of SEQ ID NO: 217, and a Cas9 domain.

317. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-316, or the gene modify ing polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the domains are arranged, in an N-terminal to C-terminal direction, two MCPs, a first linker comprising the amino acid sequence of SEQ ID NO: 217. the RT domain, a second linker comprising the amino acid sequence of SEQ ID NO: 217, and a Cas9 domain.

318. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-317, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the domains are arranged, in an N-terminal to C-terminal direction, a first amino acid sequence according to SEQ ID NO: 18003, an alanine residue, a second amino acid sequence according to SEQ ID NO: 18003, a first linker comprising the amino acid sequence of SEQ ID NO: 217, the RT domain, a second linker comprising the amino acid sequence of SEQ ID NO: 217, and a Cas9 domain.

319. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-318, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the domains are arranged, in an N-terminal to C-terminal direction, a first amino acid sequence according to SEQ ID NO: 18002, an alanine residue, a second amino acid sequence according to SEQ ID NO: 18003, a first linker comprising the amino acid sequence of SEQ ID NO: 217, the RT domain, a second linker comprising the amino acid sequence of SEQ ID NO: 217, and a Cas9 domain.

320. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-319, or tire gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the domains are arranged, in an N-terminal to C-terminal direction, four MCPs, a first linker comprising the amino acid sequence of SEQ ID NO: 217, the RT domain, a second linker comprising the amino acid sequence of SEQ ID NO: 217, and a Cas9 domain. 321. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-320, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the domains are arranged, in an N-terminal to C -terminal direction, a first amino acid sequence according to SEQ ID NO: 18003, an alanine residue, a second amino acid sequence according to SEQ ID NO: 18003, optionally a linker sequence, a third amino acid sequence according to SEQ ID NO: 18003, an alanine residue, a fourth amino acid sequence according to SEQ ID NO: 18003, a first linker comprising the amino acid sequence of SEQ ID NO: 217, the RT domain, a second linker comprising the amino acid sequence of SEQ ID NO: 217, and a Cas9 domain.

322. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-321, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the domains are arranged, in an N-terminal to C-terminal direction, a first amino acid sequence according to SEQ ID NO: 18002, an alanine residue, a second amino acid sequence according to SEQ ID NO: 18003, optionally a linker sequence, a third amino acid sequence according to SEQ ID NO: 18002, an alanine residue, a fourth amino acid sequence according to SEQ ID NO: 18003, a first linker comprising the amino acid sequence of SEQ ID NO: 217, the RT domain, a second linker comprising the amino acid sequence of SEQ ID NO: 217, and a Cas9 domain.

323. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-322, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the first amino acid sequence according to SEQ ID NO: 18003 is immediately adjacent to the alanine residue that is C- tenninal of the first amino acid sequence according to SEQ ID NO: 18003.

324. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-323, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the first amino acid sequence according to SEQ ID NO: 18002 is immediately adjacent to the alanine residue that is C- terminal of the first amino acid sequence according to SEQ ID NO: 18002.

325. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-324, orthe gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the second amino acid sequence according to SEQ ID NO: 18003 is immediately adjacent to the alanine residue that is N- terminal of the second amino acid sequence according to SEQ ID NO: 18003. 326. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-325, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the third amino acid sequence according to SEQ ID NO: 18003 is immediately adjacent to the alanine residue that is C- terminal of the third amino acid sequence according to SEQ ID NO: 18003.

327. The system or polypeptide system of any of embodiments 67-100, 102-156. or 248-326, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the third amino acid sequence according to SEQ ID NO: 18002 is immediately adjacent to the alanine residue that is C- terminal of the third amino acid sequence according to SEQ ID NO: 18002.

328. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-327, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, wherein the fourth amino acid sequence according to SEQ ID NO: 18003 is immediately adjacent to the alanine residue that is N- terminal of the fourth amino acid sequence according to SEQ ID NO: 18003.

329. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-328, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, which comprises an amino acid sequence according to SEQ ID NO: 18005 or 18006, or a sequence with at least 80%, 85%, 90%. 95%, 98%, or 99% identity thereto.

330. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-329, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, which comprises an amino acid sequence according to Table S5 or Table S6, or a sequence with at least 80%, 85%. 90%. 95%. 98%, or 99% identity thereto.

331. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-329, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, which comprises an amino acid sequence according to Table Nl, or a sequence with at least 80%, 85%. 90%, 95%, 98%, or 99% identity thereto.

332. The system or polypeptide system of any of embodiments 67-100, 102- 156, or 248-329, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, which comprises an amino acid sequence according to Table N2, or a sequence with at least 80%, 85%, 90%, 95%, 98%, or 99% identity thereto. 333. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-329, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, which comprises an amino acid sequence according to Table N4, or a sequence with at least 80%, 85%, 90%, 95%, 98%, or 99% identity thereto.

334. The system or polypeptide system of any of embodiments 67-100, 102-156, or 248-329, or the gene modifying polypeptide of any of embodiments 68, 71-80, or 217-247, which comprises the amino acid sequence of SEQ ID NO: 17,101, or a sequence with at least 80%, 85%, 90%, 95%, 98%, or 99% identity thereto.

335. The template RNA, system, or polypeptide of any of embodiments 1-162. or 167-334, which induces an insertion having at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to a desired insertion sequence.

336. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-335, which induces an insertion having 100% sequence identity to a desired insertion sequence.

337. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-336, which induces an insertion having the same length as a desired insertion sequence.

338. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-337, which induces an insertion having the same length as a desired insertion sequence wherein the insertion does not comprise a position of non-identity to a desired insertion sequence.

339. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-338, which induces an insertion having the same length as a desired insertion sequence in at least about 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%. 14%, 15%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 36%, 37%, 38%, 39%, or 40% of cells.

340. The template RNA, system, or polypeptide of any of embodiments 1 -162, or 167-339, which induces an insertion having the same length as a desired insertion sequence, and wherein sequencing of the insertion does not reveal a position of non-identity to a desired insertion sequence (e.g., sequencing reveals that each position of the insertion is identical to the desired insertion sequence, or sequencing categorizes one or more positions of the insertion as ambiguous and all other positions of the insertion as identical to the desired insertion sequence).

341. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-340, which induces an insertion having at least 80%, 85%, 90%, 95%, 96%. 97%, 98%, 99%, or 100% sequence identity to a desired insertion sequence in at least about 4%. 5%, 6%, 7%, 8%. 9%, 10%, 11%, 12%, 13%,

14%, 15%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 36%, 37%, 38%, 39%, or 40% of cells.

342. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-341, which induces an insertion having 100% sequence identity to a desired insertion sequence in at least about 4%,

5%, 6%. 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 20%, 21%, 22%, 23%, 24%, 25%, 30%. 35%.

36%, 37%, 38%, 39%, or 40% of cells.

343. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-342, which induces an insertion having 100% sequence identity to a desired insertion sequence in at least about 8% of cells.

344. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-343, which induces an insertion having 100% sequence identity to a desired insertion sequence in at least about 11% of cells.

345. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-344, which induces an insertion having 100% sequence identity to a desired insertion sequence in at least about 24% of cells.

346. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-345, which induces an insertion having 100% sequence identity to a desired insertion sequence in at least about 37% of cells.

347. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-346, which induces insertions at two copies of a target locus in at least about 4%, 5%, 6%, 7%, 8%, 9%, 10%, 1 1 %, 12%, 13%, 14%, 15%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 36%, 37%, 38%, 39%, or 40% of cells. 348. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-347, wherein the gene modifying polypeptide comprises, in N-terminal to C-terminal order, a Cas domain (e.g., a Cas9 domain), an RBD, and a reverse transcriptase (RT) domain.

349. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-348, wherein the gene modifying polypeptide comprises, in N-terminal to C-terminal order, a Cas domain (e.g.. a Cas9 domain), a reverse transcriptase (RT) domain, and an RBP domain.

350. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-349, wherein the gene modifying polypeptide comprises, in N-terminal to C-terminal order, a reverse transcriptase (RT) domain, an RBP domain, and a Cas domain (e.g., a Cas9 domain).

351. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-350, wherein the template RNA comprises an end block sequence that promotes nicking at a target site by a Cas domain (e.g., a Cas9 domain).

352. The template RNA, system, or polypeptide of any of embodiments 1-162. or 167-351, wherein the template RNA comprises an end block sequence comprising a gRNA spacer having a length greater than 15 nucleotides (e.g., at least 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides).

353. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-352, wherein the template RNA comprises an end block sequence comprising a gRNA spacer having a length of at least 20 nucleotides.

354. The template RNA, system, or polypeptide of any of embodiments 1-162, or 167-353, wherein the template RNA comprises at least 4 copies of the RBD recruitment site (RRS), e.g., at least 4 copies of an MS2 sequence.

355. The template RNA, system, or polypeptide of any of embodiments 1-162 or 167-354, which produces perfect editing at about 5%, 10%, or 15%, or about 1-5%, 5-10%, 10-15%, or 15-20% of target nucleic acids. 356. A method for modifying a target nucleic acid in a cell (e.g., a human cell), the method comprising contacting the cell with the system of any one of the preceding embodiments, or nucleic acid encoding the same, thereby modifying the target nucleic acid.

357. The method of embodiment 356, wherein presence of the second polypeptide, compared to an otherwise similar system lacking tire second polypeptide, results in one or more of: increased unwinding of the target nucleic acid: increased number of target nucleic acids that are modified; increased length of insertion into the target nucleic acid; or reduced MMR activity at the target nucleic acid.

358. The method of embodiment 356 or 357. wherein the cell is in vivo or ex vivo.

359. A system comprising:

I) template RNA comprising: a) a heterologous object sequence comprising, from 5’ to 3’: i) optionally, a post-edit homology region, ii) a mutation region, to introduce a mutation into a target nucleic acid sequence wherein the mutation region, and iii) optionally, a pre-edit homology region, and b) a primer binding site sequence (PBS sequence) that binds a first portion of the target nucleic acid sequence, wherein first portion is in the first strand of the target nucleic acid sequence, and wherein the PBS sequence is 3’ of the heterologous object sequence, c) an RBD recruitment site (RRS), wherein tire RRS is 5 ’ of the heterologous object sequence or 3’ of the PBS sequence; and d) an end block sequence which is 5' of the heterologous object sequence (e.g., wherein the end block sequence is 5’ of both of the heterologous object sequence and the RRS), wherein the end block sequence comprises: i) agRNA spacer having a length of 12-17 nt (e.g., 15 nt), wherein the gRNA spacer is complementary to a second portion of the target nucleic acid sequence wherein tire second portion is on the first strand of the target nucleic acid sequence; and ii) a gRNA scaffold; and

II) a gRNA configured to produce a second strand nick (a "‘second strand nick gRNA”), comprising: i) a gRNA spacer having a length of at least 18 nt, wherein the gRNA spacer is complementary to a further portion of the first target nucleic acid sequence; and ii) a gRNA scaffold, wherein: the second portion is situated between the first portion and the further portion; or the further portion is situated between tire first portion and the second portion.

360. The system of embodiment 359, which is capable of producing an insertion, deletion, or replacement in the target nucleic acid sequence.

361. The system of embodiment 359, wherein the heterologous object sequence (e.g., between the postedit homology region and the mutation region) comprises a deletion relative to a portion of the target nucleic acid sequence, tire portion comprising at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 100, 200, 300, or 400 contiguous nucleotides, or 2-10, 10-20, 20-50, 50-100, 100- 200, or 200-500 contiguous nucleotides of the target nucleic acid sequence.

In one aspect, the disclosure relates to a system for modifying DNA, comprising (a) a nucleic acid encoding a gene modifying polypeptide capable of target primed reverse transcription, the polypeptide comprising (i) a reverse transcriptase domain and (ii) a Cas9 nickase that binds DNA and has endonuclease activity, and (b) a template RNA comprising (i) a gRNA spacer that is complementary to a first portion of a human gene, (ii) a gRNA scaffold that binds the polypeptide, (iii) a heterologous object sequence comprising a mutation region, and (iv) a primer binding site (PBS) sequence comprising at least 3, 4, 5, 6, 7, or 8 bases of 100% homology to a target DNA strand at the 3 ' end of the template RNA.

The gRNA spacer may comprise at least 15 bases of 100% homology to the target DNA at the 5 ' end of the template RNA. The template RNA may further comprise a PBS sequence comprising at least 5 bases of at least 80% homology to the target DNA strand. The template RNA may comprise one or more chemical modifications. The domains of the gene modifying polypeptide may be joined by a peptide linker. The polypeptide may comprise one or more peptide linkers. The gene modifying polypeptide may further comprise a nuclear localization signal. The polypeptide may comprise more than one nuclear localization signal, e.g., multiple adjacent nuclear localization signals or one or more nuclear localization signals in different regions of the polypeptide, e.g., one or more nuclear localization signals in the N-terminus of the polypeptide and one or more nuclear localization signals in the C-terminus of the polypeptide. The nucleic acid encoding the gene modify ing polypeptide may encode one or more intein domains.

Introduction of the system into a target cell may result in insertion of at least 1, 2, 3, 4, 5, 10, 15, 20, 25, 30. 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 500, or 1000 base pairs of exogenous DNA. Introduction of the system into a target cell may result in deletion, wherein the deletion is less than 2, 3, 4, 5, 10, 50, or 100 base pairs of genomic DNA upstream or downstream of the insertion. Introduction of the system into a target cell may result in substitution, e.g., substitution of 1, 2, or 3 nucleotides, e.g., consecutive nucleotides. The heterologous object sequence may be at least 5, 10, 25, 50, 100, 150, 200, 250, 300, 400, 500. 600, or 700 base pairs.

In one aspect, the disclosure relates to a pharmaceutical composition comprising the system described above and a pharmaceutically acceptable excipient or carrier, wherein the pharmaceutically acceptable excipient or carrier is selected from the group consisting of a plasmid vector, a viral vector, a vesicle, and a lipid nanoparticle. In one aspect, the disclosure relates to a pharmaceutical composition comprising tire system described above and multiple pharmaceutically acceptable excipients or carriers, wherein the pharmaceutically acceptable excipients or carriers are selected from the group consisting of a plasmid vector, a viral vector, a vesicle, and a lipid nanoparticle, e.g., where the system described above is delivered by two distinct excipients or carriers, e.g., two lipid nanoparticles, two viral vectors, or one lipid nanoparticle and one viral vector. The viral vector may be an adeno-associated vims (AAV).

In one aspect, the disclosure relates to a host cell (e.g., a mammalian cell, e.g., a human cell) comprising tire system described above.

The system may be introduced in vivo, in vitro, ex vivo, or in situ. The nucleic acid of (a) may be integrated into the genome of the host cell. In some embodiments, the nucleic acid of (a) is not integrated into the genome of the host cell. In some embodiments, the heterologous object sequence is inserted at only one target site in the host cell genome. The heterologous object sequence may be inserted at two or more target sites in the host cell genome, e.g., at the same corresponding site in two homologous chromosomes or at two different sites on the same or different chromosomes. The heterologous object sequence may encode a mammalian polypeptide, or a fragment or a variant thereof. The components of the system may be delivered on 1, 2, 3, 4, or more distinct nucleic acid molecules. The system may be introduced into a host cell by electroporation or by using at least one vehicle selected from a plasmid vector, a viral vector, a vesicle, and a lipid nanoparticle.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

FIG. 1 is a series of diagrams showing components of an exemplary trans gene modifying system. The exemplary system comprises three components: (1) a gene modifying polypeptide, (2) a template RNA, and (3) a gRNA. The gene modifying polypeptide includes a nickase Cas9 (nCas9). an RNA binding domain (RBD), and a polymerase (in this example a retroviral reverse transcriptase (RT)). The template contains an RBD recruitment site (RRS), a primer binding site sequence (PBS sequence) (Priming) and a heterologous object sequence (template region), as well as an end protection/ end block sequence that, in this embodiment, (a) protects the structure from exonucleases, and/or (b) terminates the RT due to the secondary structure. The third component is a gRNA. In a fully assembled trans gene modifying reaction, the gRNA associates with the nCas9 of the gene modifying polypeptide, and directs the polypeptide to the DNA. The nCas9 then introduces a nick into the DNA. The RBD of the polypeptide recruits the template to the site of the nick through its interaction with tire RRS on the template RNA. The Cas9 induced nick results in a 3’ flap, that can anneal to the PBS sequence of the template RNA. The RT can then reverse transcribe the template until it hits the end protection structure. The highly structured end protection will terminate the reverse transcription. Cellular repair processes will incorporate the edited strand into the genome.

FIGS. 2A-2B are a series of diagrams showing exemplary polypeptides that can be used in a trans gene modifying system as described herein. There are several ways by which a polypeptide containing an nCas9-RT-RBD can be assembled: (A) by direction fusion, (B) by using either intein or dimerization (homo or hetero) domains that covalently or non-covalently assemble the full polypeptide, respectively. (A) In a direct fusion approach, a linker connects the nCas9 with the RBD, which in turn is connected through a linker with the RT (e.g., as shown). Exemplary possible configurations are listed in the panel below Fig. 2A, and RBDs /linkers are listed in a separate table. An RBP repeat can be present once or multiple (e g., n=1-5) times in a RBD. (B) The polypeptide can also be assembled using various intein or dimerization domains. In some instances, the nCas9 is linked to a dimerization domain (FD#1), and the RED is linked to its partner dimerization domain. The nCas9 is linked to a second dimerization domain (FD2), while the RT is linked to its partner. The dimerization domain can either result in covalent linkage (e.g., when using inteins), or in non-covalent assembly of the polypeptide (e.g., using chemical or light induced dimerization). Two dimerization reactions are utilized, upon which a polypeptide complex is assembled. Exemplary possible variations are described herein (e.g., intein dimerization domains, chemically-induced dimerization domains, light-induced dimerization domains, antibody-peptide dimerization domains, coiled-coil dimerization domains). The dimerization domains can be present once or multiple (n=l-30) times, e.g., as tandem repeats.

FIGS. 3A-3C are a series of diagrams showing an exemplary template RNA and subregions thereof. (A) Schematic of an exemplary template RNA. Uris template includes (3’ to 5') of one or several (n=l-10) RRS at tire 3' end, a linker, followed by a PBS sequence (priming) (8-17 nts), followed by a heterologous object sequence (template). The template region contains, in some embodiments, a pre-edit homology region (0-20 nts), the mutation region having a desired modification to the genome (e.g., an insertion, deletion, or point mutation(s)), and a post-edit homology region (e.g., n=5-500 nts). Lastly, an end protection/ end block sequence is present at the 5’ end of the template RNA. Exemplary possible configurations are listed in the panel below Fig. 3A. (B) Exemplary variations for the various template RNA components are listed. Exemplary sequences for such components are described herein. (C) Schematic of an exemplary template RNA wherein the RRS is situated betw een the pre-edit homology region and tire mutation region.

FIGS. 4A-4B are a series of diagrams showing, among other things, increased unwinding of a target nucleic acid, as well as engagement and modulation of a second strand of the target nucleic acid, e.g., to increase gene modifying efficiency and/or to pennit long insertions. There are several ways in which the second strand can be engaged in the context of trans gene modification. (A) In one exemplary- configuration, a second Cas9-gRNA complex can be introduced in trans. This second Cas9 complex can be, for example, a nickase Cas9 (nCas9) to direct a nick on the second strand . This nick could be used to initiate second strand synthesis after the RT reaction, and/or to signal to the cell endogenous Mismatch repair system that the first (edited) strand should be maintained and copied. Alternatively, tire Cas9 can be, for example, a catalytically inactive (dead) Cas9 (dCas9). Without wishing to be bound by theory, in some embodiments this would unwind the DNA and could facilitate the repair of especially longer insertions. The Cas9 in this scenario can be of the same or orthogonal species as the Cas9 present in the trans rewriting polypeptide. Thus, Fig. 4A shows an exemplary 5-component system comprising 3 RNAs and 2 different polypeptides. As described herein, the system illustrated in Fig. 4A could be altered to become a 4-component system, e.g., by fusing the template RNA to the gRNA that binds the top strand of the target nucleic acid sequence. (B) In an alternate configuration, the second strand modulation is recruited by the template RNA, by using a gRNA (full or partial) as an end structure. This gRNA can either be a full gRNA with a scaffold and a 20nt spacer, or a partial gRNA with a scaffold and a spacer of 17 or fewer nucleotides. A full gRNA will engage the polypeptide complex and can position the nick from the nCas9 in the polypeptide complex to the second strand. Placement of this nick could be used to initiate second strand synthesis after the RT reaction, and/or to signal to the cell endogenous mismatch repair system that the first (edited) strand should be maintained and copied. A spacer region (e.g., having a length of less than or equal to 17 nucleotides, e.g., about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or 17 nucleotides) can lead to binding of the polypeptide complex, but will not result in a nick. This would unwind the DNA and may facilitate the repair of insertions (e.g., longer insertions). Thus, Fig. 4B shows an exemplary 3-component system comprising two RNAs and one polypeptide (which is present in two copies). As described herein, the system illustrated in Fig. 4B could be altered to become a 4-component system, e.g., by replacing the right hand copy of the gene modifying polypeptide with a different Cas protein.

FIG. 5 shows a graph of % GFP positive cells after treating the GFP reporter-expressing cell line with a gene modifying system comprising a ttRNA having the characteristics indicated on the X-axis or with a control gene modifying system. “Short spacer” indicates a 15 nt spacer and “long spacer” indicates a 20 nt spacer. “Homology2” refers to the post-edit homology region.

FIGS. 6A-6D show graphs of % GFP positive cells after treating the GFP reporter-expressing cell line with a gene modifying system comprising a ttRNA having the characteristics indicated on the X-axis and above the graph.

FIGS. 7A-7D are a series of graphs showing percentage perfect editing at the GFP locus, determined using next-generation sequence data from amplicon sequencing, after treating GFP reporterexpressing cells with a gene modifying system comprising a ttRNA having the indicated characteristics.

FIGS. 8A-8B are a series of graphs showing percentage GFP -positive cells after treating GFP reporter-expressing cells with a gene modifying system comprising a ttRNA with 4 MS2 sequences and a 5’ end block comprising a gRNA scaffold and either a short 15-nt spacer or a long 20-nt spacer.

FIGS. 9A-9B are a series of graphs showing percentage perfect editing at the GFP locus, determined using next-generation sequence data from amplicon sequencing, after treating GFP reporterexpressing cells with a gene modifying system comprising a gene modifying system comprising a ttRNA with 4 MS2 sequences and a 5’ end block comnprising a gRNA scaffold and either a short 15-nt spacer or a long 20-nt spacer.

FIGS. 10A-10C are a series of diagrams illustrating a gene modifying system utilizing a trans template, and the target nucleic acid corresponding to such a system. Each is described in more detail below.

FIG. 10A depicts a target nucleic acid annotated with the positions of different parts of a template RNA (specifically, a trans template RNA) and gRNA of a gene modifying system. Arrows indicate the position of tire primary gRNA nick (directed by the gRNA) and the second nick (which can be generated by the end block sequence of the trans template RNA, described further in Fig. 10B). The position on the target nucleic acid that corresponds to the pre-edit homology region of the trans template RNA is labeled “Homology Ann 1”. The position on the target nucleic acid that corresponds to the post-edit homology region is labeled “Post-edit homology arm”. The post-edit homology ann of tire DNA is divided into two parts: one labeled “extension” and one labeled “primer”. The DNA region labeled “extension” (which in this example is 35 bp long) corresponds to the part of the trans template RNA called the extension homology region. However, the length of the extension homology region need not be identical to the length of the DNA region labeled “extension”. Rather, different lengths of extension homology region can be selected, for instance, between 0-35 nucleotides. In this example, an extension homology region of 0 nucleotides can be used to create a deletion of 35 nucleotides, because the trans template RNA is missing 35 nucleotides relative to the target nucleic acid. In contrast, in this example, an extension homology region of 35 nucleotides does not result in a deletion, because the trans template RNA comprises all 35 nucleotides corresponding to the DNA region labeled “extension”. Extension homology regions of intermediate length can be selected to make deletions of intermediate length. As mentioned above, the post-edit homology arm also contains a region labeled “primer”. This is the region immediately 5' of the site of the second strand nick. Without wishing to be bound by theory, in some embodiments, the region of the DNA labeled “primer” acts as a primer as described below with respect to FIG. 10B.

FIG. 10B depicts a target nucleic acid and a gene modifying system comprising a template RNA (specifically, a trans template RNA), a gRNA, and two gene modifying polypeptides (or two copies of the same gene modifying polypeptide). The gRNA, here labeled “sgRNA4”, positions the first gene modifying polypeptide on the target nucleic acid, where it can produce a first strand nick. Hie gene modifying polypeptide comprises a Cas9 nickase domain, an RNA binding domain (RBD), which here comprises two copies of the MCP domain, and an RT domain. The regions and their functions of the trans template RNA in this figure (labeled “trans-template” in the figure) are now described from 3’ to 5’. Without being bound by theory, the trans template RNA associates with the gene modifying polypeptide by virtue of the trans template RNA’s RRS (here, an MS2 sequence) binding to the RBD of the gene modifying polypeptide. In the trans template RNA shown in this figure, adjacent to the RRS is the primer binding site (PBS). The PBS can be seen binding to the nicked first strand of the target nucleic acid, where it may promote target-primed reverse transcription (TPRT). Next, the template RNA may optionally comprise a pre-edit homology region. Following the pre-edit homology region, the trans template RNA comprises a mutation region. Here, the mutation region comprises an insertion sequence (labeled “insertion seq” in the figure), designed to insert a sequence of interest into the target nucleic acid. Following the mutation region, the trans template RNA typically comprises a post-edit homology region. Following the post-edit homology region is an end block sequence at the 5’ end (labeled “5" end block” in the figure). The 5’ end block in this figure is a gRNA that comprises a gRNA scaffold region shown as a hairpin and a gRNA spacer region shown pairing with the first strand of the target nucleic acid. Without wishing to be bound by theory, the 5 ’ end block may recruit a gene modifying polypeptide and unwind the target nucleic acid and produce a second strand nick. The gene modifying polypeptide that produces the second strand nick may have the same sequence or a different sequence from the gene modifying polypeptide that produces the first strand nick.

FIG. 10C depicts a target nucleic acid annotated with the positions of different parts of a template RNA (specifically, a trans template RNA) and gRNA of a gene modifying system as described above with respect to FIG. 10A. The position on the target nucleic acid between the primary gRNA nick and the second nick is labeled “variable spacing”, indicating that the gene editing system can be configured to place the second strand nick at a desired point in the target nucleic acid, to control tire size of deletion being generated. In this example, within the region of the target nucleic acid labeled “variable spacing”, is a region labeled “variable # bp deleted”, between the position on tire target nucleic acid that corresponds to the pre-edit homology region (labeled as “Homology Arm 1”) and the extension homology region of the post-edit homology region (labeled as “extension 0-35bp”) . This illustrates the position of the deletion generated by the gene modifying system. In this example, because the template RNA lacks a sequence according to the box labeled “variable # bp deleted”, the edited DNA comprises a deletion that corresponds to the sequence that the template RNA lacks. In this scenario, the deleted target sequence may be replaced with any insertion sequence encoded in the mutation region of the template. Lastly, as similarly noted above for FIG. 10A. the length of the extension homology region in FIG. 10C need not be identical to the length of the DNA region labeled “extension”. Rather, different lengths of extension homology region can be selected, for instance, between 0-35 nucleotides. In this example, an extension homology region of 0 nucleotides can be used to create a deletion of 35 nucleotides, because the trans template RNA is missing 35 nucleotides relative to the target nucleic acid. In contrast, in this example, an extension homology region of 35 nucleotides does not result in a deletion, because the trans template RNA comprises all 35 nucleotides corresponding to the DNA region labeled “extension’’. Extension homology regions of intermediate length can be selected to make deletions of intermediate length.

FIGS. 11A-11C are a series of diagrams illustrating target nucleic acid corresponding to gene modifying systems utilizing trans templates having, in this example, different length of extension homology region. FIGS. 11A-11C depict a target nucleic acid annotated with the positions of different parts of a template RNA (specifically, a trans template RNA) and gRNA of a gene modifying system, with annotations as described above with respect to FIG. 1 OA. In particular, FIG. 11 A depicts that a target nucleic acid region labeled “extension contiguous to homology arm 1” corresponds to a full length of extension homology region of the trans template RNA (in this example, 35 nucleotides). FIG. 1 IB depicts a target nucleic acid labeled “short extension” corresponds to a short extension homology region of the trans template RNA which is next to the 3' end of the primer homology region of the trans template RNA. In this example, the length of extension homology region can have a length of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, or 34 nucleotides. FIG. 11C depicts a target nucleic acid labeled “no extension” that has no corresponding extension homology region of the trans template RNA. In other words, the extension homology region of the trans template RNA has a length of 0 nucleotide.

FIGS. 12A-12C are a series of diagrams illustrating a gene modify ing system utilizing a trans template, and the target nucleic acid corresponding to such a system. Each is described in more detail below.

FIG. 12A depicts a target nucleic acid and a gene modifying system comprising a template RNA (specifically, a trans template RNA), two gRNAs, and three gene modifying polypeptides (or three copies of tire same gene modifying polypeptide). The first gRNA, here labeled “sgRNA4”, positions tire first gene modifying polypeptide on the target nucleic acid, where it can produce a first strand nick. The gene modifying polypeptide comprises a Cas9 nickase domain, an RNA binding domain (RBD), which here comprises two copies of the MCP domain, and an RT domain. The regions and their functions of the trans template RNA in this figure (labeled “trans-template” in the figure) are described above with respect to FIG. 10B. In particular, the trans template RNA comprises an end block sequence at the 5’ end (labeled “template anchor” in the figure). The 5’ end block in this figure comprises a gRNA scaffold region shown as a hairpin and a gRNA spacer region shown pairing with the first strand of the target nucleic acid. Without wishing to be bound by theory, a 5’ end block acting as a template anchor may recruit a second gene modifying polypeptide (labeled “Second complex (anchoring)”) and unwind the target nucleic acid, but does not produce a nick because the spacer is too short. The second gRNA, labeled ‘'2 ^nd nick gRNA”, comprises a gRNA scaffold region shown as a hairpin and a gRNA spacer region shown pairing with the first strand of the target nucleic acid. Without wishing to be bound by theory, the second gRNA may recruit a third gene modifying polypeptide (labeled “Third complex (nicking)”) and bind tire target nucleic acid at the position that corresponds to the post-edit homology region of the trans template RNA and produce a second strand nick. The second and the third gene modifying polypeptide may have the same amino acid sequence or a different amino acid sequence from the gene modifying polypeptide that produces the first strand nick. The gene modifying polypeptide that produces the second strand nick may have the same amino acid sequence or a different amino acid sequence from the gene modifying polypeptide that produces the first strand nick. In contrast to the system illustrated in FIG. 10B, the system described in FIG. 12A allows the site of the second nick to be at a different position from the site of the template anchor.

FIG. 12B and 12C further illustrate the position of tire template anchor and the second strand nick on the target nucleic acid. FIGS. 12B and 12C depict target nucleic acid annotated with the positions of different parts of a template RNA (specifically, a trans template RNA) and gRNA of gene modifying systems, with annotations as described above with respect to FIG. 10A. In particular, in some embodiments, the template anchoring induced by the 5 ’ end block of the trans template RNA and the second gene modifying polypeptide can be located between the position of the target nucleic acid that corresponds to the pre-edit homology region (labeled “Homology Arm 1”) and the post-edit homology region (labeled “Post-edit homology region”), as shown in FIG. 12B. In some embodiments, the template anchoring induced by the 5 ’ end block of the trans template RNA and the second gene modifying polypeptide can be located outside of the region between the position of tire target nucleic acid that corresponds to the pre-edit homology region (labeled “Homology Ann 1”) and the post-edit homology region (labeled “Post-edit homology region”), as shown in FIG. 12C. In other words, FIG. 12C illustrates embodiments wherein the position of the target nucleic acid that corresponds to the post-edit homology region is situated between the template anchor and the position of the target nucleic acid that corresponds to the pre-edit homology region (labeled “Homology Arm 1”). A system as described in FIG. 12B or 12C can be used, in some instances, to direct a replacement or deletion to the target nucleic acid.

FIG. 13 is a graph showing percentage GFP -positive cells after treating cells comprising variant lengths of disruption sequence in a GFP reporter cassette with a gene modify ing system comprising a gene modifying polypeptide, a gRNA and a ttRNA having 5' end block comprising a gRNA.

FIG. 14 is a series of graphs showing percentage of GFP-positive cells after treating a 150-bp insertion GFP reporter-expressing cell line with a gene modifying system comprising a ttRNA having 4 MS2 repeats or 1 MS2 repeat. The gene modifying polypeptides in the system included an RT-Cas9-MCP configuration and an MCP-RT-Cas9 configuration. Also tested was a variant that included an N55K mutation in the MCP region.

FIG. 15A and 15B are a series of graphs showing editing of GFP reporter cells treated with a gene modifying system comprising a gRNA, and a gene modifying polypeptide and ttRNA encoding cognate RBP/RRS pairs (e.g. MCP variants with MS2 variants; PCP variants with PP7 variants; Com variants with com variants). The gene modifying polypeptides included the following configurations: Cas9-RBP-RT, RT-RBP-Cas9, and Cas9-RT-RBP. (A) Percentage GFP-positive cells after treatment with the indicated gene modifying systems. (B) Percentage of cells that showed perfect editing at the GFP locus after treatment with the indicated gene modifying systems.

FIG. 16 is a graph showing percentage GFP-positive cells after treating a 150 bp insertion GFP reporter-expressing cell line with a gene modifying system comprising a gRNA. ttRNA and a gene modifying polypeptide comprising an exemplary Marathon RT domain. The gene modifying polypeptides included various configurations (i.e.. Config 1. Config 2, and Config 3 as described in Example 3), or with H2O only or no-gRNA negative control gene modifying systems.

FIG. 17 is a graph showing percentage perfect editing at the GFP locus after treating a 150 bp insertion GFP reporter-expressing cell line with a gene modifying system comprising a gRNA, a gene modify ing polypeptide, and a ttRNA having the indicated primer length and the indicated length of an extension to the homology region.

DETAILED DESCRIPTION

Definitions The term “expression cassette,” as used herein, refers to a nucleic acid construct comprising nucleic acid elements sufficient for the expression of the nucleic acid molecule of the instant invention.

The term “extension homology region” of a template RNA, as used herein, refers to a 3 ’ portion of the post-edit homology region that has sequence identity to the sequence immediately adjacent to the second strand nick on the side closer to the first strand nick.

A “gRNA spacer”, as used herein, refers to a portion of a nucleic acid that has complementarity to a target nucleic acid and can, together with a gRNA scaffold, target a Cas protein to the target nucleic acid.

A “gRNA scaffold”, as used herein, refers to a portion of a nucleic acid that can bind a Cas protein and can. together with a gRNA spacer, target the Cas protein to the target nucleic acid. In some embodiments, the gRNA scaffold comprises a crRNA sequence, tetraloop, and tracrRNA sequence. A ''gene modifying polypeptide'', as used herein, refers to a polypeptide comprising a retroviral reverse transcriptase, or a polypeptide comprising an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity to a retroviral reverse transcriptase, which is capable of integrating a nucleic acid sequence (e.g., a sequence provided on a template nucleic acid) into a target DNA molecule (e.g.. in a mammalian host cell, such as a genomic DNA molecule in the host cell). In some embodiments, the gene modifying polypeptide is capable of integrating the sequence substantially without relying on host machinery. In some embodiments, the gene modifying polypeptide integrates a sequence into a random position in a genome, and in some embodiments, the gene modifying polypeptide integrates a sequence into a specific target site. In some embodiments, a gene modify ing polypeptide includes one or more domains that, collectively, facilitate 1) binding the template nucleic acid, 2) binding the target DNA molecule, and 3) facilitate integration of the at least a portion of the template nucleic acid into the target DNA. Gene modifying polypeptides include both naturally occurring polypeptides as well as engineered variants of the foregoing, e.g., having one or more amino acid substitutions to the naturally occurring sequence. Gene modifying polypeptides also include heterologous constructs, e.g., where one or more of the domains recited above are heterologous to each other, yvhether through a heterologous fusion (or other conjugate) of otherwise wild-type domains, as well as fusions of modified domains, e.g., by yvay of replacement or fusion of a heterologous sub-domain or other substituted domain. Exemplary gene modifying polypeptides, and systems comprising them and methods of using them, that can be used in the methods provided herein are described, e.g., in PCT/US2021/020948, yyhich is incorporated herein by reference yvith respect to gene modifying polypeptides that comprise a retroviral reverse transcriptase domain. In some embodiments, a gene modify ing polypeptide integrates a sequence into a gene. In some embodiments, a gene modifying polypeptide integrates a sequence into a sequence outside of a gene. A "‘gene modifying system,” as used herein, refers to a system comprising a gene modifying polypeptide and a template nucleic acid.

The term ‘'domain” as used herein refers to a structure of a biomolecule that contributes to a specified function of the biomolecule. A domain may comprise a contiguous region (e g., a contiguous sequence) or distinct, non-contiguous regions (e.g., non-contiguous sequences) of a biomolecule. Examples of protein domains include, but are not limited to, an endonuclease domain, a DNA binding domain, a reverse transcription domain; an example of a domain of a nucleic acid is a regulatory’ domain, such as a transcription factor binding domain. In some embodiments, a domain (e.g., a Cas domain) can comprise two or more smaller domains (e.g., a DNA binding domain and an endonuclease domain).

The term “end block sequence,” as used herein, refers to an RNA sequence having a secondary structure that impairs reverse transcription and/or impairs exonuclease activity’. In some instances, an end block sequence comprises a stem-loop sequence. As used herein, the term “exogenous”, when used with reference to a biomolecule (such as a nucleic acid sequence or polypeptide) means that the biomolecule was introduced into a host genome, cell or organism by the hand of man. For example, a nucleic acid that is as added into an existing genome, cell, tissue or subject using recombinant DNA techniques or other methods is exogenous to the existing nucleic acid sequence, cell, tissue or subject.

As used herein, “first strand” and “second strand”, as used to describe the individual DNA strands of target DNA, distinguish the two DNA strands based upon which strand the reverse transcriptase domain initiates polymerization, e.g., based upon where target primed synthesis initiates. The first strand refers to the strand of the target DNA upon which the reverse transcriptase domain initiates polymerization, e.g., where target primed synthesis initiates. The second strand refers to the other strand of the target DNA. First and second strand designations do not describe the target site DNA strands in other respects: for example, in some embodiments the first and second strands are nicked by a polypeptide described herein, but the designations ‘first’ and ‘second’ strand have no bearing on the order in which such nicks occur.

A “genomic safe harbor site” (GSH site) is a site in a host genome that is able to accommodate the integration of new genetic material, e.g., such that the inserted genetic element does not cause significant alterations of the host genome posing a risk to the host cell or organism. A GSH site generally meets 1, 2, 3, 4, 5, 6, 7, 8 or 9 of the following criteria: (i) is located >300kb from a cancer-related gene; (ii) is >300kb from a miRNA/other functional small RNA: (iii) is >50kb from a 5' gene end: (iv) is >50kb from a replication origin; (v) is >50kb away from any ultraconservcrcd element; (vi) has low transcriptional activity (i.e. no rnRNA +/- 25 kb); (vii) is not in a copy number variable region; (viii) is in open chromatin; and/or (ix) is unique, with 1 copy in tire human genome. Examples of GSH sites in the human genome that meet some or all of these criteria include (i) the adeno-associated virus site 1 (AAV S 1 ), a naturally occurring site of integration of AAV virus on chromosome 19; (ii) the chemokine (C-C motif) receptor 5 (CCR5) gene, a chemokine receptor gene known as an HIV-1 coreceptor: (iii) the human ortholog of tire mouse Rosa26 locus; (iv) tire ribosomal DNA (“rDNA”) locus. Additional GSH sites are known and described, e.g., in Pellenz et al. epub August 20, 2018 (doi.org/10.1101/396390).

The term “heterologous,” as used herein to describe a first element in reference to a second element means that the first element and second element do not exist in nature disposed as described. For example, a heterologous polypeptide, nucleic acid molecule, construct or sequence refers to (a) a polypeptide, nucleic acid molecule or portion of a polypeptide or nucleic acid molecule sequence that is not native to a cell in which it is expressed, (b) a polypeptide or nucleic acid molecule or portion of a polypeptide or nucleic acid molecule that has been altered or mutated relative to its native state, or (c) a polypeptide or nucleic acid molecule with an altered expression as compared to the native expression levels under similar conditions. For example, a heterologous regulatory sequence (e.g., promoter, enhancer) may be used to regulate expression of a gene or a nucleic acid molecule in a way that is different than the gene or a nucleic acid molecule is normally expressed in nature. In another example, a heterologous domain of a polypeptide or nucleic acid sequence (e.g., a DNA binding domain of a polypeptide or nucleic acid encoding a DNA binding domain of a polypeptide) may be disposed relative to other domains or may be a different sequence or from a different source, relative to other domains or portions of a polypeptide or its encoding nucleic acid. In certain embodiments, a heterologous nucleic acid molecule may exist in a native host cell genome, but may have an altered expression level or have a different sequence or both. In other embodiments, heterologous nucleic acid molecules may not be endogenous to a host cell or host genome but instead may have been introduced into a host cell by transformation (e.g.. transfection, electroporation), wherein the added molecule may integrate into tire host genome or can exist as extra-chromosomal genetic material either transiently (e.g., mRNA) or semi- stably for more than one generation (e.g., episomal viral vector, plasmid or other self-replicating vector).

As used herein, '‘insertion” of a sequence into a target site refers to the net addition of DNA sequence at the target site, e.g., where there are new nucleotides in the heterologous object sequence with no cognate positions in the unedited target site. In some embodiments, a nucleotide alignment of the PBS sequence and heterologous object sequence to the target nucleic acid sequence would result in an alignment gap in tire target nucleic acid sequence.

As used herein, a ‘'deletion” generated by a heterologous object sequence in a target site refers to the net deletion of DNA sequence at the target site, e.g., where there are nucleotides in the unedited target site with no cognate positions in the heterologous object sequence. In some embodiments, a nucleotide alignment of the PBS sequence and heterologous object sequence to the target nucleic acid sequence would result in an alignment gap in the molecule comprising the PBS sequence and heterologous object sequence.

The term ‘'inverted terminal repeats” or '‘ITRs” as used herein refers to AAV viral cis-elements named so because of their symmetry. These elements promote efficient multiplication of an AAV genome. It is hypothesized that the minimal elements for ITR function are a Rep-binding site (RBS; 5 - GCGCGCTCGCTCGCTC-3' for AAV2) and a terminal resolution site (TRS; 5 -AGTTGG-3' for AAV2) plus a variable palindromic sequence allowing for hairpin formation. According to the present invention, an ITR comprises at least these three elements (RBS, TRS, and sequences allowing the formation of an hairpin). In addition, in the present invention, the term ‘‘ITR” refers to ITRs of known natural AAV serotypes (e.g. ITR of a serotype 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or 11 AAV), to chimeric ITRs formed by the fusion of ITR elements derived from different serotypes, and to functional variants thereof. “Functional variant” refers to a sequence presenting a sequence identity of at least 80%, 85%, 90%, preferably of at least 95% with a known ITR and allowing multiplication of the sequence that includes said ITR in the presence of Rep proteins. The term “mutation region,” as used herein, refers to a region in a template RNA having one or more sequence difference relative to the corresponding sequence in a target nucleic acid. The sequence difference may comprise, for example, a substitution, insertion, frameshift, or deletion.

The term “mutated” when applied to nucleic acid sequences means that nucleotides in a nucleic acid sequence are inserted, deleted, or changed compared to a reference (e.g., native) nucleic acid sequence. A single alteration may be made at a locus (a point mutation), or multiple nucleotides may be inserted, deleted, or changed at a single locus. In addition, one or more alterations may be made at any number of loci within a nucleic acid sequence. A nucleic acid sequence may be mutated by any method known in the art.

“Nucleic acid molecule” refers to both RNA and DNA molecules including, without limitation, complementary DNA (“cDNA”), genomic DNA (“gDNA”), and messenger RNA (“mRNA”), and also includes synthetic nucleic acid molecules, such as those that are chemically synthesized or recombinantly produced, such as RNA templates, as described herein. The nucleic acid molecule can be double-stranded or single-stranded, circular, or linear. If single-stranded, the nucleic acid molecule can be the sense strand or the antisense strand. Unless otherwise indicated, and as an example for all sequences described herein under the general format “SEQ ID NO:,” “nucleic acid comprising SEQ ID NO: 1” refers to a nucleic acid, at least a portion which has either (i) the sequence of SEQ ID NO: 1, or (ii) a sequence complimentary to SEQ ID NO: 1. The choice between the two is dictated by the context in which SEQ ID NO: 1 is used. For instance, if the nucleic acid is used as a probe, the choice between the two is dictated by the requirement that the probe be complementary to tire desired target. Nucleic acid sequences of the present disclosure may be modified chemically or biochemically or may contain non-natural or derivatized nucleotide bases, as will be readily appreciated by those of skill in the art. Such modifications include, for example, labels, methylation, substitution of one or more naturally occurring nucleotides with an analog, inter-nucleotide modifications such as uncharged linkages (for example, methyl phosphonates, phosphotriesters, phosphoramidates, carbamates, etc.), charged linkages (for example, phosphorothioates, phosphorodithioates, etc.), pendant moieties, (for example, polypeptides), intercalators (for example, acridine, psoralen, etc.), chelators, alkylators, and modified linkages (for example, alpha anomeric nucleic acids, etc.). Also included are chemically modified bases (see, for example. Table 13), backbones (see, for example, Table 14), and modified caps (see, for example. Table 15). Also included are synthetic molecules that mimic polynucleotides in their ability to bind to a designated sequence via hydrogen bonding and other chemical interactions. Such molecules are known in the art and include, for example, those in which peptide linkages substitute for phosphate linkages in the backbone of a molecule, e.g., peptide nucleic acids (PNAs). Other modifications can include, for example, analogs in which the ribose ring contains a bridging moiety or other structure such as modifications found in “locked” nucleic acids (LNAs). In various embodiments, tire nucleic acids are in operative association with additional genetic elements, such as tissue-specific expression-control sequence(s) (e.g., tissue-specific promoters and tissue-specific microRNA recognition sequences), as well as additional elements, such as inverted repeats (e.g., inverted terminal repeats, such as elements from or derived from viruses, e.g., AAV ITRs) and tandem repeats, inverted repeats/direct repeats, homology regions (segments with various degrees of homology to a target DNA), untranslated regions (UTRs) (5 3 ', or both 5 ' and 3 ' UTRs), and various combinations of the foregoing. The nucleic acid elements of the systems provided by the invention can be provided in a variety of topologies, including single-stranded, double-stranded, circular, linear, linear with open ends, linear with closed ends, and particular versions of these, such as doggybone DNA (dbDNA). closed-ended DNA (ceDNA).

As used herein, a “gene expression unit” is a nucleic acid sequence comprising at least one regulatory nucleic acid sequence operably linked to at least one effector sequence. A first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter or enhancer is operably linked to a coding sequence if the promoter or enhancer affects tire transcription or expression of the coding sequence. Operably linked DNA sequences may be contiguous or noncontiguous. Where necessary to join two protein-coding regions, operably linked sequences may be in the same reading frame. The terms “host genome” or “host cell”, as used herein, refer to a cell and/or its genome into which protein and/or genetic material has been introduced. It should be understood that such terms are intended to refer not only to the particular subject cell and/or genome, but to the progeny of such a cell and/or the genome of the progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term “host cell” as used herein. A host genome or host cell may be an isolated cell or cell line grown in culture, or genomic material isolated from such a cell or cell line, or may be a host cell or host genome which composing living tissue or an organism. In some instances, a host cell may be an animal cell or a plant cell, e.g., as described herein. In certain instances, a host cell may be a mammalian cell, a human cell, avian cell, reptilian cell, bovine cell, horse cell, pig cell, goat cell, sheep cell, chicken cell, or turkey cell. In certain instances, a host cell may be a com cell, soy cell, wheat cell, or rice cell.

As used herein, “operative association” describes a functional relationship between two nucleic acid sequences, such as a 1) promoter and 2) a heterologous object sequence, and means, in such example, the promoter and heterologous object sequence (e.g., a gene of interest) are oriented such that, under suitable conditions, the promoter drives expression of the heterologous object sequence. For instance, a template nucleic acid carrying a promoter and a heterologous object sequence may be singlestranded, e.g., either the (+) or (-) orientation. An “operative association” between the promoter and the heterologous object sequence in this template means that, regardless of whether the template nucleic acid will be transcribed in a particular state, when it is in the suitable state (e.g., is in the (+) orientation, in the presence of required catalytic factors, and NTPs, etc.), it is accurately transcribed. Operative association applies analogously to other pairs of nucleic acids, including other tissue-specific expression control sequences (such as enhancers, repressors and microRNA recognition sequences), IR/DR, ITRs, UTRs, or homology regions and heterologous object sequences or sequences encoding a retroviral RT domain.

The term “primer binding site sequence” or “PBS sequence.” as used herein, refers to a portion of a template RNA capable of binding to a region comprised in a target nucleic acid sequence. In some instances, a PBS sequence is a nucleic acid sequence comprising at least 3, 4, 5, 6, 7, or 8 bases with 100% identity to the region comprised in the target nucleic acid sequence. In some embodiments the primer region comprises at least 5, 6, 7, 8 bases with 100% identity to the region comprised in the target nucleic acid sequence. Without wishing to be bound by theory, in some embodiments when a template RNA comprises a PBS sequence and a heterologous object sequence, the PBS sequence binds to a region comprised in a target nucleic acid sequence, allowing a reverse transcriptase domain to use that region as a primer for reverse transcription, and to use the heterologous object sequence as a template for reverse transcription. The term “primer homology region” of a template RNA, as used herein, refers to to a 5' portion of the post-edit homology region that has sequence identity to the sequence immediately adjacent to the second strand nick on the side further from the first strand nick. In some embodiments, the primer homology region directs reverse transcription of a nascent DNA strand that can hybridize to the “primer” region of the second strand of the target DNA, i.e., second strand of the target DNA immediately 5 ’ to the second strand nick.

As used herein, a “stem-loop sequence” refers to a nucleic acid sequence (e.g., RNA sequence) with sufficient self-complementarity to fomi a stem-loop, e.g., having a stem comprising at least two (e.g., 3, 4, 5. 6, 7, 8, 9. or 10) base pairs, and a loop with at least three (e.g., four) base pairs. The stem may comprise mismatches or bulges.

As used herein, a “tissue-specific expression-control sequence” means nucleic acid elements that increase or decrease the level of a transcript comprising the heterologous object sequence in a target tissue in a tissue-specific manner, e.g., preferentially in on-target tissue(s), relative to off-target tissue(s). In some embodiments, a tissue-specific expression-control sequence preferentially drives or represses transcription, activity, or the half-life of a transcript comprising the heterologous object sequence in the target tissue in a tissue-specific manner, e.g., preferentially in an on-target tissue(s), relative to an off- target tissue(s). Exemplary tissue-specific expression-control sequences include tissue-specific promoters, repressors, enhancers, or combinations thereof, as well as tissue-specific microRNA recognition sequences. Tissue specificity refers to on-target (tissue(s) where expression or activity of the template nucleic acid is desired or tolerable) and off-target (tissue(s) where expression or activity of the template nucleic acid is not desired or is not tolerable). For example, a tissue-specific promoter drives expression preferentially in on-target tissues, relative to off-target tissues. In contrast, a microRNA that binds the tissue-specific microRNA recognition sequences is preferentially expressed in off-target tissues, relative to on-target tissues, thereby reducing expression of a template nucleic acid in off-target tissues. Accordingly, a promoter and a microRNA recognition sequence that are specific for the same tissue, such as the target tissue, have contrasting functions (promote and repress, respectively, with concordant expression levels, i.e., high levels of the microRNA in off-target tissues and low levels in on-target tissues, while promoters drive high expression in on-target tissues and low expression in off-target tissues) with regard to the transcription, activity, or half-life of an associated sequence in that tissue.

Introduction

This disclosure relates to methods compositions for targeting, editing, modifying or manipulating a DNA sequence (e.g., inserting a heterologous object sequence into a target site of a mammalian genome) at one or more locations in a DNA sequence in a cell, tissue or subject, e.g., in vivo or in vitro. The heterologous object DNA sequence may include, e.g., a substitution, a deletion, an insertion, e.g., a coding sequence, a regulatory sequence, or a gene expression unit.

This disclosure relates, in part, to anchoring of a trans template RNA to a gene modifying polypeptide :sgRNA: target genomic DNA complex by two or more interactions. Without wishing to be bound by theory, it is contemplated that such anchoring can achieve high rewriting activity, e.g., for achieving single or several nucleotide long edits. For example, 1) an RRS:RBD interaction and 2) a 5’ end block Cas9 scaffold and spacer to target DNA interaction (mediated via an additional gene modifying polypeptide) represent exemplary interactions that together anchor a trans template RNA to a gene modifying polypeptide:sgRNA:target genomic DNA complex to enable rewriting. It is contemplated that the RRS:RBD interaction is critical in the absence of the 5’ end block spacer. It is further contemplated that the presence of both can provide high rewriting activity and the presence of the 5' end block spacer in combination with a weaker RRS:RBD interaction rescues rewriting activity. The disclosure relates, in part, to trans template RNAs designed to facilitate long edits (e.g., long insertions, e.g., insertions of greater than or equal to 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 225, 250, 275, or 300 nucleotides) in the genome of a host cell, tissue, or subject, in vivo or in vitro. The disclosure relates, in part, to trans template RNA elements comprising a 5’ end block gRNA spacer, where the gRNA spacer has a length sufficient to support nicking of a target sequence in genomic DNA. Without wishing to be bound by theory, it has been found that a 5’ end block gRNA spacer that supports nicking enables a trans template RNA-containing gene modifying system to achieve long edits (e.g., long insertions). The disclosure further relates, in part, to trans template RNA elements comprising long postedit homology regions (e.g., comprising at least 30, 35, 40, 45, 50, 55, or 60 nucleotides). Without wishing to be bound by theory, it has been found that a long post-edit homology region enables a trans template RNA-containing gene modifying system to achieve long edits (e.g., long insertions).

The disclosure also provides methods for treating disease using reverse transcriptase-based systems for altering a genomic DNA sequence of interest, e.g., by inserting, deleting, or substituting one or more nucleotides into/from the sequence of interest. The disclosure provides, in part, methods for treating disease using a gene modifying system comprising a gene modifying polypeptide component and a template nucleic acid (e.g., template RNA) component. In some embodiments, a gene modifying system can be used to introduce an alteration into a target site in a genome. In some embodiments, the gene modifying polypeptide component comprises a writing domain (e.g., a reverse transcriptase domain), a DNA-binding domain, and an endonuclease domain (e.g., nickase domain). In some embodiments, the template nucleic acid (e.g., template RNA) comprises a sequence (e.g., a gRNA spacer) that binds a target site in tire genome (e.g., that binds to a second strand of the target site), a sequence (e g., a gRNA scaffold) that binds the gene modifying polypeptide component, a heterologous object sequence, and a PBS sequence. Without wishing to be bound by theory, it is thought that the template nucleic acid (e.g., template RNA) binds to the second strand of a target site in the genome, and binds to the gene modifying polypeptide component (e.g., localizing the polypeptide component to the target site in the genome). It is thought that the endonuclease (e.g., nickase) of the gene modifying polypeptide component cuts the target site (e.g., the first strand of the target site), e.g., allowing the PBS sequence to bind to a sequence adjacent to the site to be altered on the first strand of the target site. It is thought that the writing domain (e.g., reverse transcriptase domain) of the polypeptide component uses the first strand of the target site that is bound to the complementary sequence comprising the PBS sequence of the template nucleic acid as a primer and the heterologous object sequence of the template nucleic acid as a template to, e.g., polymerize a sequence complementary to the heterologous object sequence. Without wishing to be bound by theory, it is thought that selection of an appropriate heterologous object sequence can result in substitution, deletion, and/or insertion of one or more nucleotides at the target site.

Gene modifying systems

In some embodiments, a gene modifying system described herein comprises: (A) a gene modifying polypeptide or a nucleic acid encoding the gene modifying polypeptide, wherein the gene modifying polypeptide comprises (i) a reverse transcriptase domain, and either (x) an endonuclease domain that contains DNA binding functionality or (y) an endonuclease domain and separate DNA binding domain; and (B) a template RNA. A gene modifying polypeptide, in some embodiments, acts as a substantially autonomous protein machine capable of integrating a template nucleic acid sequence into a target DNA molecule (e.g., in a mammalian host cell, such as a genomic DNA molecule in the host cell), substantially without relying on host machinery. For example, the gene modifying protein may comprise a DNA-binding domain, a reverse transcriptase domain, and an endonuclease domain. In some embodiments, the DNA-binding function may involve an RNA component that directs the protein to a DNA sequence, e.g., a gRNA spacer. In other embodiments, the gene modifying polypeptide may comprise a reverse transcriptase domain and an endonuclease domain. The RNA template element of a gene modifying system is typically heterologous to the gene modifying polypeptide element and provides an object sequence to be inserted (reverse transcribed) into the host genome. In some embodiments, the gene modifying polypeptide is capable of target primed reverse transcription. In some embodiments, the gene modifying polypeptide is capable of second-strand synthesis.

In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising the amino acid sequence, or a functional portion thereof, of an exemplary gene modifying polypeptide as listed in any of Tables S 1 -S3, or an amino acid sequence having at least 70%. 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto, or a nucleic acid molecule encoding the gene modifying polypeptide. In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising the amino acid sequence of an RT domain of an exemplary gene modify ing polypeptide as listed in any of Tables S1-S3, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto, or a nucleic acid molecule encoding the gene modifying polypeptide. In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising the amino acid sequence of a DBD of an exemplary gene modifying polypeptide as listed in any of Tables SI -S3, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto, or a nucleic acid molecule encoding the gene modifying polypeptide. In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising tire amino acid sequence of an RBD of an exemplary gene modifying polypeptide as listed in any of Tables S1-S3, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto, or a nucleic acid molecule encoding the gene modifying polypeptide. In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising the amino acid sequence of the RT domain, DBD, and RBD of an exemplary gene modifying polypeptide as listed in any of Tables S1-S3, or amino acid sequences having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto, or a nucleic acid molecule encoding the gene modifying polypeptide.

In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising the amino acid sequence, or a functional portion thereof, of an exemplary gene modifying polypeptide as listed in Table SI, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%. 98%, or 99% identity thereto, or a nucleic acid molecule encoding the gene modifying polypeptide. In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising the amino acid sequence of an RT domain of an exemplary gene modifying polypeptide as listed in Table SI, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identify thereto, or a nucleic acid molecule encoding the gene modifying polypeptide. In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising the amino acid sequence of a DBD of an exemplary gene modifying polypeptide as listed in Table SI. or an amino acid sequence having at least 70%, 75%, 80%. 85%, 90%, 95%, 96%, 97%, 98%, or 99% identify thereto, or a nucleic acid molecule encoding the gene modifying polypeptide. In some embodiments, a gene modify ing system described herein comprises a gene modifying polypeptide comprising the amino acid sequence of an RBD of an exemplary gene modifying polypeptide as listed in Table SI, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%. 98%, or 99% identify thereto, or a nucleic acid molecule encoding the gene modifying polypeptide. In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising the amino acid sequence of the RT domain, DBD, and RBD of an exemplary gene modify ing polypeptide as listed in Table SI, or amino acid sequences having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identify thereto, or a nucleic acid molecule encoding the gene modifying polypeptide.

In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising the amino acid sequence, or a functional portion thereof, of an exemplary gene modifying polypeptide as listed in Table S2, or an amino acid sequence having at least 70%, 75%, 80%. 85%, 90%, 95%, 96%, 97%, 98%, or 99% identify thereto, or a nucleic acid molecule encoding the gene modifying polypeptide. In some embodiments, a gene modify ing system described herein comprises a gene modifying polypeptide comprising the amino acid sequence of an RT domain of an exemplary gene modifying polypeptide as listed in Table S2, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto, or a nucleic acid molecule encoding the gene modifying polypeptide. In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising the amino acid sequence of a DBD of an exemplary gene modifying polypeptide as listed in Table S2. or an amino acid sequence having at least 70%, 75%, 80%. 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto, or a nucleic acid molecule encoding the gene modifying polypeptide. In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising the amino acid sequence of an RBD of an exemplary' gene modifying polypeptide as listed in Table S2, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%. 98%. or 99% identity thereto, or a nucleic acid molecule encoding the gene modifying polypeptide. In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising the amino acid sequence of the RT domain, DBD, and RBD of an exemplary gene modifying polypeptide as listed in Table S2, or amino acid sequences having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto, or a nucleic acid molecule encoding tire gene modifying polypeptide.

In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising the amino acid sequence, or a functional portion thereof, of an exemplary gene modifying polypeptide as listed in Table S3, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto, or a nucleic acid molecule encoding the gene modifying polypeptide. In some embodiments, a gene modify ing system described herein comprises a gene modifying polypeptide comprising the amino acid sequence of an RT domain of an exemplary gene modifying polypeptide as listed in Table S3, or an amino acid sequence having at least 70%, 75%, 80%. 85%, 90%, 95%, 96%, 97%. 98%. or 99% identity thereto, or a nucleic acid molecule encoding the gene modifying polypeptide. In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising the amino acid sequence of a DBD of an exemplary' gene modifying polypeptide as listed in Table S3, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto, or a nucleic acid molecule encoding the gene modifying polypeptide. In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising the amino acid sequence of an RBD of an exemplary gene modifying polypeptide as listed in Table S3, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto, or a nucleic acid molecule encoding the gene modifying polypeptide. In some embodiments, a gene modifying system described herein comprises a gene modifying polypeptide comprising tire amino acid sequence of the RT domain, DBD, and RBD of an exemplary gene modifying polypeptide as listed in Table S3, or amino acid sequences having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto, or a nucleic acid molecule encoding the gene modify ing polypeptide.

In some embodiments, a gene modify ing system described herein comprises a template RNA comprising a nucleic acid sequence as listed in Table S4, or a nucleic acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%. 97%. 98%, or 99% identity thereto. In some embodiments, a gene modifying system described herein comprises a template RNA comprising a 5’ end block sequence of a template sequence as listed in Table S4, or a nucleic acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying system described herein comprises a template RNA comprising a PBS sequence of a template sequence as listed in Table S4, or a nucleic acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying system described herein comprises a template RNA comprising a linker sequence of a template sequence as listed in Table S4, or a nucleic acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying system described herein comprises a template RNA comprising one or more (e.g., 1, 2, 3, or 4) RRS sequences of a template sequence as listed in Table S4, or nucleic acid sequences having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying system described herein comprises a template RNA comprising a 3’ end block sequence of a template sequence as listed in Table S4, or a nucleic acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying system described herein comprises a template RNA comprising one or more (e.g., 1, 2, 3, or 4) of (e.g., in 5' to 3’ order) a 5’ end block sequence, optionally a PBS sequence, one or more (e.g., 1, 2, 3, or 4) RRS sequences, and a 3’ end block sequence of a template sequence as listed in Table S4, or nucleic acid sequences having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

In some embodiments the gene modifying system is combined with a second polypeptide. In some embodiments, the second polypeptide may comprise an endonuclease domain. In some embodiments, the second polypeptide may comprise a polymerase domain, e.g., a reverse transcriptase domain. In some embodiments, tire second polypeptide may comprise a DNA-dependent DNA polymerase domain. In some embodiments, the second polypeptide aids in completion of the genome edit, e.g., by contributing to second-strand synthesis or DNA repair resolution.

A functional gene modifying polypeptide can be made up of unrelated DNA binding, reverse transcription, and endonuclease domains. This modular structure allows combining of functional domains, e.g., dCas9 (DNA binding), MMLV reverse transcriptase (reverse transcription), FokI (endonuclease). In some embodiments, multiple functional domains may arise from a single protein, e.g., Cas9 or Cas9 nickase (DNA binding, endonuclease).

In some embodiments, a gene modifying polypeptide includes one or more domains that, collectively, facilitate 1) binding the template nucleic acid, 2) binding the target DNA molecule, and 3) facilitate integration of tire at least a portion of tire template nucleic acid into tire target DNA. In some embodiments, the gene modifying polypeptide is an engineered polypeptide that comprises one or more amino acid substitutions to a corresponding naturally occurring sequence. In some embodiments, the gene modifying polypeptide comprises two or more domains that are heterologous relative to each other, e.g., through a heterologous fusion (or other conjugate) of otherwise wild-type domains, or well as fusions of modified domains, e.g., by way of replacement or fusion of a heterologous sub-domain or other substituted domain. For instance, in some embodiments, one or more of: the RT domain is heterologous to the DBD; the DBD is heterologous to the endonuclease domain; or the RT domain is heterologous to the endonuclease domain.

In some embodiments, a template RNA molecule for use in the system comprises, from 5 ' to 3 '

(1) a gRNA spacer; (2) a gRNA scaffold; (3) heterologous object sequence (4) a primer binding site (PBS) sequence. In some embodiments:

(1) Is a gRNA spacer of -18-22 nt, e.g., is 20 nt

(2) Is a gRNA scaffold comprising one or more hairpin loops, e.g., 1, 2, of 3 loops for associating the template with a Cas domain, e.g., a nickase Cas9 domain. In some embodiments, the gRNA scaffold comprises the sequence, from 5' to 3', GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAA AGTGGGACCGAGTCGGTCC (SEQ ID NO: 8).

(3) In some embodiments, tire heterologous object sequence is, e.g., 7-74. e.g., 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, or 70-80 nt or, 80-90 nt in length. In some embodiments, the first (most 5') base of the sequence is not C.

(4) In some embodiments, the PBS sequence that binds the target priming sequence after nicking occurs is e.g., 3-20 nt, e.g., 7-15 nt, e.g., 12-14 nt. In some embodiments, the PBS sequence has 40-60% GC content.

In some embodiments, a second gRNA associated with the system may help drive complete integration. In some embodiments, the second gRNA may target a location that is 0-200 nt away from the first-strand nick, e.g., 0-50, 50-100, 100-200 nt away from the first-strand nick. In some embodiments, the second gRNA can only bind its target sequence after the edit is made, e.g., the gRNA binds a sequence present in the heterologous object sequence, but not in the initial target sequence.

In some embodiments, a gene modifying system described herein is used to make an edit in HEK293, K562, U2OS, or HeLa cells. In some embodiment, a gene modifying system is used to make an edit in primary cells, e.g., primary cortical neurons from E18.5 mice.

In some embodiments, a gene modifying polypeptide as described herein comprises a reverse transcriptase or RT domain (e.g., as described herein) that comprises a MoMLV RT sequence or variant thereof. In embodiments, the MoMLV RT sequence comprises one or more mutations selected from D200N, L603W, T330P, T306K, W313F, D524G, E562Q, D583N, P51L, S67R, E67K, T197A, H204R, E302K, F309N, L435G, N454K, H594Q, D653N, R1 IOS, and K103L. In embodiments, the MoMLV RT sequence comprises a combination of mutations, such as D200N, L603W. and T330P. optionally further including T306K and/or W313F.

In some embodiments, an endonuclease domain (e.g., as described herein) comprises nCAS9, e.g., comprising the H840A mutation.

In some embodiments, the heterologous object sequence (e.g., of a system as described herein) is about 1-50, 50-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, 900- 1000, or more, nucleotides in length.

In some embodiments, the RT and endonuclease domains are joined by a flexible linker, e.g., comprising the amino acid sequence SGGSSGGSSGSETPGTSESATPESSGGSSGGSS (SEQ ID NO: 6).

In some embodiments, the endonuclease domain is N-terminal relative to the RT domain. In some embodiments, the endonuclease domain is C-terminal relative to the RT domain.

In some embodiments, the system incorporates a heterologous object sequence into a target site by TPRT, e.g., as described herein.

In some embodiments, a gene modifying polypeptide comprises a DNA binding domain. In some embodiments, a gene modifying polypeptide comprises an RNA binding domain. In some embodiments, the RNA binding domain comprises an RNA binding domain of B-box protein, MS2 coat protein, dCas, or an element of a sequence of a table herein. In some embodiments, the RNA binding domain is capable of binding to a template RNA with greater affinity than a reference RNA binding domain.

In some embodiments, a gene modifying system is capable of producing an insertion into the target site of at least 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 nucleotides (and optionally no more than 500, 400, 300, 200, or 100 nucleotides). In some embodiments, a gene modifying system is capable of producing an insertion into the target site of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 nucleotides (and optionally no more than 500, 400, 300, 200, or 100 nucleotides). In some embodiments, a gene modifying system is capable of producing an insertion into the target site of at least 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5,

5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5 or 10 kilobases (and optionally no more than 1, 5, 10, or 20 kilobases). In some embodiments, a gene modifying system is capable of producing a deletion of at least 81, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160. 170, 180. 190, or 200 nucleotides (and optionally no more than 500, 400. 300, or 200 nucleotides). In some embodiments, a gene modifying system is capable of producing a deletion of at least 81, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 nucleotides (and optionally no more than 500, 400, 300, or 200 nucleotides). In some embodiments, a gene modifying system is capable of producing a deletion of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 nucleotides (and optionally no more than 500, 400, 300, or 200 nucleotides). In some embodiments, a gene modifying system is capable of producing a deletion of at least 0.2, 0.3, 0.4, 0.5, 0.6. 0.7, 0.8, 0.9, 1.

1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5 or 10 kilobases (and optionally no more than 1, 5, 10, or 20 kilobases). In some embodiments, a gene modifying system is capable of producing a substitution into the target site of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, or 100 or more nucleotides. In some embodiments, a gene modifying system is capable of producing a substitution in tire target site of 1-2. 2-3, 3-4, 4-5, 5-10, 10-15, 15-20, 20-30, 30-40. 40-50, 50-60, 60-70, 70-80. 80-90, or 90-100 nucleotides.

In some embodiments, the substitution is a transition mutation. In some embodiments, the substitution is a transversion mutation. In some embodiments, the substitution converts an adenine to a thymine, an adenine to a guanine, an adenine to a cytosine, a guanine to a thymine, a guanine to a cytosine, a guanine to an adenine, a thymine to a cytosine, a thymine to an adenine, a thymine to a guanine, a cytosine to an adenine, a cytosine to a guanine, or a cytosine to a thymine.

In some embodiments, an insertion, deletion, substitution, or combination thereof, increases or decreases expression (e.g. transcription or translation) of a gene. In some embodiments, an insertion, deletion, substitution, or combination thereof, increases or decreases expression (e.g. transcription or translation) of a gene by altering, adding, or deleting sequences in a promoter or enhancer, e.g. sequences that bind transcription factors. In some embodiments, an insertion, deletion, substitution, or combination thereof alters translation of a gene (e.g. alters an amino acid sequence), inserts or deletes a start or stop codon, alters or fixes the translation frame of a gene. In some embodiments, an insertion, deletion, substitution, or combination thereof alters splicing of a gene, e.g. by inserting, deleting, or altering a splice acceptor or donor site. In some embodiments, an insertion, deletion, substitution, or combination thereof alters transcript or protein half-life. In some embodiments, an insertion, deletion, substitution, or combination thereof alters protein localization in the cell (e.g. from the cytoplasm to a mitochondria, from the cytoplasm into the extracellular space (e.g. adds a secretion tag)). In some embodiments, an insertion, deletion, substitution, or combination thereof alters (e.g. improves) protein folding (e.g. to prevent accumulation of misfolded proteins). In some embodiments, an insertion, deletion, substitution, or combination thereof, alters, increases, decreases the activity of a gene, e.g. a protein encoded by the gene.

Exemplary gene modifying polypeptides, and systems comprising them and methods of using them are described, e.g., in PCT/US2021/020948, which is incorporated herein by reference with respect to retroviral RT domains, including the amino acid and nucleic acid sequences therein.

Exemplary gene modifying polypeptides and retroviral RT domain sequences are also described, e.g., in International Application No. PCT/US21/20948 fded March 4, 2021, e.g., at Table 30, Table 31, and Table 44 therein; the entire application is incorporated by reference herein with respect to retroviral RTs, e.g., in said sequences and tables. Accordingly, a gene modifying polypeptide described herein may comprise an amino acid sequence according to any of the Tables mentioned in this paragraph, or a domain thereof (e.g., a retroviral RT domain), or a functional fragment or variant of any of the foregoing, or an amino acid sequence having at least 70%, 80%, 85%, 90%, 95%, or 99% identity thereto.

In some embodiments, a polypeptide for use in any of the systems described herein can be a molecular reconstruction or ancestral reconstruction based upon the aligned polypeptide sequence of multiple homologous proteins. In some embodiments, a reverse transcriptase domain for use in any of the systems described herein can be a molecular reconstruction or an ancestral reconstruction, or can be modified at particular residues, based upon alignments of reverse transcriptase domains from the same or different sources. A skilled artisan can, based on the Accession numbers provided herein, align polypeptides or nucleic acid sequences, e.g., by using routine sequence analysis tools as Basic Local Alignment Search Tool (BLAST) or CD-Search for conserved domain analysis. Molecular reconstructions can be created based upon sequence consensus, e.g. using approaches described in Ivies et al., Cell 1997, 501 - 510 ; Wagstaff et al.. Molecular Biology and Evolution 2013, 88-99.

Polypeptide components of gene modifying systems

In some embodiments, the gene modifying polypeptide possesses the functions of DNA target site binding, template nucleic acid (e.g., RNA) binding, DNA target site cleavage, and template nucleic acid (e.g., RNA) writing, e.g., reverse transcription. In some embodiments, each functions is contained within a distinct domain. In some embodiments, a function may be attributed to two or more domains (e g., two or more domains, together, exhibit the functionality). In some embodiments, two or more domains may have the same or similar function (e.g., two or more domains each independently have DNA-binding functionality, e.g., for two different DNA sequences). In other embodiments, one or more domains may be capable of enabling one or more functions, e.g., a Cas9 domain enabling both DNA binding and target site cleavage. In some embodiments, the domains are all located within a single polypeptide. In some embodiments, a first domain is in one polypeptide and a second domain is in a second polypeptide. For example, in some embodiments, the sequences may be split between a first polypeptide and a second polypeptide, e.g., wherein the first polypeptide comprises a reverse transcriptase (RT) domain and wherein the second polypeptide comprises a DNA-binding domain and an endonuclease domain, e.g., a nickase domain. As a further example, in some embodiments, the first polypeptide and the second polypeptide each comprise a DNA binding domain (e.g., a first DNA binding domain and a second DNA binding domain). In some embodiments, the first and second polypeptide may be brought together post- translationally via a split-intein to form a single gene modifying polypeptide.

In some aspects, a gene modifying polypeptide described herein comprises (e.g., a system described herein comprises a gene modifying polypeptide that comprises): 1) a Cas domain (e.g., a Cas nickase domain, e.g., a Cas9 nickase domain); 2) a reverse transcriptase (RT) domain of Table 1, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto, wherein the RT domain is C-terminal of the Cas domain: and a linker disposed between the RT domain and the Cas domain, wherein the linker has a sequence from the same row of Table 1 as the RT domain, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.

In some embodiments, the RT domain has a sequence with 100% identity to the RT domain of Table 1 and the linker has a sequence with 100% identity to the linker sequence from the same row of Table 1 as the RT domain. In some embodiments, the Cas domain comprises a sequence of Table 8, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity thereto. In some embodiments, the gene modifying polypeptide comprises an amino acid sequence according to any of SEQ ID Nos: 1-3332 in the sequence listing, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto.

In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence, or a functional portion thereof, of an exemplary gene modifying polypeptide as listed in any of Tables S1-S3, or an amino acid sequence having at least 70%. 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modify ing polypeptide described herein comprises the amino acid sequence of an RT domain of an exemplary gene modifying polypeptide as listed in any of Tables S1-S3, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence of a DBD of an exemplary gene modifying polypeptide as listed in any of Tables S 1 -S3, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence of an RBD of an exemplary gene modifying polypeptide as listed in any of Tables S1-S3, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%. 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence of tire RT domain, DBD, and RBD of an exemplary gene modifying polypeptide as listed in any of Tables SI -S3, or amino acid sequences having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence, or a functional portion thereof, of an exemplary gene modifying polypeptide as listed in Table SI, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%. 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence of an RT domain of an exemplary gene modifying polypeptide as listed in Table SI, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence of a DBD of an exemplary gene modifying polypeptide as listed in Table SI, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence of an RBD of an exemplary gene modifying polypeptide as listed in Table SI, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence of the RT domain, DBD, and RBD of an exemplary’ gene modifying polypeptide as listed in Table SI, or amino acid sequences having at least 70%, 75%, 80%. 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence, or a functional portion thereof, of an exemplary gene modifying polypeptide as listed in Table S2, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence of an RT domain of an exemplary gene modify ing polypeptide as listed in Table S2, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%. or 99% identity thereto. In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence of a DBD of an exemplary gene modifying polypeptide as listed in Table S2, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence of an RBD of an exemplary gene modifying polypeptide as listed in Table S2, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence of the RT domain, DBD, and RBD of an exemplary gene modifying polypeptide as listed in Table S2, or amino acid sequences having at least 70%, 75%, 80%. 85%. 90%. 95%. 96%, 97%, 98%, or 99% identity thereto.

In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence, or a functional portion thereof, of an exemplary gene modifying polypeptide as listed in Table S3, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence of an RT domain of an exemplary gene modify ing polypeptide as listed in Table S3, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence of a DBD of an exemplary gene modifying polypeptide as listed in Table S3, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence of an RBD of an exemplary gene modify ing polypeptide as listed in Table S3, or an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide described herein comprises the amino acid sequence of the RT domain, DBD, and RBD of an exemplary gene modifying polypeptide as listed in Table S3, or amino acid sequences having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

In some embodiments, a gene modifying polypeptide described herein comprises a DBD, RT domain, and one or more RBDs (e.g., as described herein).

In certain embodiments, the gene modifying polypeptide comprises, in N-terminal to C-terminal order, a DBD (e g., a Cas domain, e.g., a Cas9 domain, e g., as described herein), one or more (e.g., 1, 2, 3, or 4) RBDs, and an RT domain. In embodiments, the DBD and the N-terminal RBD are connected by a linker (e.g., as described herein). In embodiments, the C-terminal RBD and the RT domain are connected by a linker (e g., as described herein).

In certain embodiments, the gene modifying polypeptide comprises, in N-terminal to C-terminal order, an RT domain, one or more (e.g., I, 2, 3, or 4) RBDs, and a DBD (e.g., a Cas domain, e.g., a Cas9 domain, e.g., as described herein). In embodiments, the RT domain and the N-terminal RBD are connected by a linker (e.g., as described herein). In embodiments, the C-terminal RBD and the DBD are connected by a linker (e.g., as described herein).

In certain embodiments, the gene modifying polypeptide comprises, in N-terminal to C-terminal order, a DBD (e g., a Cas domain, e.g., a Cas9 domain, e.g., as described herein), an RT domain, and one or more (e.g., 1, 2. 3, or 4) RBDs. In embodiments, the DBD and RT domain are connected by a linker (e.g., as described herein). In embodiments, the RT domain and the the N-terminal RBD are connected by a linker (e.g., as described herein).

In some embodiments, the gene modifying polypeptide comprises an N-terminal methionine residue.

In some embodiments, the gene modify ing polypeptide comprises one or more nuclear localization sequences (NLSes), e.g., as described herein.

In some embodiments, tire gene modifying polypeptide comprises a GG amino acid sequence between the Cas domain and the linker, an AG amino acid sequence between the RT domain and the second NLS, and/or a GG amino acid sequence between the linker and the RT domain. In some embodiments, the gene modifying polypeptide comprises a sequence of SEQ ID NO: 4000 which comprises the first NLS and the Cas domain, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity thereto. In some embodiments, the gene modifying polypeptide comprises a sequence of SEQ ID NO: 4001 which comprises the second NLS, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%. 98%. or 99% identify thereto.

Exemplary N-terminal NLS-Cas9 domain

MPAAKRVKLDGGDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKN LIGALLF DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKH ERHP I FGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDN SDV DKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNL IALS LGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDI LRVN TEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEI FFDQSKNGYAGYIDGGASQEEFY KFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSI PHQIHLGELHAILRRQEDFYPFLKDNR EKIEKILTFRI PYYVGPLARGNSRFAWMTRKSEETITPWNFEEWDKGASAQSFIERMTNFDKN LPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTV KQLK EDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKI IKDKDFLDNEENEDILEDIVLTLTLFEDR EMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFA NRNF MQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKWDELVKVMGRH KPE NIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQ NGRD MYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKARGKSDNVPSEEWKKMKNY WRQ LLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDE NDKL I REVKVI TLKS KLVSDFRKDFQF YKVRE I NNYHHAHDAYLNAWGTAL I KKYPKLE S E FVYGD Y KVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIV WDKG RDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSP TVAY SVLWAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLI IKLPKYSLFE LENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHY LDEI IEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENI IHLFTLTNLGAPAAFKYFDTTIDR KRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDGG (SEQ ID NO: 4000)

Exemplary C-terminal sequence comprising an NLS

AGKRTADGSEFEKRTADGSEFESPKKKAKVE (SEQ ID NO: 4001)

Gene modifying domain (RT Domain)

In certain aspects of the present invention, the gene modifying domain of the gene modifying system possesses reverse transcriptase activity and is also referred to as a reverse transcriptase domain (a RT domain). In some embodiments, the RT domain comprises an RT catalytic portion and RNA-binding region (e.g., a region that binds the template RNA).

In some embodiments, a nucleic acid encoding the reverse transcriptase is altered from its natural sequence to have altered codon usage, e.g. improved for human cells. In some embodiments the reverse transcriptase domain is a heterologous reverse transcriptase from a retrovirus. In some embodiments, the RT domain comprising a gene modifying polypeptide has been mutated from its original amino acid sequence, e.g., has at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 substitutions. In some embodiments, the RT domain is derived from the RT of a retrovirus, e.g., HIV-1 RT, Moloney Murine Leukemia Virus (MMLV) RT, avian myeloblastosis virus (AMV) RT, or Rous Sarcoma Vims (RSV) RT.

In some embodiments, the retroviral reverse transcriptase (RT) domain exhibits enhanced stringency of target-primed reverse transcription (TPRT) initiation, e.g., relative to an endogenous RT domain. In some embodiments, the RT domain initiates TPRT when the 3 nt in the target site immediately upstream of the first strand nick, e.g., the genomic DNA priming the RNA template, have at least 66% or 100% complementarity to the 3 nt of homology in the RNA template. In some embodiments, the RT domain initiates TPRT when there are less than 5 nt mismatched (e.g., less than 1, 2, 3, 4, or 5 nt mismatched) between the template RNA homology and the target DNA priming reverse transcription. In some embodiments, the RT domain is modified such that the stringency for mismatches in priming the TPRT reaction is increased, e.g., wherein the RT domain does not tolerate any mismatches or tolerates fewer mismatches in the priming region relative to a wild-type (e.g., unmodified) RT domain. In some embodiments, the RT domain comprises a HIV-1 RT domain. In embodiments, the HIV-1 RT domain initiates lower levels of synthesis even with three nucleotide mismatches relative to an alternative RT domain (e g., as described by Jamburuthugoda and Eickbush J Mol Biol 407(5):661-672 (2011); incorporated herein by reference in its entirety). In some embodiments, the RT domain forms a dimer (e.g., a heterodimer or homodimer). In some embodiments, the RT domain is monomeric. In some embodiments, an RT domain, naturally functions as a monomer or as a dimer (e.g., heterodimer or homodimer). In some embodiments, an RT domain naturally functions as a monomer, e.g., is derived from a virus wherein it functions as a monomer. In embodiments, the RT domain is selected from an RT domain from murine leukemia virus (MLV; sometimes referred to as MoMLV) (e.g., P03355), porcine endogenous retrovirus (PERV) (e.g., UniProt Q4VFZ2). mouse mammary tumor vims (MMTV) (e.g., UniProt P03365), Mason-Pfizer monkey vims (MPMV) (e.g., UniProt P07572). bovine leukemia vims (BLV) (e.g., UniProt P03361), human T-cell leukemia virus-1 (HTLV-1) (e.g., UniProt P03362), human foamy vims (HFV) (e.g., UniProt P14350), simian foamy vims (SFV) (e.g., UniProt P23074), or bovine foamy/ syncytial vims (BFV/BSV) (e.g., UniProt 041894), or a functional fragment or variant thereof (e.g., an amino acid sequence having at least 70%, 80%, 90%, 95%, or 99% identity thereto). In some embodiments, an RT domain is dimeric in its natural functioning. In some embodiments, the RT domain is derived from a vims wherein it functions as a dimer. In embodiments, the RT domain is selected from an RT domain from avian sarcoma/leukemia vims (ASLV) (e.g., UniProt A0A142BKH1), Rous sarcoma vims (RSV) (e.g., UniProt P03354), avian myeloblastosis vims (AMV) (e.g., UniProt Q83133), human immunodeficiency vims type I (HIV-1) (e.g., UniProt P03369), human immunodeficiency vims type II (HIV-2) (e.g., UniProt P15833), simian immunodeficiency vims (SIV) (e.g., UniProt P05896), bovine immunodeficiency vims (BIV) (e.g., UniProt P19560), equine infectious anemia vims (EIAV) (e.g., UniProt P03371), or feline immunodeficiency vims (FIV) (e.g., UniProt Pl 6088) (Herschhom and Hizi Cell Mol Life Set 67( 16): 2717-2747 (2010)), or a functional fragment or variant thereof (e.g., an amino acid sequence having at least 70%, 80%, 90%, 95%, or 99% identity thereto). Naturally heterodimeric RT domains may, in some embodiments, also be functional as homodimers. In some embodiments, dimeric RT domains are expressed as fusion proteins, e.g., as homodimeric fusion proteins or heterodimeric fusion proteins. In some embodiments, the RT function of the system is fulfilled by multiple RT domains (e.g., as described herein). In further embodiments, the multiple RT domains are fused or separate, e g., may be on the same polypeptide or on different polypeptides.

In some embodiments, a gene modifying system described herein comprises an integrase domain, e.g., wherein the integrase domain may be part of the RT domain. In some embodiments, an RT domain (e.g., as described herein) comprises an integrase domain. In some embodiments, an RT domain (e.g., as described herein) lacks an integrase domain, or comprises an integrase domain that has been inactivated by mutation or deleted. In some embodiment, a gene modifying system described herein comprises an RNase H domain, e.g., wherein the RNase H domain may be part of the RT domain. In some embodiments, the RNase H domain is not part of the RT domain and is covalently linked via a flexible linker. In some embodiments, an RT domain (e g., as described herein) comprises an RNase H domain, e.g.. an endogenous RNAse H domain or a heterologous RNase H domain. In some embodiments, an RT domain (e.g., as described herein) lacks an RNase H domain. In some embodiments, an RT domain (e.g., as described herein) comprises an RNase H domain that has been added, deleted, mutated, or swapped for a heterologous RNase H domain. In some embodiments, the polypeptide comprises an inactivated endogenous RNase H domain. In some embodiments, an endogenous RNase H domain from one of the other domains of the polypeptide is genetically removed such that it is not included in the polypeptide, e.g.. the endogenous RNase H domain is partially or completely truncated from the comprising domain. In some embodiments, mutation of an RNase H domain yields a polypeptide exhibiting lower RNase activity, e.g., as determined by the methods described in Kotewicz et al. Nucleic Acids Res 16(l):265-277 (1988) (incorporated herein by reference in its entirety), e.g., lower by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% compared to an otherwise similar domain without the mutation. In some embodiments, RNase H activity is abolished.

In some embodiments, an RT domain is mutated to increase fidelity compared to an otherwise similar domain without the mutation. For instance, in some embodiments, a YADD or YMDD motif in an RT domain (e.g., in a reverse transcriptase) is replaced with YVDD. In embodiments, replacement of the YADD or YMDD or YVDD results in higher fidel ity in retroviral reverse transcriptase activity (e.g., as described in Jamburuthugoda and Eickbush J Mol Biol 2011; incorporated herein by reference in its entirety).

In some embodiments, a gene modifying polypeptide described herein comprises an RT domain having an amino acid sequence according to Table 6, or a sequence having at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto. In some embodiments, a nucleic acid described herein encodes an RT domain having an amino acid sequence according to Table 6, or a sequence having at least 70%, 80%, 85%, 90%, 95%, 97%. 98%, or 99% identity thereto.

Table 6: Exemplary reverse transcriptase domains from retroviruses

In some embodiments, reverse transcriptase domains are modified, for example by site-specific mutation. In some embodiments, reverse transcriptase domains are engineered to have improved properties, e.g. SuperScript IV (SSIV) reverse transcriptase derived from the MMLV RT. In some embodiments, the reverse transcriptase domain may be engineered to have lower error rates, e.g., as described in W02001068895, incorporated herein by reference. In some embodiments, the reverse transcriptase domain may be engineered to be more thermostable. In some embodiments, the reverse transcriptase domain may be engineered to be more processive. In some embodiments, the reverse transcriptase domain may be engineered to have tolerance to inhibitors. In some embodiments, the reverse transcriptase domain may be engineered to be faster. In some embodiments, the reverse transcriptase domain may be engineered to better tolerate modified nucleotides in the RNA template. In some embodiments, the reverse transcriptase domain may be engineered to insert modified DNA nucleotides. In some embodiments, the reverse transcriptase domain is engineered to bind a template RNA. In some embodiments, one or more mutations are chosen from D200N, L603W, T330P, D524G, E562Q, D583N, P51L, S67R, E67K, T197A, H204R, E302K, F309N, W313F, L435G, N454K, H594Q, L671P, E69K, or D653N in the RT domain of murine leukemia virus reverse transcriptase or a corresponding mutation at a corresponding position of another RT domain.

In some embodiments, an RT domain (e.g., as listed in Table 6) comprises one or more mutations as listed in Table 2 below. In some embodiment, an RT domain as listed in Table 6 comprises one, two, three, four, five, or six of the mutations listed in the corresponding row of Table 2 below. Table 2. Exemplary RT domain mutations (relative to corresponding wild-type sequences as listed in the corresponding row of Table 6)

In some embodiments, a gene modifying polypeptide comprises the RT domain from a retroviral reverse transcriptase, e.g., a wild-type M-MLV RT, e.g., comprising the following sequence:

M-MLV (WT):

TLNIEDEYRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATST PVSIKQYP MSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDI HPTVP

NPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTR LPQGFKN SPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRA SAKKA QICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKTPRQLREFLGTAGFCRLWIPGFAE MAA

PLYPLTKTGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKG VLTQKLG PWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQ PPD RWLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEGLQHNCLDILAEAHGTRPDL TDQP LPDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMA EGK

KLNVYTDSRYAFATAHIHGEIYRRRGLLTSEGKEIKNKDEILALLKALFLPKRLSII HCPGHQKGH SAEARGNRMADQAARKAAITETPDTSTLLI (SEQ ID NO: 2)

In some embodiments, a gene modifying polypeptide comprises the RT domain from a retroviral reverse transcriptase, e.g., an M-MLV RT, e.g., comprising the following sequence:

TLNIEDEHRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATST PVSIKQYP

MSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRV EDIHPTVP

NPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTR LPQGFKN SPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRA SAKKA

QICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKTPRQLREFLGTAGFCRLWIPG FAEMAA

PLYPLTKTGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKG VLTQKLG

PWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEAL VKQPPD

RWLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEGLQHNCLDILAEAHGTR PDLTDQP LPDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMA EGK KLNVYTDSRYAFATAHIHGEIYRRRGLLTSEGKEIKNKDEILALLKALFLPKRLSIIHCP GHQKGH SAEARGNRMADQAARKAAITETPDTSTLL (SEQ ID NO: 3)

In some embodiments, a gene modifying polypeptide comprises the RT domain from a retroviral reverse transcriptase comprising tire sequence of amino acids 659-1329 of NP 057933. In embodiments, the gene modifying polypeptide further comprises one additional amino acid at tire N-terminus of the sequence of amino acids 659-1329 of NP 057933, e.g., as shown below:

TLNIEDEHRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPL1IPEKATST PVS1KQYP MSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDI HPT

VPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTW TRLP QGFKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGN L

GYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKTPRQLREFLGTA GFCRL WIPGFAEMAAPLYPLTKTGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDE KQGY

AKGVLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLV ILAPH AVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEGLQHNCLDI LAE AHGTRPDLTDOPLPDADHTWYTDGSSLLOEGORKAGAAVTTETEVIWAKALPAGTSAQRA ELI ALTQALKMAEGKKLNVYTDSRYAFATAHIHGEIYRRRGLLTSEGKEIKNKDEILALLKAL FLPKR LSIIHCPGHQKGHSAEARGNRMADQAARKAA (SEO ID NO: 4)

Core RT (bold), annotated per above RNAseH (underlined), annotated per above

In embodiments, the gene modifying polypeptide further comprises one additional amino acid at the C-terminus of the sequence of amino acids 659-1329 of NP 057933. In embodiments, the gene modifying polypeptide comprises an RNaseHl domain (e.g., amino acids 1178-1318 of NP 057933).

In some embodiments, a retroviral reverse transcriptase domain, e.g., M-MLV RT, may comprise one or more mutations from a wild-type sequence that may improve features of the RT, e.g., thermostability, processivity, and/or template binding. In some embodiments, an M-MLV RT domain comprises, relative to the M-MLV (WT) sequence above, one or more mutations, e.g., selected from D200N, L603W, T330P, T306K, W313F, D524G, E562Q, D583N, P51L, S67R, E67K, T197A, H204R, E302K, F309N, L435G, N454K, H594Q, D653N, R1 IOS, K103L, e.g., a combination of mutations, such as D200N, L603W, and T330P, optionally further including T306K and W313F. In some embodiments, an M-MLV RT used herein comprises the mutations D200N, L603W, T330P, T306K and W313F. In embodiments, the mutant M-MLV RT comprises the following amino acid sequence:

M-MLV (PE2):

TLNIEDEYRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATST PVSIKQYP MSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDI HPTVP NPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQ GFKN SPTLFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRA SAKKA QICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKTPRQLREFLGKAGFCRLFIPGFAE MAAP LYPLTKPGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQ KLGP WRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQP PDR WLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEGLQHNCLDILAEAHGTRPDLT DQPL PDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAE GKK LNVYTDSRYAFATAH1HGE1YRRRGWLTSEGKEIKNKDE1LALLKALFLPKRLS11HCPG HQKGHS

AEARGNRMADQAARKAAITETPDTSTLLI (SEQ ID NO: 5) In some embodiments, a writing domain (e.g., RT domain) comprises an RNA-binding domain, e.g., that specifically binds to an RNA sequence. In some embodiments, a template RNA comprises an RNA sequence that is specifically bound by the RNA-binding domain of the writing domain.

In some embodiments, the reverse transcription domain only recognizes and reverse transcribes a specific template, e.g., a template RNA of the system. In some embodiments, the template comprises a sequence or structure that enables recognition and reverse transcription by a reverse transcription domain. In some embodiments, the template comprises a sequence or structure that enables association with an RNA-binding domain of a polypeptide component of a genome engineering system described herein. In some embodiments, the genome engineering system reverse preferably transcribes a template comprising an association sequence over a template lacking an association sequence.

The writing domain may also comprise DNA-dependent DNA polymerase activity , e.g., comprise enzymatic activity capable of writing DNA into the genome from a template DNA sequence. In some embodiments, DNA-dependent DNA polymerization is employed to complete second-strand synthesis of a target site edit. In some embodiments, the DNA-dependent DNA polymerase activity is provided by a DNA polymerase domain in the polypeptide. In some embodiments, the DNA-dependent DNA polymerase activity is provided by a reverse transcriptase domain that is also capable of DNA-dependent DNA polymerization, e.g., second-strand synthesis. In some embodiments, the DNA-dependent DNA polymerase activity is provided by a second polypeptide of the system. In some embodiments, the DNA- dependent DNA polymerase activity is provided by an endogenous host cell polymerase that is optionally recruited to the target site by a component of the genome engineering system.

In some embodiments, the reverse transcriptase domain has a lower probability of premature termination rate (/’off) in vitro relative to a reference reverse transcriptase domain. In some embodiments, the reference reverse transcriptase domain is a viral reverse transcriptase domain, e.g., the RT domain from M-MLV.

In some embodiments, the reverse transcriptase domain has a lower probability of premature termination rate (Poff) in vitro of less than about 5 x 10" ³ /nt, 5 x 10 ^-4 /nt, or 5 x 10 ^-6 /nt, e.g., as measured on a 1094 nt RNA. In embodiments, the in vitro premature termination rate is determined as described in Bibillo and Eickbush (2002) J Biol Chem 277(38):34836-34845 (incorporated by reference herein its entirety).

In some embodiments, the reverse transcriptase domain is able to complete at least about 30% or 50% of integrations in cells. The percent of complete integrations can be measured by dividing the number of substantially full-length integration events (e.g., genomic sites that comprise at least 98% of the expected integrated sequence) by the number of total (including substantially full-length and partial) integration events in a population of cells. In embodiments, the integrations in cells is determined (e.g., across the integration site) using long-read amplicon sequencing, e.g., as described in Karst et al. (2020) bioRxiv doi.org/10.1101/645903 (incorporated by reference herein in its entirety).

In some embodiments, an integration event results in a perfect editing event, e.g., wherein the resultant edited sequence perfectly matches a desired expected edited sequence. In embodiments, whether an integration event results in a perfectly edited sequence is detennined by identifying a perfectly- edited read using next-generation sequencing (e.g., from amplicon sequencing, e.g., as described herein). In embodiments, a perfectly edited read is a read that indicates that the edit contains the desired correct insertion size; optionally such a perfectly edited read may include one or more “N” base calls (i.e., wherein no clear base identification was made at certain sequence positions). In embodiments, a perfectly edited read includes up to 1%, up to 5%, up to 10%, up to 15%, up to 20%, up to 25%, up to 30%, up to 35%, or up to 40% "N” base calls (e.g., base calls that do not result in a read of non-identity relative to the desired expected edited sequence). In embodiments, a perfectly edited read is a read that indicates that the edit has 100% sequence identity to the desired expected edited sequence.

In some embodiments, a gene modifying system as described herein (e.g., comprising a template RNA or gene modifying polypeptide as described herein) induces insertions at two copies of a target locus in a cell. In some embodiments, a gene modifying system as described herein (e.g., comprising a template RNA or gene modifying polypeptide as described herein) induces insertions at two copies of a target locus in at least about 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 36%, 37%, 38%, 39%, or 40% of cells in a population of cells. In some embodiments, a gene modifying system as described herein (e.g., comprising a template RNA or gene modifying polypeptide as described herein) induces insertions at two copies of a target locus in at least about 1%, 2%, 3%. 4%, 5%, 6%. 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 36%, 37%, 38%, 39%, or 40% of cells comprising at least one edit induced by the gene modifying system. In certain embodiments, the insertions at the two copies of the target locus share at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity. In certain embodiments, the insertions at the two copies of the target locus have 100% sequence identity. In certain embodiments, the insertions at the two copies of the target locus have about the same length. In certain embodiments, the insertions at the two copies of the target locus include no more than 1. 2, 3, 4, 5. 6, 7, 8, 9, 10, 15, 20. 25, 30, 35, 40, 45, or 50 positions of non-identity relative to each other.

In embodiments, quantifying integrations in cells comprises counting the fraction of integrations that contain at least about 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% of the DNA sequence corresponding to the template RNA (e.g., a template RNA having a length of at least 0.05, 0.1, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 3, 4, or 5 kb, e.g., a length between 0.5-0.6, 0.6-0.7, 0.7-0.8, 0.8-0.9, 1 .0- 1.2, 1.2-1.4, 1.4-1.6, 1.6-1.8, 1.8-2.0, 2-3, 3-4, or 4-5 kb).

In some embodiments, the reverse transcriptase domain is capable of polymerizing dNTPs in vitro. In embodiments, the reverse transcriptase domain is capable of polymerizing dNTPs in vitro at a rate between 0.1 - 50 nt/sec (e.g., between 0.1-1, 1-10, or 10-50 nt/sec). In embodiments, polymerization of dNTPs by tire reverse transcriptase domain is measured by a single -molecule assay, e.g., as described in Schwartz and Quake (2009) PNAS 106(48):20294-20299 (incorporated by reference in its entirety).

In some embodiments, the reverse transcriptase domain has an in vitro error rate (e.g., misincorporation of nucleotides) of between 1 x 10" ³ - 1 x 10" ⁴ or 1 x 10" ⁴ - 1 x 10" ⁵ substitutions/nt , e.g., as described in Yasukawa et al. (2017) Biochem Biophys Res Commun 492(2): 147-153 (incorporated herein by reference in its entirety). In some embodiments, the reverse transcriptase domain has an error rate (e.g., misincorporation of nucleotides) in cells (e.g.. HEK293T cells) of between 1 x 10' ³ - 1 x 10' ⁴ or 1 x 10' ⁴ - 1 x 10' ⁵ substitutions/nt, e.g., by long-read amplicon sequencing, e.g., as described in Karst et al. (2020) bioRxiv doi.org/10.1101/645903 (incorporated by reference herein in its entirety).

In some embodiments, the reverse transcriptase domain is capable of performing reverse transcription of a target RNA in vitro. In some embodiments, tire reverse transcriptase requires a primer of at least 3 nucleotides to initiate reverse transcription of a template. In some embodiments, reverse transcription of the target RNA is determined by detection of cDNA from the target RNA (e.g., when provided with a ssDNA primer, e.g., which anneals to the target with at least 3, 4, 5, 6, 7, 8, 9, or 10 nt at the 3' end), e.g., as described in Bibillo and Eickbush (2002) J Biol Chem 277(38):34836-34845 (incorporated herein by reference in its entirety).

In some embodiments, the reverse transcriptase domain performs reverse transcription at least 5 or 10 times more efficiently (e.g., by cDNA production), e.g., when converting its RNA template to cDNA, for example, as compared to an RNA template lacking the protein binding motif (e.g., a 3' UTR). In embodiments, efficiency of reverse transcription is measured as described in Yasukawa et al. (2017) Biochem Biophys Res Commun 492(2): 147-153 (incorporated by reference herein in its entirety).

In some embodiments, the reverse transcriptase domain specifically binds a specific RNA template with higher frequency (e g., about 5 or 10-fold higher frequency) than any endogenous cellular RNA, e.g., when expressed in cells (e.g., HEK293T cells). In embodiments, frequency of specific binding between the reverse transcriptase domain and the template RNA are measured by CLIP-seq, e.g., as described in Lin and Miles (2019) Nucleic Acids Res 47(1 1 ):5490-5501 (incorporated herein by reference in its entirety).

Template nucleic acid binding domain The gene modifying polypeptide typically contains regions capable of associating with the template nucleic acid (e.g., template RNA). In some embodiments, the template nucleic acid binding domain is an RNA binding domain. In some embodiments, the RNA binding domain is a modular domain that can associate with RNA molecules containing specific signatures, e.g., structural motifs. In other embodiments, the template nucleic acid binding domain (e.g., RNA binding domain) is contained within the reverse transcription domain, e.g., the reverse transcriptase-derived component has a known signature for RNA preference.

In other embodiments, the template nucleic acid binding domain (e.g., RNA binding domain) is contained within the target DNA binding domain. For example, in some embodiments, the DNA binding domain is a CRISPR-associated protein that recognizes the structure of a template nucleic acid (e.g., template RNA) comprising a gRNA. In some embodiments, a gene modifying polypeptide comprises a DNA-binding domain comprising a CRISPR-associated protein that associates with a gRNA scaffold that allows the DNA-binding domain to bind a target genomic DNA sequence. In some embodiments, the gRNA scaffold and gRNA spacer is comprised within the template nucleic acid (e.g., template RNA), thus the DNA-binding domain is also the template nucleic acid binding domain. In some embodiments, the polypeptide possesses RNA binding function in multiple domains, e.g., can bind a gRNA structure in a CRISPR-associated DNA binding domain and an additional sequence or structure in a reverse transcriptase domain.

In some embodiments, the RNA binding domain is capable of binding to a template RNA with greater affinity than a reference RNA binding domain. In some embodiments, the reference RNA binding domain is an RNA binding domain from Cas9 of S. pyogenes. In some embodiments, the RNA binding domain is capable of binding to a template RNA with an affinity between 100 pM - 10 nM (e.g., between 100 pM-1 nM or 1 nM - 10 nM ). In some embodiments, the affinity of a RNA binding domain for its template RNA is measured in vitro, e.g.. by thennophoresis. e.g., as described in Asmari et al. Methods 146: 107-119 (2018) (incorporated by reference herein in its entirety). In some embodiments, the affinity of a RNA binding domain for its template RNA is measured in cells (e.g., by FRET or CLIP-Seq).

In some embodiments, the RNA binding domain is associated with the template RNA in vitro at a frequency at least about 5-fold or 10-fold higher than with a scrambled RNA. In some embodiments, the frequency of association between the RNA binding domain and the template RNA or scrambled RNA is measured by CLIP-seq, e.g.. as described in Lin and Miles (2019) Nucleic Acids Res 47(11): 5490-5501 (incorporated by reference herein in its entirety). In some embodiments, the RNA binding domain is associated with the template RNA in cells (e.g., in HEK293T cells) at a frequency at least about 5-fold or 10-fold higher than with a scrambled RNA. In some embodiments, the frequency of association between the RNA binding domain and the template RNA or scrambled RNA is measured by CLIP-seq, e.g., as described in Lin and Miles (2019), supra.

RNA binding domains (RBDs)

In some embodiments, a gene modifying polypeptide as described herein comprises an RNA binding domain (RBD). In some embodiments, a gene modifying polypeptide as described herein comprises an RBD comprising the amino acid sequence of an RBD as listed in Table 31, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, tire RBD of a gene modifying polypeptide as described herein binds to an RNA binding partner, e.g.. as listed in Table 31. In embodiments, the RBD comprises the amino acid sequence of an RBD as listed in any one row of Table 31. or an amino acid sequence having at least 75%, 80%. 85%. 90%, 95%, 96%, 97%, 98%, or 99% identity thereto, and binds to the RNA binding partner listed in the same row of Table 31. In embodiments, the RBD comprises, in N-terminal to C-terminal direction, a first amino acid sequence according to SEQ ID NO: 18003, an alanine residue, and a second amino acid sequence according to SEQ ID NO: 18003. Table 31. Exemplary RNA binding domain sequences

Endonuclease domains and DNA binding domains

In some embodiments, a gene modifying polypeptide possesses the function of DNA target site cleavage via an endonuclease domain. In some embodiments, a gene modifying polypeptide comprises a DNA binding domain, e.g., for binding to a target nucleic acid. In some embodiments, a domain (e.g., a Cas domain) of the gene modifying polypeptide comprises two or more smaller domains, e.g., a DNA binding domain and an endonuclease domain. It is understood that when a DNA binding domain (e.g., a Cas domain) is said to bind to a target nucleic acid sequence, in some embodiments, the binding is mediated by agRNA. In some embodiments, a domain has two functions. For example, in some embodiments, the endonuclease domain is also a DNA-binding domain. In some embodiments, the endonuclease domain is also a template nucleic acid (e.g., template RNA) binding domain. For example, in some embodiments, a polypeptide comprises a CRISPR-associated endonuclease domain that binds a template RNA comprising a gRNA, binds a target DNA sequence (e.g., with complementarity to a portion of the gRNA), and cuts the target DNA sequence. In some embodiments, an endonuclease domain or endonuclease/DNA-binding domain from a heterologous source can be used or can be modified (e.g., by insertion, deletion, or substitution of one or more residues) in a gene modifying system described herein.

In some embodiments, a nucleic acid encoding the endonuclease domain or endonuclease/DNA binding domain is altered from its natural sequence to have altered codon usage, e.g. improved for human cells. In some embodiments, the endonuclease element is a heterologous endonuclease element, such as a Cas endonuclease (e.g., Cas9), atype-II restriction endonuclease (e.g., Fokl), a meganuclease (e.g.. I- Scel), or other endonuclease domain.

In certain aspects, the DNA-binding domain of a gene modifying polypeptide described herein is selected, designed, or constructed for binding to a desired host DNA target sequence. In certain embodiments, the DNA-binding domain of the polypeptide is a heterologous DNA-binding element. In some embodiments the heterologous DNA binding element is a zinc-finger element or a TAL effector element, e.g., a zinc-finger or TAL polypeptide or functional fragment thereof. In some embodiments the heterologous DNA binding element is a sequence-guided DNA binding element, such as Cas9, Cpfl, or other CRISPR-related protein that has been altered to have no endonuclease activity. In some embodiments the heterologous DNA binding element retains endonuclease activity. In some embodiments, the heterologous DNA binding element retains partial endonuclease activity to cleave ssDNA, e.g., possesses nickase activity. In specific embodiments, the heterologous DNA-binding domain can be any one or more of Cas9, TAL domain, ZF domain, Myb domain, combinations thereof, or multiples thereof.

In some embodiments, DNA-binding domains are modified, for example by site-specific mutation, increasing or decreasing DNA-binding elements (for example, number and/or specificity of zinc fingers), etc., to alter DNA-binding specificity and affinity. In some embodiments a nucleic acid sequence encoding the DNA binding domain is altered from its natural sequence to have altered codon usage, e.g. improved for human cells. In embodiments, the DNA binding domain comprises one or more modifications relative to a wild-type DNA binding domain, e.g., a modification via directed evolution, e.g., phage-assisted continuous evolution (PACE).

In some embodiments, the DNA binding domain comprises a meganuclease domain (e.g., as described herein, e.g., in the endonuclease domain section), or a functional fragment thereof. In some embodiments, the meganuclease domain possesses endonuclease activity, e.g., double-strand cleavage and/or nickase activity. In other embodiments, the meganuclease domain has reduced activity, e.g., lacks endonuclease activity, e.g., the meganuclease is catalytically inactive. In some embodiments, a catalytically inactive meganuclease is used as a DNA binding domain, e.g., as described in Fonfara et al. Nucleic Acids Res 40(2): 847-860 (2012), incorporated herein by reference in its entirety.

In some embodiments, a gene modifying polypeptide comprises a modification to a DNA-binding domain, e.g., relative to the wild-type polypeptide. In some embodiments, the DNA-binding domain comprises an addition, deletion, replacement, or modification to the amino acid sequence of the original DNA-binding domain. In some embodiments, the DNA-binding domain is modified to include a heterologous functional domain that binds specifically to a target nucleic acid (e.g., DNA) sequence of interest. In some embodiments, the functional domain replaces at least a portion (e.g., the entirety of) the prior DNA-binding domain of the polypeptide. In some embodiments, the functional domain comprises a zinc finger (e.g., a zinc finger that specifically binds to the target nucleic acid (e.g., DNA) sequence of interest. In some embodiments, the functional domain comprises a Cas domain (e.g., a Cas domain that specifically binds to the target nucleic acid (e.g., DNA) sequence of interest. In some embodiments, the Cas domain comprises a Cas9 or a mutant or variant thereof (e.g., as described herein). In embodiments, the Cas domain is associated with a guide RNA (gRNA), e.g., as described herein. In embodiments, the Cas domain is directed to a target nucleic acid (e.g., DNA) sequence of interest by the gRNA. In embodiments, the Cas domain is encoded in the same nucleic acid (e g., RNA) molecule as the gRNA. In embodiments, the Cas domain is encoded in a different nucleic acid (e.g., RNA) molecule from the gRNA.

In some embodiments, the DNA binding domain is capable of binding to a target sequence (e.g., a dsDNA target sequence) with greater affinity than a reference DNA binding domain. In some embodiments, the reference DNA binding domain is a DNA binding domain from Cas9 of S. pyogenes. In some embodiments, the DNA binding domain is capable of binding to a target sequence (e.g., a dsDNA target sequence) with an affinity between 100 pM - 10 nM (e.g., between 100 pM-1 nM or 1 nM - 10 nM).

In some embodiments, the affinity of a DNA binding domain for its target sequence (e.g., dsDNA target sequence) is measured in vitro, e.g., by thennophoresis, e g., as described in Asmari et al. Methods 146: 107-119 (2018) (incorporated by reference herein in its entirety).

In embodiments, the DNA binding domain is capable of binding to its target sequence (e.g., dsDNA target sequence), e.g, with an affinity between 100 pM - 10 nM (e.g., between 100 pM-1 nM or 1 nM - 10 nM) in the presence of a molar excess of scrambled sequence competitor dsDNA, e.g., of about 100-fold molar excess. In some embodiments, the DNA binding domain is found associated with its target sequence (e.g., dsDNA target sequence) more frequently than any other sequence in the genome of a target cell, e.g., human target cell, e.g., as measured by ChlP-seq (e.g., in HEK293T cells), e.g., as described in He and Pu (2010) Curr. Protoc Mol Biol Chapter 21 (incorporated herein by reference in its entirety). In some embodiments, the DNA binding domain is found associated with its target sequence (e.g., dsDNA target sequence) at least about 5-fold or 10-fold, more frequently than any other sequence in the genome of a target cell, e.g., as measured by ChlP-seq (e.g., in HEK293T cells), e.g., as described in He and Pu (2010), supra.

In some embodiments, the endonuclease domain has nickase activity and cleaves one strand of a target DNA. In some embodiments, nickase activity reduces the formation of double -stranded breaks at the target site. In some embodiments, the endonuclease domain creates a staggered nick structure in the first and second strands of a target DNA. In some embodiments, a staggered nick structure generates free 3’ overhangs at the target site. In some embodiments, free 3’ overhangs at the target site improve editing efficiency, e.g., by enhancing access and annealing of a 3' homology region of a template nucleic acid. In some embodiments, a staggered nick structure reduces tire formation of double -stranded breaks at the target site.

In some embodiments, the endonuclease domain cleaves both strands of a target DNA, e.g., results in blunt-end cleavage of a target with no ssDNA overhangs on either side of the cut-site. The amino acid sequence of an endonuclease domain of a gene modifying system described herein may be at least about 50%. at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%. at least about 99% identical to the amino acid sequence of an endonuclease domain described herein, e.g., an endonuclease domain as described herein.

In certain embodiments, the heterologous endonuclease is Fokl or a functional fragment thereof. In certain embodiments, tire heterologous endonuclease is a Holliday junction rcsolvasc or homolog thereof, such as the Holliday junction resolving enzyme from Sulfolobus solfataricus — Ssol Hje (Govindaraju et al., Nucleic Acids Research 44:7, 2016). In certain embodiments, the heterologous endonuclease is the endonuclease of the large fragment of a spliceosomal protein, such as Prp8 (Mahbub et al., Mobile DNA 8: 16, 2017). In certain embodiments, the heterologous endonuclease is derived from a CRISPR-associated protein, e.g., Cas9. In certain embodiments, the heterologous endonuclease is engineered to have only ssDNA cleavage activity, e.g., only nickase activity, e.g., be a Cas9 nickase, e.g., SpCas9 with D10A, H840A, or N863A mutations. Table 8 provides exemplary Cas proteins and mutations associated with nickase activity. In still other embodiments, homologous endonuclease domains are modified, for example by site-specific mutation, to alter DNA endonuclease activity. In still other embodiments, endonuclease domains are modified to reduce DNA-sequence specificity, e.g., by truncation to remove domains that confer DNA-sequence specificity or mutation to inactivate regions conferring DNA-sequence specificity.

In some embodiments, the endonuclease domain has nickase activity and does not fonn doublestranded breaks. In some embodiments, the endonuclease domain forms single -stranded breaks at a higher frequency than double-stranded breaks, e.g., at least 90%, 95%, 96%, 97%, 98%, or 99% of the breaks are single-stranded breaks, or less than 10%, 5%, 4%, 3%, 2%, or 1% of the breaks are doublestranded breaks. In some embodiments, the endonuclease forms substantially no double -stranded breaks. In some embodiments, the endonuclease does not fonn detectable levels of double -stranded breaks.

In some embodiments, the endonuclease domain has nickase activity that nicks the target site DNA of the first strand; e.g., in some embodiments, the endonuclease domain cuts the genomic DNA of the target site near to the site of alteration on the strand that will be extended by the writing domain. In some embodiments, the endonuclease domain has nickase activity that nicks the target site DNA of the first strand and does not nick the target site DNA of the second strand. For example, when a polypeptide comprises a CRISPR-associated endonuclease domain having nickase activity, in some embodiments, said CRISPR-associated endonuclease domain nicks the target site DNA strand containing the PAM site (e.g., and does not nick the target site DNA strand that does not contain the PAM site). As a further example, when a polypeptide comprises a CRISPR-associated endonuclease domain having nickase activity, in some embodiments, said CRISPR-associated endonuclease domain nicks the target site DNA strand not containing the PAM site (e.g., and does not nick the target site DNA strand that contains the PAM site).

In some other embodiments, the endonuclease domain has nickase activity that nicks the target site DNA of the first strand and the second strand. Without wishing to be bound by theory, after a writing domain (e.g., RT domain) of a polypeptide described herein polymerizes (e.g., reverse transcribes) from the heterologous object sequence of a template nucleic acid (e.g., template RNA), the cellular DNA repair machinery must repair the nick on the first DNA strand. The target site DNA now contains two different sequences for the first DNA strand: one corresponding to tire original genomic DNA (e.g., having a free 5' end) and a second corresponding to that polymerized from the heterologous object sequence (e.g.. having a free 3' end). It is thought that the two different sequences equilibrate with one another, first one hybridizing the second strand, then the other, and which sequence the cellular DNA repair apparatus incorporates into its repaired target site may be a stochastic process. Without wishing to be bound by theory, it is thought that introducing an additional nick to the second-strand may bias the cellular DNA repair machinery to adopt the heterologous object sequence-based sequence more frequently than the original genomic sequence (Anzalone et al. Nature 576: 149-157 (2019)). In some embodiments, the additional nick is positioned at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, or 150 nucleotides 5' or 3' of the target site modification (e.g., the insertion, deletion, or substitution) or to the nick on tire first strand.

Alternatively or additionally, without wishing to be bound by theory, it is thought that an additional nick to the second strand may promote second-strand synthesis. In some embodiments, where the gene modifying system has inserted or substituted a portion of the first strand, synthesis of a new sequence corresponding to the insertion/substitution in the second strand is necessary.

In some embodiments, the polypeptide comprises a single domain having endonuclease activity (e.g., a single endonuclease domain) and said domain nicks both the first strand and tire second strand. For example, in such an embodiment the endonuclease domain may be a CRISPR-associated endonuclease domain, and the template nucleic acid (e.g., template RNA) comprises a gRNA spacerthat directs nicking of the first strand and an additional gRNA spacer that directs nicking of the second strand. In some embodiments, the polypeptide comprises a plurality of domains having endonuclease activity, and a first endonuclease domain nicks the first strand and a second endonuclease domain nicks the second strand (optionally, tire first endonuclease domain does not (e.g., cannot) nick the second strand and the second endonuclease domain does not (e.g., cannot) nick the first strand).

In some embodiments, the endonuclease domain is capable of nicking a first strand and a second strand. In some embodiments, the first and second strand nicks occur at the same position in the target site but on opposite strands. In some embodiments, the second strand nick occurs in a staggered location, e.g., upstream or downstream, from the first nick. In some embodiments, the endonuclease domain generates a target site deletion if the second strand nick is upstream of the first strand nick. In some embodiments, the endonuclease domain generates a target site duplication if the second strand nick is downstream of the first strand nick. In some embodiments, the endonuclease domain generates no duplication and/or deletion if the first and second strand nicks occur in the same position of the target site. In some embodiments, the endonuclease domain has altered activity depending on protein conformation or RNA-binding status, e.g., which promotes the nicking of the first or second strand (e.g., as described in Christensen et al. PNAS 2006; incorporated by reference herein in its entirety).

In some embodiments, the endonuclease domain comprises a meganuclease, or a functional fragment thereof. In some embodiments, the endonuclease domain comprises a homing endonuclease, or a functional fragment thereof. In some embodiments, the endonuclease domain comprises a meganuclease from the LAGLIDADG, GIY-YIG, HNH, His-Cys Box, or PD-(D/E) XK families, or a functional fragment or variant thereof, e.g., which possess conserved amino acid motifs, e.g., as indicated in the family names. In some embodiments, the endonuclease domain comprises a meganuclease, or fragment thereof, chosen from, e.g., I-SmaMI (Uniprot F7WD42), I-Scel (Uniprot P03882), I-Anil (Umprot P03880), I-Dmol (Uniprot P21505), I-Crel (Uniprot P05725), I-TevI (Uniprot P13299), I-Onul (Uniprot Q4VWW5), or I-Bmol (Uniprot Q9ANR6). In some embodiments, the meganuclease is naturally monomeric, e.g., I-Scel, I-TevI, or dimeric, e.g., I-Crel, in its functional form. For example, the LAGLID ADG meganucleases with a single copy of the LAGLID ADG motif generally form homodimers, whereas members with two copies of the LAGLID ADG motif are generally found as monomers. In some embodiments, a meganuclease that normally forms as a dimer is expressed as a fusion, e.g., the two subunits are expressed as a single ORF and, optionally, connected by a linker, e.g., an I-Crel dimer fusion (Rodriguez-Fomes et al. Gene Therapy 2020; incorporated by reference herein in its entirety)- In some embodiments, a meganuclease, or a functional fragment thereof, is altered to favor nickase activity’ for one strand of a double-stranded DNA molecule, e.g., I-Scel (K122I and/or K223I) (Niu et al. J Mol Biol 2008). I-Aml (K227M) (McConnell Smith et al. PNAS 2009). I-Dmol (Q42A and/or K120M) (Molina et al. J Biol Chem 2015). In some embodiments, a meganuclease or functional fragment thereof possessing this preference for single-strand cleavage is used as an endonuclease domain, e.g., with nickase activity. In some embodiments, an endonuclease domain comprises a meganuclease, or a functional fragment thereof, which naturally targets or is engineered to target a safe harbor site, e.g., an I-Crel targeting SH6 site (Rodriguez-Fomes et al., supra). In some embodiments, an endonuclease domain comprises a meganuclease, or a functional fragment thereof, with a sequence tolerant catalytic domain, e.g., I-TevI recognizing the minimal motif CNNNG (Kleinstiver et al. PNAS 2012). In some embodiments, atarget sequence tolerant catalytic domain is fused to a DNA binding domain, e.g., to direct activity, e.g., by fusing I-TevI to: (i) zinc fingers to create Tev-ZFEs (Kleinstiver et al. PNAS 2012), (ii) other meganucleases to create MegaTevs (Wolfs et al. Nucleic Acids Res 2014), and/or (iii) Cas9 to create TevCas9 (Wolfs et al. PNAS 2016).

In some embodiments, the endonuclease domain comprises a restriction enzyme, e.g., a Type IIS or Type IIP restriction enzyme. In some embodiments, the endonuclease domain comprises a Type IIS restriction enzyme, e.g., FokI, or a fragment or variant thereof. In some embodiments, the endonuclease domain comprises a Type IIP restriction enzyme, e.g., PvuII, or a fragment or variant thereof. In some embodiments, a dimeric restriction enzyme is expressed as a fusion such that it functions as a single chain, e.g., a FokI dimer fusion (Minczuk et al. Nucleic Acids Res 36(12):3926-3938 (2008)).

The use of additional endonuclease domains is described, for example, in Guha and Edgell Int J Mol Sci 18(22):2565 (2017), which is incorporated herein by reference in its entirety.

In some embodiments, a gene modifying polypeptide comprises a modification to an endonuclease domain, e.g., relative to a wild-type Cas protein. In some embodiments, the endonuclease domain comprises an addition, deletion, replacement, or modification to the amino acid sequence of the wild-type Cas protein. In some embodiments, the endonuclease domain is modified to include a heterologous functional domain that binds specifically to and/or induces endonuclease cleavage of a target nucleic acid (e.g., DNA) sequence of interest. In some embodiments, the endonuclease domain comprises a zinc finger. In embodiments, the endonuclease domain comprising tire Cas domain is associated with a guide RNA (gRNA), e.g., as described herein. In some embodiments, the endonuclease domain is modified to include a functional domain that does not target a specific target nucleic acid (e.g., DNA) sequence. In embodiments, the endonuclease domain comprises a Fokl domain.

In some embodiments, the endonuclease domain is associated with the target dsDNA in vitro at a frequency at least about 5-fold or 10-fold higher than with a scrambled dsDNA. In some embodiments, the endonuclease domain is associated with the target dsDNA in vitro at a frequency at least about 5 -fold or 10-fold higher than with a scrambled dsDNA, e.g., in a cell (e.g., a HEK293T cell). In some embodiments, the frequency of association between the endonuclease domain and the target DNA or scrambled DNA is measured by ChlP-seq, e.g., as described in He and Pu (2010) Curr. ProtocMol Biol Chapter 21 (incorporated by reference herein in its entirety).

In some embodiments, the endonuclease domain can catalyze the formation of a nick at a target sequence, e.g., to an increase of at least about 5-fold or 10-fold relative to a non-target sequence (e.g., relative to any other genomic sequence in the genome of the target cell). In some embodiments, tire level of nick formation is determined using NickSeq, e.g., as described in Elacqua et al. (2019) bioRxiv doi.org/10.1101/867937 (incorporated herein by reference in its entirety).

In some embodiments, the endonuclease domain is capable of nicking DNA in vitro. In embodiments, the nick results in an exposed base. In embodiments, the exposed base can be detected using a nuclease sensitivity' assay, e.g., as described in Chaudhry and Weinfeld (1995) Nucleic Acids Res 23(19):3805-3809 (incorporated by reference herein in its entirety). In embodiments, the level of exposed bases (e.g., detected by the nuclease sensitivity assay) is increased by at least 10%, 50%, or more relative to a reference endonuclease domain. In some embodiments, the reference endonuclease domain is an endonuclease domain from Cas9 of S. pyogenes.

In some embodiments, the endonuclease domain is capable of nicking DNA in a cell. In embodiments, tire endonuclease domain is capable of nicking DNA in aHEK293T cell. In embodiments, an unrepaired nick that undergoes replication in the absence of Rad51 results in increased NHEJ rates at the site of the nick, which can be detected, e.g., by using a Rad51 inhibition assay, e.g., as described in Bothmer et al. (2017) Nat Commun 8: 13905 (incorporated by reference herein in its entirety). In embodiments, NHEJ rates are increased above 0-5%. In embodiments, NHEJ rates are increased to 20- 70% (e.g., between 30%-60% or 40-50%), e.g., upon Rad51 inhibition. In some embodiments, the endonuclease domain releases the target after cleavage. In some embodiments, release of the target is indicated indirectly by assessing for multiple turnovers by the enzyme, e.g., as described in Yourik at al. RNA 25( 1): 35-44 (2019) (incorporated herein by reference in its entirety) and shown in FIG. 2. In some embodiments, the k _exp of an endonuclease domain is 1 x 10’ ³ - 1 x 10'5 min-1 as measured by such methods.

In some embodiments, the endonuclease domain has a catalytic efficiency (kfyK^) greater than about 1 x 10 ⁸ s ^-1 M ^-1 in vitro. In embodiments, the endonuclease domain has a catalytic efficiency greater than about 1 x 10 ⁵ , 1 x 10 ⁶ , 1 x 10 ⁷ , or 1 x 10 ⁸ , s' ¹ M ¹ in vitro. In embodiments, catalytic efficiency is determined as described in Chen et al. (2018) Science 360(6387):436-439 (incorporated herein by reference in its entirety). In some embodiments, the endonuclease domain has a catalytic efficiency (Ccat/ATm) greater than about 1 x 10 ⁸ s ^-1 M ^-1 in cells. In embodiments, the endonuclease domain has a catalytic efficiency greater than about 1 x 10 ⁵ . 1 x 10 ⁶ . 1 x 10 ⁷ , or 1 x 10 ⁸ s ^-1 M ^-1 in cells.

Gene modifying polypeptides comprising Cas domains

In some embodiments, a gene modifying polypeptide described herein comprises a Cas domain. In some embodiments, the Cas domain can direct the gene modifying polypeptide to a target site specified by a gRNA spacer, thereby modifying a target nucleic acid sequence in “cis”. In some embodiments, a gene modifying polypeptide is fused to a Cas domain. In some embodiments, a gene modify ing polypeptide comprises a CRISPR/Cas domain (also referred to herein as a CRISPR-associated protein). In some embodiments, a CRISPR/Cas domain comprises a protein involved in the clustered regulatory interspaced short palindromic repeat (CRISPR) system, e.g., a Cas protein, and optionally binds a guide RNA, e.g., single guide RNA (sgRNA).

CRISPR systems are adaptive defense systems originally discovered in bacteria and archaea. CRISPR systems use RNA-guided nucleases termed CRISPR-associated or “Cas” endonucleases (e. g., Cas9 or Cpfl) to cleave foreign DNA. For example, in a typical CRISPR-Cas system, an endonuclease is directed to a target nucleotide sequence (e. g., a site in the genome that is to be sequence-edited) by sequence-specific, non-coding “guide RNAs” that target single- or double-stranded DNA sequences. Three classes (I-III) of CRISPR systems have been identified. The class II CRISPR systems use a single Cas endonuclease (rather than multiple Cas proteins). One class II CRISPR system includes a type II Cas endonuclease such as Cas9, a CRISPR RNA (“crRNA”), and a trans-activating crRNA (“tracrRNA”). The crRNA contains a “spacer” sequence, atypically about 20-nucleotide RNA sequence that corresponds to a target DNA sequence (“protospacer”). In the wild-type system, and in some engineered systems, crRNA also contains a region that binds to the tracrRNA to form a partially double-stranded structure that is cleaved by RNase III, resulting in a crRNA/tracrRNA hybrid molecule. A crRNA/tracrRNA hybrid then directs the Cas endonuclease to recognize and cleave a target DNA sequence. A target DNA sequence is generally adjacent to a “protospacer adjacent motif’ (“PAM”) that is specific for a given Cas endonuclease and required for cleavage activity at a target site matching the spacer of the crRNA. CRISPR endonucleases identified from various prokaryotic species have unique PAM sequence requirements, e.g., as listed for exemplary Cas enzymes in Table 7; examples of PAM sequences include 5 -NGG (Streptococcus pyogenes), 5 -NNAGAA (Streptococcus thermophilus CRISPR1), 5 -NGGNG (Streptococcus thermophilus CRISPR3), and 5 -NNNGATT (Neisseria meningiditis). Some endonucleases, e.g., Cas9 endonucleases, are associated with G-rich PAM sites, e. g., 5 -NGG, and perform blunt-end cleaving of the target DNA at a location 3 nucleotides upstream from (5' from) the PAM site. Another class II CRISPR system includes the type V endonuclease Cpfl, which is smaller than Cas9; examples include AsCpfl (from Acidaminococcus sp.) and LbCpfl (from Lachnospiraceae sp.). Cpfl -associated CRISPR arrays are processed into mature crRNAs without the requirement of a tracrRNA; in other words, a Cpfl system, in some embodiments, comprises only Cpfl nuclease and a crRNA to cleave a target DNA sequence. Cpfl endonucleases, are typically associated with T-rich PAM sites, e. g., 5'-TTN. Cpfl can also recognize a 5'-CTA PAM motif. Cpfl typically cleaves a target DNA by introducing an offset or staggered double-strand break with a 4- or 5 -nucleotide 5 ' overhang, for example, cleaving a target DNA with a 5-nucleotide offset or staggered cut located 18 nucleotides downstream from (3 ' from) from a PAM site on the coding strand and 23 nucleotides downstream from the PAM site on tire complimentary strand; the 5-nucleotide overhang that results from such offset cleavage allows more precise genome editing by DNA insertion by homologous recombination than by insertion at blunt-end cleaved DNA. See, e.g., Zetsche et al. (2015) Cell, 163:759 - 771.

A variety of CRISPR associated (Cas) genes or proteins can be used in the technologies provided by the present disclosure and the choice of Cas protein will depend upon the particular conditions of the method. Specific examples of Cas proteins include class II systems including Casl, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9, CaslO, Cpfl, C2C1, or C2C3. In some embodiments, a Cas protein, e.g., a Cas9 protein, may be from any of a variety of prokaryotic species. In some embodiments a particular Cas protein, e.g., a particular Cas9 protein, is selected to recognize a particular protospacer-adjacent motif (PAM) sequence. In some embodiments, a DNA-binding domain or endonuclease domain includes a sequence targeting polypeptide, such as a Cas protein, e.g., Cas9. In certain embodiments a Cas protein, e.g., a Cas9 protein, may be obtained from a bacteria or archaea or synthesized using known methods. In certain embodiments, a Cas protein may be from a gram-positive bacteria or a gram -negative bacteria. In certain embodiments, a Cas protein may be from a Streptococcus (e.g., a S. pyogenes, or a S. thermophilus), a Francisella (e.g., an F. novicida), a Staphylococcus (e.g., an S. aureus), an Acidaminococcus (e.g., an Acidaminococcus sp. BV3L6), a Neisseria (e.g., an N. meningitidis), a Cryptococcus, a Corynebacterium, a Haemophilus, a Eubacterium, a Pasteurella, a Prevotella, a Veillonella, or a Marinobacter.

In some embodiments, a gene modifying polypeptide may comprise tire amino acid sequence of SEQ ID NO: 4000 below, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identity thereto. In embodiments, the amino acid sequence of SEQ ID NO: 4000 below, or the sequence having at least 70%. 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identity thereto, is positioned at the N-terminal end of the gene modifying polypeptide. In embodiments, the amino acid sequence of SEQ ID NO: 4000 below, or the sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identify thereto, is positioned within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, or 30 amino acids of the N-terminal end of the gene modifying polypeptide.

Exemplary N-terminal NLS-Cas9 domain

MPAAKRVKLDGGDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKN LIGALLF DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKH ERHP I FGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDN SDV DKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNL IALS LGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDI LRVN TEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEI FFDQSKNGYAGYIDGGASQEEFY KFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSI PHQIHLGELHAILRRQEDFYPFLKDNR EKIEKILTFRI PYYVGPLARGNSRFAWMTRKSEETITPWNFEEWDKGASAQSFIERMTNFDKN

LPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRK VTVKQLK EDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKI IKDKDFLDNEENEDILEDIVLTLTLFEDR EMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFA NRNF MQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKWDELVKVMGRH KPE NIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQ NGRD MYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKARGKSDNVPSEEWKKMKNY WRQ LLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDE NDKL I REVKVI TLKS KLVSDFRKDFQF YKVRE I NNYHHAHDAYLNAWGTAL I KKYPKLE S E FVYGD Y

KVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETG EIVWDKG RDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSP TVAY SVLWAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLI IKLPKYSLFE LENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHY LDEI IEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENI IHLFTLTNLGAPAAFKYFDTTIDR KRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDGG (SEQ ID NO: 4000)

In some embodiments, a gene modifying polypeptide may comprise the amino acid sequence of SEQ ID NO: 4001 below, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identify thereto. In embodiments, the amino acid sequence of SEQ ID NO: 4001 below, or the sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identity thereto, is positioned at the C-terminal end of the gene modifying polypeptide. In embodiments, the amino acid sequence of SEQ ID NO: 4001 below, or the sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identity thereto, is positioned within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, or 30 amino acids of the C-terminal end of the gene modifying polypeptide.

Exemplary C-terminal sequence comprising an NLS

AGKRTADGSEFEKRTADGSEFESPKKKAKVE (SEQ ID NO: 4001)

Exemplary benchmarking sequence

MPAAKRVKLDGGDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKN LIGALLF DSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKH ERHP I FGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDN SDV DKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNL IALS LGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDI LRVN TEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEI FFDQSKNGYAGYIDGGASQEEFY KFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSI PHQIHLGELHAILRRQEDFYPFLKDNR EKIEKILTFRI PYYVGPLARGNSRFAWMTRKSEETITPWNFEEWDKGASAQSFIERMTNFDKN LPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTV KQLK EDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKI IKDKDFLDNEENEDILEDIVLTLTLFEDR EMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFA NRNF MQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKWDELVKVMGRH KPE

NIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLY YLQNGRD MYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKARGKSDNVPSEEWKKMKNY WRQ LLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDE NDKL I REVKVI TLKS KLVSDFRKDFQF YKVRE I NNYHHAHDAYLNAWGTAL I KKYPKLE S E FVYGD Y KVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIV WDKG RDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSP TVAY SVLWAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLI IKLPKYSLFE LENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHY LDEI IEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENI IHLFTLTNLGAPAAFKYFDTTIDR

KRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDGGSGGSSGGSSGSETPGTSESA TPESSGG SSGGSSGGTLNIEDEYRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLI I PLKATS TPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLR EVNK

RVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEM GI SGQLT

WTRLPQGFKNSPTLFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTR ALLQTLG

NLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKTPRQLREFLG KAGFCRL FI PGFAEMAAPLYPLTKPGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQ GY

AKGVLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLV ILAPHAV

EALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPWALNPATLLPLPEEGLQHNCLDI LAEAHG

TRPDLTDQPLPDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALPAGTSAQRA ELIALTQ

ALKMAEGKKLNVYTDSRYAFATAHIHGEI YRRRGWLTSEGKEIKNKDEILALLKALFLPKRLSI IHCPGHQKGHSAEARGNRMADQAARKAAITETPDTSTLLIENSSPSGGSKRTADGSEFEA GKRT

ADGSEFEKRTADGSEFESPKKKAKVE (SEQ ID NO: 4002)

In some embodiments, a gene modifying polypeptide may comprise a Cas domain as listed in

Table 7 or 8, or a functional fragment thereof, or a sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% identity thereto.

Table 7. CRISPR/Cas Proteins, Species, and Mutations

Table 8 Amino Acid Sequences of CRISP RCas Proteins, Species, and Mutations

In some embodiments, a Cas protein requires a protospacer adjacent motif (PAM) to be present in or adjacent to a target DNA sequence for the Cas protein to bind and/or function. In some embodiments, the PAM is or comprises, from 5' to 3', NGG, YG, NNGRRT, NNNRRT, NGA, TYCV, TATV, NTTN, or NNNGATT, where N stands for any nucleotide, Y stands for C or T, R stands for A or G, and V stands for A or C or G. In some embodiments, a Cas protein is a protein listed in Table 7 or 8. In some embodiments, a Cas protein comprises one or more mutations altering its PAM. In some embodiments, a Cas protein comprises E1369R, E1449H, and R1556A mutations or analogous substitutions to the amino acids corresponding to said positions. In some embodiments, a Cas protein comprises E782K, N968K, and R1015H mutations or analogous substitutions to the amino acids corresponding to said positions. In some embodiments, a Cas protein comprises DI 135V, R1335Q, and T1337R mutations or analogous substitutions to the amino acids corresponding to said positions. In some embodiments, a Cas protein comprises S542R and K607R mutations or analogous substitutions to the amino acids corresponding to said positions. In some embodiments, a Cas protein comprises S542R, K548V, and N552R mutations or analogous substitutions to the amino acids corresponding to said positions. Exemplary advances in the engineering of Cas enzymes to recognize altered PAM sequences are reviewed in Collias et al Nature Communications 12:555 (2021), incorporated herein by reference in its entirety.

In some embodiments, the Cas protein is catalytically active and cuts one or both strands of the target DNA site. In some embodiments, cutting the target DNA site is followed by formation of an alteration, e.g., an insertion or deletion, e.g., by the cellular repair machinery.

In some embodiments, the Cas protein is modified to deactivate or partially deactivate the nuclease, e.g., nuclease-deficient Cas9. Whereas wild-type Cas9 generates double-strand breaks (DSBs) at specific DNA sequences targeted by a gRNA. a number of CRISPR endonucleases having modified functionalities are available, for example: a ‘‘nickase” version of Cas9 that has been partially deactivated generates only a single-strand break; a catalytically inactive Cas9 (“dCas9”) does not cut target DNA. In some embodiments, dCas9 binding to a DNA sequence may interfere with transcription at that site hysteric hindrance. In some embodiments, dCas9 binding to an anchor sequence may interfere with (e.g., decrease or prevent) genomic complex (e.g.. ASMC) formation and/or maintenance. In some embodiments, a DNA-binding domain comprises a catalytically inactive Cas9, e.g., dCas9. Many catalytically inactive Cas9 proteins are known in the art. In some embodiments, dCas9 comprises mutations in each endonuclease domain of the Cas protein, e.g., D10A and H840A or N863A mutations. In some embodiments, a catalytically inactive or partially inactive CRISPR/Cas domain comprises a Cas protein comprising one or more mutations, e.g., one or more of the mutations listed in Table 7. In some embodiments, a Cas protein described on a given row of Table 7 comprises one. two, three, or all of the mutations listed in the same row of Table 7. In some embodiments, a Cas protein, e.g., not described in Table 7, comprises one, two, three, or all of the mutations listed in a row of Table 7 or a corresponding mutation at a corresponding site in that Cas protein.

In some embodiments, a Cas9 derivative with enhanced activity may be used in the gene modification polypeptide. In some embodiments, a Cas9 derivative may comprise mutations that improve activity of the HNH endonuclease domain, e.g., SpyCas9 R221K, N394K. or mutations that improve R- loop formation, e.g.. SpyCas9 L1245V, or comprise a combination of such mutations, e.g., SpyCas9 R221K/N394K, SpyCas9 N394K/L1245V, SpyCas9 R221K/L1245V, or SpyCas9 R221K/N394K/L1245V (see, e.g., Spencer and Zhang Sci Rep 7: 16836 (2017), the Cas9 derivatives and comprising mutations of which are incorporated herein by reference). In some embodiments, a Cas9 derivative may comprise one or more types of mutations described herein, e.g., PAM-modifying mutations, protein stabilizing mutations, activity enhancing mutations, and/or mutations partially or fully inactivating one or two endonuclease domains relative to the parental enzyme (e.g., one or more mutations to abolish endonuclease activity towards one or both strands of a target DNA, e.g., a nickase or catalytically dead enzyme). In some embodiments, a Cas9 enzyme used in a system described herein may comprise mutations that confer nickase activity toward the enzyme (e.g., SpyCas9 N863A or H840A) in addition to mutations improving catalytic efficiency (e.g., SpyCas9 R221K, N394K, and/or L1245V). In some embodiments, a Cas9 enzyme used in a system described herein is a SpyCas9 enzyme or derivative that further comprises an N863A mutation to confer nickase activity in addition to R221K and N394K mutations to improve catalytic efficiency.

In some embodiments, a catalytically inactive, e.g., dCas9, or partially deactivated Cas9 protein comprises a DI 1 mutation (e.g., DI 1A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises aH969 mutation (e.g., H969A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a N995 mutation (e.g., N995A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, comprises mutations at one, two, or three of positions Dl l, H969, and N995 (e.g., DI 1A, H969A, and N995A mutations) or analogous substitutions to the amino acids corresponding to said positions.

In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a DIO mutation (e.g., a D10A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a H557 mutation (e.g.. a H557A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, comprises a DIO mutation (e.g., a D10A mutation) and a H557 mutation (e.g., a H557A mutation) or analogous substitutions to the amino acids corresponding to said positions.

In some embodiments, a catalytically inactive Cas9 protein, e g., dCas9, or partially deactivated Cas9 protein comprises a D839 mutation (e.g., a D839A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a H840 mutation (e.g., a H840A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a N863 mutation (e.g.. aN863A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, comprises a DIO mutation (e g., D10A), a D839 mutation (e.g., D839A), a H840 mutation (e.g., H840A), and a N863 mutation (e.g., N863A) or analogous substitutions to the amino acids corresponding to said positions.

In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a E993 mutation (e.g., a E993A mutation) or an analogous substitution to the amino acid corresponding to said position.

In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a D917 mutation (e.g., a D917A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a a E1006 mutation (e.g., a E1006A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a D 1255 mutation (e.g.. a D1255A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, comprises a D917 mutation (e.g., D917A), a E1006 mutation (e.g., E1006A), and a D1255 mutation (e.g., D1255A) or analogous substitutions to the amino acids corresponding to said positions. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a D16 mutation (e.g., a D16A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a D587 mutation (e.g., a D587A mutation) or an analogous substitution to tire amino acid corresponding to said position. In some embodiments, a partially deactivated Cas domain has nickase activity. In some embodiments, a partially deactivated Cas9 domain is a Cas9 nickase domain. In some embodiments, the catalytically inactive Cas domain or dead Cas domain produces no detectable double strand break formation. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a H588 mutation (e.g., a H588A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, or partially deactivated Cas9 protein comprises a N611 mutation (e.g., a N611A mutation) or an analogous substitution to the amino acid corresponding to said position. In some embodiments, a catalytically inactive Cas9 protein, e.g., dCas9, comprises a D16 mutation (e.g., D16A), a D587 mutation (e.g., D587A), a H588 mutation (e.g., H588A), and a N611 mutation (e.g., N611A) or analogous substitutions to the amino acids corresponding to said positions.

In some embodiments, a DNA-binding domain or endonuclease domain may comprise a Cas molecule comprising or linked (e.g., covalently) to a gRNA (e.g., a template nucleic acid, e.g., template RNA, comprising a gRNA).

In some embodiments, an endonuclease domain or DNA binding domain comprises a Streptococcus pyogenes Cas9 (SpCas9) or a functional fragment or variant thereof. In some embodiments, the endonuclease domain or DNA binding domain comprises a modified SpCas9. In embodiments, the modified SpCas9 comprises a modification that alters protospacer-adjacent motif (PAM) specificity. In embodiments, the PAM has specificity' for the nucleic acid sequence 5'-NGT-3'. In embodiments, the modified SpCas9 comprises one or more amino acid substitutions, e.g., at one or more of positions LI 111, DI 135, G1218, E1219, A1322, of R1335, e.g.. selected from LI 111R, DI 135V, G1218R, E1219F, A1322R, R1335V. In embodiments, the modified SpCas9 comprises the amino acid substitution T1337R and one or more additional amino acid substitutions, e.g., selected from Li l l i, DI 135L, S1136R, G1218S, E1219V, D1332A, D1332S, D1332T, D1332V, D1332L. D1332K. D1332R, R1335Q, T1337, T1337L. T1337Q. T13371, T1337V. T1337F, T1337S, T1337N. T1337K. T1337H, T1337Q, and T1337M, or corresponding amino acid substitutions thereto. In embodiments, the modified SpCas9 comprises: (i) one or more amino acid substitutions selected from D1135L, S1136R, G1218S, E1219V, A1322R, R1335Q, and T1337; and (ii) one or more amino acid substitutions selected from LI 111R, G1218R, E1219F, D1332A, D1332S, D1332T, D1332V, D1332L, D1332K, D1332R. T1337L, T1337I, T1337V, T1337F, T1337S, T1337N, T1337K, T1337R, T1337H, T1337Q, and T1337M, or corresponding amino acid substitutions thereto.

In some embodiments, the endonuclease domain or DNA binding domain comprises a Cas domain, e.g., a Cas9 domain. In embodiments, the endonuclease domain or DNA binding domain comprises a nuclease -active Cas domain, a Cas nickase (nCas) domain, or a nuclease -inactive Cas (dCas) domain. In embodiments, the endonuclease domain or DNA binding domain comprises a nuclease-active Cas9 domain, a Cas9 nickase (nCas9) domain, or a nuclease-inactive Cas9 (dCas9) domain. In some embodiments, the endonuclease domain or DNA binding domain comprises a Cas9 domain of Cas9 (e.g., dCas9 and nCas9), Casl2a/Cpfl, Casl2b/C2cl, Casl2c/C2c3, Casl2d/CasY, Casl2e/CasX, Casl2g, Casl2h, or Casl2i. In some embodiments, the endonuclease domain or DNA binding domain comprises a Cas9 (e.g., dCas9 and nCas9), Casl2a/Cpfl, Casl2b/C2cl, Casl2c/C2c3, Casl2d/CasY, Casl2e/CasX, Cas 12g. Casl2h, or Casl2i. In some embodiments, the endonuclease domain or DNA binding domain comprises an S. pyogenes or an S. thermophilus Cas9, or a functional fragment thereof. In some embodiments, the endonuclease domain or DNA binding domain comprises a Cas9 sequence, e.g., as described in Chylinski, Rhun, and Charpentier (2013) RNA Biology 10:5, 726-737; incorporated herein by reference. In some embodiments, the endonuclease domain or DNA binding domain comprises the HNH nuclease subdomain and/or the RuvCl subdomain of a Cas, e.g., Cas9, e.g., as described herein, or a variant thereof. In some embodiments, the endonuclease domain or DNA binding domain comprises Casl2a/Cpfl, Casl2b/C2cl, Casl2c/C2c3, Casl2d/CasY, Casl2e/CasX, Casl2g, Casl2h, or Casl2i. In some embodiments, the endonuclease domain or DNA binding domain comprises a Cas polypeptide (e.g., enzyme), or a functional fragment thereof. In embodiments, the Cas polypeptide (e.g., enzyme) is selected from Casl, CaslB, Cas2, Cas3, Cas4. Cas5, Cas5d, Cas5t, Cas5h, Cas5a, Cas6, Cas7, Cas8, Cas8a, Cas8b, Cas8c, Cas9 (e.g., Csnl or Csxl2), CaslO, CaslOd. Casl2a/Cpfl, Casl2b/C2cl. Casl2c/C2c3, Casl2d/CasY, Casl2e/CasX, Casl2g, Casl2h, Casl2i, Csyl , Csy2, Csy3, Csy4, Csel, Cse2, Cse3, Cse4, Cse5e, Cscl, Csc2, Csa5, Csnl, Csn2, Csml, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Csxl4, CsxlO, Csxl6, CsaX, Csx3, Csxl, CsxlS, Csxl l, Csfl, Csf2, CsO, Csf4, Csdl, Csd2, Cstl, Cst2, Cshl, Csh2, Csal, Csa2, Csa3, Csa4, Csa5, Type II Cas effector proteins, Type V Cas effector proteins, Type VI Cas effector proteins, CARF, DinG, Cpfl. Casl2b/C2cl, Casl2c/C2c3, Casl2b/C2cl, Casl2c/C2c3, SpCas9(K855A), eSpCas9(l. l), SpCas9-HFl, hyper accurate Cas9 variant (HypaCas9), homologues thereof, modified or engineered versions thereof, and/or functional fragments thereof. In embodiments, the Cas9 comprises one or more substitutions, e.g., selected from H840A, D10A, P475A, W476A, N477A, DI 125A, W1126A, and DI 127A. In embodiments, the Cas9 comprises one or more mutations at positions selected from: DIO, G12, G17, E762, H840, N854, N863, H982, H983, A984, D986, and/or A987, e.g., one or more substitutions selected from D10A, G12A, G17A, E762A, H840A, N854A, N863A, H982A, H983A, A984A, and/or D986A. In some embodiments, the endonuclease domain or DNA binding domain comprises a Cas (e.g., Cas9) sequence from Corynebacterium ulcerans, Coryncbactcrium diphtheria, Spiroplasma syrphidicola, Prevotella intermedia, Spiroplasma taiwanense, Streptococcus iniae, Belliella baltica, Psychroflexus torquis, Streptococcus thermophilus, Listeria innocua, Campylobacter jejuni, Neisseria meningitidis, Streptococcus pyogenes, or Staphylococcus aureus, or a fragment or variant thereof.

In some embodiments, the endonuclease domain or DNA binding domain comprises a Cpfl domain, e.g., comprising one or more substitutions, e.g., at position D917, E1006A, D1255 or any combination thereof, e.g., selected from D917A, E1006A, D1255A, D917A/E1006A, D917A/D1255A, E1006A/D1255A, and D917A/E1006A/D1255A.

In some embodiments, the endonuclease domain or DNA binding domain comprises spCas9, spCas9-VRQR(SEQ ID NO: 19), spCas9- VRER(SEQ ID NO: 20), xCas9 (sp), saCas9, saCas9-KKH, spCas9-MQKSER(SEQ ID NO: 21), spCas9-LRKIQK(SEQ ID NO: 22), or spCas9- LRVSQL(SEQ ID NO: 23).

In some embodiments, a gene modifying polypeptide has an endonuclease domain comprising a Cas9 nickase, e.g., Cas9 H840A. In embodiments, the Cas9 H840A has the following amino acid sequence:

Cas9 nickase (H840A):

DKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGET AEATRLKR TARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEV AYHEK YPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQT YNQLF EENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNF DLAEDA KLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMI KRYDE HHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTE ELLVK LNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYV GPLARGN SRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFT VYNE LTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGV EDRF NASLGTYHDLLKI1KDKDFLDNEENEDILED1VLTLTLFEDREMIEERLKTYAHLFDDKV MKQLK RRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQ VSGQG DSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNS RERM KRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDAI VPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERG GLS ELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKD FQFYK

VREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGK ATAKYF

FYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNI VKKTEVQT GGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKE LLGI

TIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKG NELALPSKY

VNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDK VLSAYNKH

RDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITG LYETRIDLSQL GGD

In some embodiments, a gene modifying polypeptide comprises a dCas9 sequence comprising a

D10A and/or H840A mutation, e.g., the following sequence:

SMDKKYSIGLAIGTNSVGWAVITDDYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSG ETAEATRL KRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVD EVAYH EKYPT1YHLRKKLVDSTDKADLRL1YLALAHMIKFRGHFL1EGDLNPDNSDVDKLF1QLV QTYNQ LFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKS NFDLAED AKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASM IKRYD EHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGT EELLV KLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYY VGPLARG NSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYF TVYN ELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISG VEDRF NASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKV MKQLK RRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQ VSGQG

DSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQ KNSRERM KRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDAI VPQSF LKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERG GLS ELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKD FQFYK VREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATA KYF FYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKK TEVQT GGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKE LLGI TIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNEL ALPSKY VNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLS AYNKH RDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYE TRIDLSQL GGD (SEQ ID NO: 7)

TAL Effectors and Zinc Finger Nucleases

In some embodiments, an endonuclease domain or DNA-binding domain comprises a TAL effector molecule. A TAL effector molecule, e.g., a TAL effector molecule that specifically binds a DNA sequence, typically comprises a plurality of TAL effector domains or fragments thereof, and optionally one or more additional portions of naturally occurring TAL effectors (e.g., N- and/or C-terminal of the plurality of TAL effector domains). Many TAL effectors are known to those of skill in the art and are commercially available, e.g., from Thermo Fisher Scientific.

Naturally occurring TALEs are natural effector proteins secreted by numerous species of bacterial pathogens including the plant pathogen Xanthomonas which modulates gene expression in host plants and facilitates bacterial colonization and survival. The specific binding of TAL effectors is based on a central repeat domain of tandemly arranged nearly identical repeats of typically 33 or 34 amino acids (the repeatvariable di-residues, RVD domain).

Members of the TAL effectors family differ mainly in the number and order of their repeats. The number of repeats typically ranges from 1.5 to 33.5 repeats and the C-terminal repeat is usually shorter in length (e.g., about 20 amino acids) and is generally referred to as a “half-repeat.” Each repeat of the TAL effector generally features a one-repeat-to-one-base-pair correlation with different repeat types exhibiting different base-pair specificity (one repeat recognizes one base-pair on the target gene sequence). Generally, the smaller the number of repeats, the weaker the protein-DNA interactions. A number of 6.5 repeats has been shown to be sufficient to activate transcription of a reporter gene (Scholze et al., 2010).

Repeat to repeat variations occur predominantly at amino acid positions 12 and 13, which have therefore been termed “hypervariable” and which are responsible for the specificity of the interaction with the target DNA promoter sequence, as shown in Table 9 listing exemplary repeat variable diresidues (RVD) and their correspondence to nucleic acid base targets.

Table 9 - RVDs and Nucleic Acid Base Specificity

Accordingly, it is possible to modify the repeats of a TAL effector to target specific DNA sequences. Further studies have shown that the RVD NK can target G. Target sites of TAL effectors also tend to include a T flanking the 5' base targeted by the first repeat, but the exact mechanism of this recognition is not known. More than 113 TAL effector sequences are known to date. Non-limiting examples of TAL effectors from Xanthomonas include, Hax2, Hax3, Hax4, AvrXa7, AvrXalO and AvrBs3.

Accordingly, the TAL effector domain of a TAL effector molecule described herein may be derived from a TAL effector from any bacterial species (e.g., Xanthomonas species such as the African strain of Xanthomonas oryzae pv. Oryzae (Yu et al. 2011), Xanthomonas campestris pv. raphani strain 756C and Xanthomonas oryzae pv. oryzicolastxain BLS256 (Bogdanove et al. 2011). In some embodiments, the TAL effector domain comprises an RVD domain as well as flanking sequence(s) (sequences on the N-terminal and/or C-terminal side of the RVD domain) also from the naturally occurring TAL effector. It may comprise more or fewer repeats than the RVD of the naturally occurring TAL effector. The TAL effector molecule can be designed to target a given DNA sequence based on the above code and others known in the art. The number of TAL effector domains (e.g., repeats (monomers or modules)) and their specific sequence can beselected based on the desired DNA target sequence. For example, TAL effector domains, e.g., repeats, may be removed or added in order to suit a specific target sequence. In an embodiment, the TAL effector molecule of the present invention comprises between 6.5 and 33.5 TAL effector domains, e.g., repeats. In an embodiment, TAL effector molecule of the present invention comprises between 8 and 33.5 TAL effector domains, e.g., repeats, e.g., between 10 and 25 TAL effector domains, e.g., repeats, e g., between 10 and 14 TAL effector domains, e.g., repeats.

In some embodiments, the TAL effector molecule comprises TAL effector domains that correspond to a perfect match to tire DNA target sequence. In some embodiments, a mismatch between a repeat and a target base-pair on tire DNA target sequence is permitted as along as it allows for the function of the polypeptide comprising the TAL effector molecule. In general, TALE binding is inversely correlated with the number of mismatches. In some embodiments, the TAL effector molecule of a polypeptide of the present invention comprises no more than 7 mismatches, 6 mismatches, 5 mismatches, 4 mismatches, 3 mismatches, 2 mismatches, or 1 mismatch, and optionally no mismatch, with the target DNA sequence. Without wishing to be bound by theory , in general the smaller the number of TAL effector domains in the TAL effector molecule, the smaller tire number of mismatches will be tolerated and still allow for the function of the polypeptide comprising the TAL effector molecule. The binding affinity is thought to depend on the sum of matching repeat-DNA combinations. For example, TAL effector molecules having 25 TAL effector domains or more may be able to tolerate up to 7 mismatches.

In addition to the TAL effector domains, the TAL effector molecule of the present invention may comprise additional sequences derived from a naturally occurring TAL effector. The length of the C- terminal and/or N-terminal sequence(s) included on each side of the TAL effector domain portion of the TAL effector molecule can vary and be selected by one skilled in the art, for example based on the studies of Zhang et al. (2011). Zhang et aL, have characterized a number of C-terminal and N-terminal truncation mutants in Hax3 derived TAL-effector based proteins and have identified key elements, which contribute to optimal binding to the target sequence and thus activation of transcription. Generally, it was found that transcriptional activity is inversely correlated with the length of N-terminus. Regarding the C-terminus. an important element for DNA binding residues within the first 68 amino acids of the Hax 3 sequence was identified. Accordingly, in some embodiments, the first 68 amino acids on the C-terminal side of the TAL effector domains of the naturally occurring TAL effector is included in the TAL effector molecule. Accordingly, in an embodiment, a TAL effector molecule comprises 1) one or more TAL effector domains derived from a naturally occurring TAL effector; 2) at least 70, 80, 90, 100, 110, 120, 130, 140, 150, 170, 180, 190, 200. 220, 230. 240, 250. 260, 270. 280 or more amino acids from the naturally occurring TAL effector on the N-terminal side of the TAL effector domains; and/or 3) at least 68. 80, 90, 100, 110, 120, 130, 140, 150, 170, 180, 190, 200, 220, 230, 240, 250, 260 or more amino acids from the naturally occurring TAL effector on the C-terminal side of the TAL effector domains.

In some embodiments, an endonuclease domain or DNA-binding domain is or comprises a Zn finger molecule. A Zn finger molecule comprises a Zn finger protein, e.g., a naturally occurring Zn finger protein or engineered Zn finger protein, or fragment thereof. Many Zn finger proteins are known to those of skill in the art and are commercially available, e g., from Sigma-Aldrich.

In some embodiments, a Zn finger molecule comprises a non-naturally occurring Zn finger protein that is engineered to bind to a target DNA sequence of choice. See, for example, Beerli, et al. (2002) Nature Biotechnol. 20: 135-141; Pabo, et al. (2001) Ann. Rev. Biochem. 70:313-340; Isalan, et al. (2001) Nature Biotechnol. 19:656-660; Segal, et al. (2001) Curr. Opin. Biotechnol. 12:632-637; Choo, et al. (2000) Curr. Opin. Struct. Biol. 10:411-416; U.S. Pat. Nos. 6,453,242; 6.534,261; 6,599.692: 6,503,717; 6,689,558; 7,030,215; 6,794,136; 7,067,317; 7,262,054; 7,070,934; 7,361,635; 7,253,273; and U.S. Patent Publication Nos. 2005/0064474; 2007/0218528; 2005/0267061, all incorporated herein by reference in their entireties.

An engineered Zn finger protein may have a novel binding specificity, compared to a naturally- occurring Zn finger protein. Engineering methods include, but are not limited to, rational design and various types of selection. Rational design includes, for example, using databases comprising triplet (or quadruplet) nucleotide sequences and individual Zn finger amino acid sequences, in which each triplet or quadruplet nucleotide sequence is associated with one or more amino acid sequences of zinc fingers which bind the particular triplet or quadruplet sequence. See, for example, U.S. Pat. Nos. 6,453,242 and 6,534,261, incorporated by reference herein in their entireties. Exemplary selection methods, including phage display and two-hybrid systems, are disclosed in U.S. Pat. Nos. 5,789,538; 5,925,523; 6,007,988; 6,013,453; 6,410,248; 6,140,466; 6,200,759; and 6,242,568; as well as International Patent Publication Nos. WO 98/37186; WO 98/53057; WO 00/27878; and WO 01/88197 and GB 2,338,237. In addition, enhancement of binding specificity for zinc finger proteins has been described, for example, in International Patent Publication No. WO 02/077227.

In addition, as disclosed in these and other references, zinc finger domains and/or multi-fingered zinc finger proteins may be linked together using any suitable linker sequences, including for example, linkers of 5 or more amino acids in length. See, also, U.S. Pat. Nos. 6,479,626; 6,903,185; and 7,153,949 for exemplary linker sequences 6 or more amino acids in length. The proteins described herein may include any combination of suitable linkers between tire individual zinc fingers of the protein. In addition, enhancement of binding specificity for zinc finger binding domains has been described, for example, in co-owned International Patent Publication No. WO 02/077227.

Zn finger proteins and methods for design and construction of fusion proteins (and polynucleotides encoding same) are known to those of skill in the art and described in detail in U.S. Pat. Nos. 6,140,0815; 789,538; 6,453,242; 6,534,261; 5,925,523; 6,007,988; 6,013,453; and 6,200,759; International Patent Publication Nos. WO 95/19431; WO 96/06166; WO 98/53057; WO 98/54311; WO 00/27878; WO 01/60970; WO 01/88197; WO 02/099084: WO 98/53058; WO 98/53059; WO 98/53060; WO 02/016536: and WO 03/016496.

In addition, as disclosed in these and other references, Zn finger proteins and/or multi -fingered Zn finger proteins may be linked together, e.g., as a fusion protein, using any suitable linker sequences, including for example, linkers of 5 or more amino acids in length. See, also, U.S. Pat. Nos. 6,479,626; 6,903,185; and 7,153,949 for exemplary linker sequences 6 or more amino acids in length. The Zn finger molecules described herein may include any combination of suitable linkers between the individual zinc finger proteins and/or multi-fingered Zn finger proteins of the Zn finger molecule.

In certain embodiments, the DNA-binding domain or endonuclease domain comprises a Zn finger molecule comprising an engineered zinc finger protein that binds (in a sequence-specific manner) to a target DNA sequence. In some embodiments, the Zn finger molecule comprises one Zn finger protein or fragment thereof. In other embodiments, tire Zn finger molecule comprises a plurality of Zn finger proteins (or fragments thereof), e.g.. 2, 3, 4, 5. 6 or more Zn finger proteins (and optionally no more than 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, or 2 Zn finger proteins). In some embodiments, the Zn finger molecule comprises at least three Zn finger proteins. In some embodiments, the Zn finger molecule comprises four, five or six fingers. In some embodiments, the Zn finger molecule comprises 8, 9, 10, 11 or 12 fingers. In some embodiments, a Zn finger molecule comprising three Zn finger proteins recognizes a target DNA sequence comprising 9 or 10 nucleotides. In some embodiments, a Zn finger molecule comprising four Zn finger proteins recognizes a target DNA sequence comprising 12 to 14 nucleotides. In some embodiments, a Zn finger molecule comprising six Zn finger proteins recognizes a target DNA sequence comprising 18 to 21 nucleotides.

In some embodiments, a Zn finger molecule comprises a two-handed Zn finger protein. Two handed zinc finger proteins are those proteins in which two clusters of zinc finger proteins are separated by intervening amino acids so that the two zinc finger domains bind to two discontinuous target DNA sequences. An example of a two handed type of zinc finger binding protein is SIP 1 , where a cluster of four zinc finger proteins is located at the amino terminus of the protein and a cluster of three Zn finger proteins is located at the carboxyl terminus (see Remade, et al. (1999) EMBO Journal 18(18): 5073-5084). Each cluster of zinc fingers in these proteins is able to bind to a unique target sequence and the spacing between the two target sequences can comprise many nucleotides.

Linkers

In some embodiments, a gene modifying polypeptide may comprise a linker, e.g., a peptide linker, e g., a linker as described in Table 1 or Table 10. In some embodiments, a gene modifying polypeptide comprises, in an N-terminal to C-terminal direction, a Cas domain (e.g., a Cas domain of Table 8), a linker of Table 10 (or a sequence having at least 70%, 80%, 85%, 90%, 95%, or 99% identity thereto), and an RT domain (e.g., an RT domain of Table 6). In some embodiments, a gene modifying polypeptide comprises a flexible linker between the endonuclease and tire RT domain, e.g., a linker comprising the amino acid sequence SGGSSGGSSGSETPGTSESATPESSGGSSGGSS. In some embodiments, an RT domain of a gene modify ing polypeptide may be located C-tenninal to the endonuclease domain. In some embodiments, an RT domain of a gene modifying polypeptide may be located N-terminal to the endonuclease domain.

Table 10. Exemplary linker sequences

In some embodiments, a linker of a gene modifying polypeptide comprises a motif chosen from: (SGGS)n(SEQ ID NO: 25), (GGGS) _n (SEQ ID NO: 26). (GGGGS)n(SEQ ID NO: 27), (G)„. (EAAAK)„ (SEQ ID NO: 28), (GGS)„, or (XP) _n

Gene modifying polypeptide selection by pooled screening

Candidate gene modifying polypeptides may be screened to evaluate a candidate’s gene editing ability. For example, an RNA gene modifying system designed for the targeted editing of a coding sequence in the human genome may be used. In certain embodiments, such a gene modifying system may be used in conjunction with a pooled screening approach.

For example, a library of gene modifying polypeptide candidates and a template guide RNA (tgRNA) may be introduced into mammalian cells to test the candidates’ gene editing abilities by a pooled screening approach. In specific embodiments, a library of gene modifying polypeptide candidates is introduced into mammalian cells followed by introduction of the tgRNA into the cells.

Representative, non-limiting examples of mammalian cells that may be used in screening include HEK293T cells, U2OS cells, HeLa cells, HepG2 cells, Huh7 cells, K562 cells, or iPS cells.

A gene modify ing polypeptide candidate may comprise 1) a Cas-nuclease. for example a wild-type Cas nuclease, e.g., a wild-type Cas9 nuclease, a mutant Cas nuclease, e.g.. a Cas nickase, for example, a Cas9 nickase such as a Cas9 N863A nickase, or a Cas nuclease selected from Table 7 or 8, 2) a peptide linker, e.g., a sequence from Table 1 or 10, that may exhibit varying degrees of length, flexibility, hydrophobicity, and/or secondary structure; and 3) a reverse transcriptase (RT), e.g. an RT domain from Table 1 or 6. A gene modifying polypeptide candidate library comprises: a plurality of different gene modifying polypeptide candidates that differ from each other with respect to one, two or all three of the Cas nuclease, peptide linker or RT domain components, or a plurality of nucleic acid expression vectors that encode such gene modifying polypeptide candidates.

For screening of gene modifying polypeptide candidates, a two-component system may be used that comprises a gene modifying polypeptide component and a tgRNA component. A gene modifying component may comprise, for example, an expression vector, e.g., an expression plasmid or lentiviral vector, that encodes a gene modifying polypeptide candidate, for example, comprises a human codon- optimized nucleic acid that encodes a gene modifying polypeptide candidate, e.g., a Cas-linker-RT fusion as described above. In a particular embodiment, a lentiviral cassette is utilized that comprises: (i) a promoter for expression in mammalian cells, e.g., a CMV promoter; (ii) a gene modifying library candidate, e.g. a Cas-linker-RT fusion comprising a Cas nuclease of Table CC, a peptide linker of Table AA and an RT of Table BB, for example a Cas-linker-RT fusion as in Table 1; (iii) a self-cleaving polypeptide, e.g., a T2A peptide; (iv) a marker enabling selection in mammalian cells, e.g., a puromycin resistance gene; and (v) a termination signal, e.g., a poly A tail.

The tgRNA component may comprise a tgRNA or expression vector, e.g., an expression plasmid, that produces the tgRNA, for example, utilizes a U6 promoter to drive expression of the tgRNA, wherein the tgRNA is a non-coding RNA sequence that is recognized by Cas and localizes it to the genomic locus of interest, and that also templates reverse transcription of the desired edit into the genome by the RT domain.

To prepare a pool of cells expressing gene modifying polypeptide library candidates, mammalian cells, e.g., HEK293T or U2OS cells, may be transduced with pooled gene modifying polypeptide candidate expression vector preparations, e.g., lentiviral preparations, of the gene modifying candidate polypeptide library. In a particular embodiment, lentiviral plasmids are utilized, and HEK293 Lenti-X cells are seeded in 15 cm plates (~12xl0 ⁶ cells) prior to lentiviral plasmid transfection. In such an embodiment, lentiviral plasmid transfection may be performed using the Lentiviral Packaging Mix (Biosettia) and transfection of the plasmid DNA for the gene modifying candidate library is performed the following day using Lipofectamine 2000 and Opti-MEM media according to the manufacturer’s protocol. In such an embodiment, extracellular DNA may be removed by a foil media change the next day and virus-containing media may be harvested 48 hours after. Lentiviral media may be concentrated using Lenti-X Concentrator (TaKaRa Biosciences) and 5 mL lentiviral aliquots may be made and stored at -80°C. Lentiviral titering is perfonned by enumerating colony forming units post-selection, e.g.. post Puromycin selection.

In some embodiments, a plurality of DNA molecules encoding a gene modifying polypeptide as described herein and a plurality of DNA molecules encoding a template RNA as described herein are present in a cell. In some embodiments, a plurality of DNA molecules encoding a gene modifying polypeptide as described herein and a plurality of DNA molecules encoding a template RNA as described herein are introduced into a cell. In certain embodiments, tire ratio of DNA molecules encoding the gene modifying polypeptide and the DNA molecules encoding the template RNA is about 6: 1, 2: 1, 1:1, or 3:5. In certain embodiments, the ratio of DNA molecules encoding tire gene modifying polypeptide and the DNA molecules encoding the template RNA is about 6: 1 to 2: 1, 2: 1 to 1 : 1, or 1 : 1 to 3:5. In certain embodiments, the system comprises a plurality of DNA molecules (e.g., plasmids) encoding a gRNA and a plurality of DNA molecules (e.g., plasmids) encoding the template RNA. In certain embodiments, the ratio of DNA molecules encoding the gRNA and the DNA molecules encoding the template RNA is about 3: 1, 1:1, 1:2, or 3:5. In certain embodiments, the ratio of DNA molecules encoding the gRNA and the DNA molecules encoding the template RNA is about 3 : 1 to 1: 1, 1 : 1 to 1 : 2, or 1 : 2 to 3 : 5. In certain embodiments, a gene modifying system as described herein comprises at least about 50, 150, 300, or 500 ng of the DNA molecule encoding the template RNA.

For monitoring gene editing of a target DNA, mammalian cells, e.g., HEK293T or U2OS cells, carrying a target DNA may be utilized. In other embodiments for monitoring gene editing of a target DNA, mammalian cells, e.g., HEK293T or U2OS cells, carrying a target DNA genomic landing pad may be utilized. In particular embodiments, the target DNA genomic landing pad may comprise a gene to be edited for treatment of a disease or disorder of interest. In other particular embodiments, the target DNA is a gene sequence that expresses a protein that exhibits detectable characteristics that may be monitored to determine whether gene editing has occurred. For example, in certain embodiments, a blue fluorescence protein (BFP)- or green fluorescence protein (GFP)-expressing genomic landing pad is utilized. In certain embodiments, mammalian cells, e.g., HEK293T or U2OS cells, comprising a target DNA, e.g., a target DNA genomic landing pad, are seeded in culture plates at 500x-3000x cells per gene modifying library candidate and transduced at a 0.2-0.3 multiplicity of infection (MOI) to minimize multiple infections per cell. Puromycin (2.5 ug/mL) may be added 48 hours post infection to allow for selection of infected cells. In such an embodiment, cells may be kept under puromycin selection for at least 7 days and then scaled up for tgRNA introduction, e.g., tgRNA electroporation.

To ascertain whether gene editing occurs, mammalian cells containing a target DNA to be edited may be infected with gene modifying polypeptide library’ candidates then transfected with tgRNA designed for use in editing of the target DNA. Subsequently, the cells may be analyzed to determine whether editing of the target locus has occurred according to the designed outcome, or whether no editing or imperfect editing has occurred, e.g., by using cell sorting and sequence analysis.

In a particular embodiment, to ascertain whether genome editing occurs, BFP- or GFP -expressing mammalian cells, e.g., HEK293T or U2OS cells, may be infected with gene modifying library candidates and then transfected or electroporated with tgRNA plasmid or RNA, e.g., by electroporation of 250,000 cells/well with 200 ng of a tgRNA plasmid designed to convert BFP-to-GFP or GFP-to-BFP, at a cell count ensuring >250x-1000x coverage per library candidate. In such an embodiment, the genome-editing capacity of the various constructs in this assay may be assessed by sorting the cells by Fluorescence-Activated Cell Sorting (FACS) for expression of the color-converted fluorescent protein (FP) at 4-10 days postelectroporation. Cells are sorted and harvested as distinct populations of unedited cells (exhibiting original florescence protein signal), edited cells (exhibiting converted fluorescence protein signal), and imperfect edit (exhibiting no florescence protein signal) cells. A sample of unsorted cells may also be harvested as the input population to determine candidate enrichment during analysis.

To determine which gene modifying library candidates exhibit genome-editing capacity in an assay, genomic DNA (gDNA) is harvested from tire sorted cell populations, and analyzed by sequencing the gene modifying library candidates in each population. Briefly, gene modifying candidates may be amplified from the genome using primers specific to the gene modifying polypeptide expression vector, e.g., the lentiviral cassette, amplified in a second round of PCR to dilute genomic DNA, and then sequenced, for example, sequenced by a next-generation sequencing platform. After quality control of sequencing reads, reads of at least about 1500 nucleotides and generally no more than about 3200 nucleotides are mapped to the gene modify ing polypeptide library sequences and those containing a minimum of about an 80% match to a library sequence are considered to be successfully aligned to a given candidate for purposes of this pooled screen. In order to identify candidates capable of performing gene editing in the assay, e.g., the BFP-to- GFP or GFP-to-BFP edit, the read count of each library candidate in the edited population is compared to its read count in the initial, unsorted population.

For purposes of pooled screening, gene modifying candidates with genome -editing capacity are identified based on enrichment in the edited (converted FP) population relative to unsorted (input) cells. In some embodiments, an enrichment of at least 1.0. 1.5, 2.0, 2.5, 3.0. 4.0, 5.0, 6.0, 7.0. 8.0, 9.0, 10, 15, 20, 25, 30, 40, 50, 60, 70. 80. 90. or at least 100-fold over the input indicates potentially useful gene editing activity, e.g., at least 2-fold enrichment. In some embodiments, the enrichment is converted to a log -value by taking the log base 2 of the enrichment ratio. In some embodiments, a log2 enrichment score of at least 0, 1, 2, 3, 4, 5, 5.5, 6.0, 6.2, 6.3, 6.4, 6.5, or at least 6.6 indicates potentially useful gene editing activity, e.g., a log2 enrichment score of at least 1.0. In particular embodiments, enrichment values observed for gene modifying candidates may be compared to enrichment values observed under similar conditions utilizing a reference, e.g., Element ID No: 17380.

In some embodiments, multiple tgRNAs may be used to screen the gene modifying candidate library. In particular embodiments, a plurality of tgRNAs may be utilized to optimize template/Cas-linker- RT fusion pairs, e.g., for gene editing of particular target genes, for example, gene targets for the treatment of disease. In specific embodiments, a pooled approach to screening gene modifying candidates may be performed using a multiplicity of different tgRNAs in an arrayed format.

In some embodiments, multiple types of edits, e.g., insertions, substitutions, and/or deletions of different lengths, may be used to screen the gene modifying candidate library. In some embodiments, multiple target sequences, e.g., different fluorescent proteins, may be used to screen the gene modifying candidate library. In some embodiments, multiple target sequences, e.g., different fluorescent proteins, may be used to screen the gene modifying candidate libraiy . In some embodiments, multiple cell types, e.g., HEK293T or U2OS, may be used to screen the gene modifying candidate library. The person of ordinary skill in the art will appreciate that a given candidate may exhibit altered editing capacity or even the gain or loss of any observable or useful activity across different conditions, including tgRNA sequence (e.g., nucleotide modifications, PBS length, RT template length), target sequence, target location, type of edit, location of mutation relative to the first-strand nick of the gene modifying polypeptide, or cell type. Tirus, in some embodiments, gene modifying libraiy candidates are screened across multiple parameters, e.g., with at least two distinct tgRNAs in at least two cell types, and gene editing activity is identified by enrichment in any single condition. In other embodiments, a candidate with more robust activity across different tgRNA and cell types is identified by enrichment in at least two conditions, e.g., in all conditions screened. For clarity, candidates found to exhibit little to no enrichment under any given condition are not assumed to be inactive across all conditions and may be screened with different parameters or reconfigured at tire polypeptide level, e.g., by swapping, shuffling, or evolving domains (e.g., RT domain), linkers, or other signals (e.g., NLS).

Sequences of exemplary Cas9-linker-RT fusions

In some embodiments, a gene modifying polypeptide comprises a linker sequence and an RT sequence. In some embodiments, a gene modifying polypeptide comprises a linker sequence as listed in Table 1, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises the amino acid sequence of an RT domain as listed in Table 1, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identify thereto. In some embodiments, a gene modifying polypeptide comprises a linker sequence as listed in Table 1, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%. 98%. or 99% identity thereto; and the amino acid sequence of an RT domain as listed in Table 1, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a gene modifying polypeptide comprises: (i) a linker sequence as listed in a row of Table 1, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto; and (ii) the amino acid sequence of an RT domain as listed in the same row of Table 1, or an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. For each RT domain named in Table 1, the corresponding amino acid sequence can be found in Table 6 herein. Dimerization domains

In some embodiments, a gene modifying system as described herein comprises a DNA binding domain (DBD), e.g., comprising a Cas domain (e.g., a Cas9 domain, e.g., an nCas9 or dCas9 domain); an RNA binding domain (RBD); and a retroviral reverse transcriptase (RT) domain. In some embodiments, the DBD is attached to the RBD via binding between two dimerization domains. In some embodiments, the DBD is attached to the RT domain via binding between two dimerization domains. In some embodiments, the RT domain is attached to the RBD via binding between two dimerization domains.

In some embodiments, a pair of dimerization domains comprised in a gene modifying polypeptide or complex as described herein can be induced to dimerize by a compound (e.g., a small molecule). In some embodiments, a pair of dimerization domains comprised in a gene modifying polypeptide or complex as described herein can be induced to dimerize by exposure to light (e.g.. of a specific color and/or wavelength). In some embodiments, a pair of dimerization domains comprised in a gene modifying polypeptide or complex as described herein comprise a Chain A sequence (or a sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto) and a Chain B sequence (or a sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto), as listed in a single row of Table 34. In embodiments, the pair of dimerization domains can be induced by the inducer listed in the same row of Table 34.

Table 34. Exemplary chemical- or light-induced dimerization domains

oc

In some embodiments, a pair of dimerization domains comprised in a gene modifying polypeptide or complex as described herein comprise an antibody, or a functional fragment thereof, and a peptide recognized by the antibody or fragment thereof. In some embodiments, a pair of dimerization domains comprised in a gene modifying polypeptide or complex as described herein comprise a Chain A sequence (or a sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto) and a Chain B sequence (or a sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto), as listed in a single row of Table 35.

Table 35. Exemplary antibody-peptide dimerization domains

In some embodiments, a dimerization domain comprised in a gene modifying polypeptide or complex as described herein comprises a coilcd-coil dimerization domain. In some embodiments, a dimerization domain comprised in a gene modifying polypeptide or complex as described herein comprises a sequence as listed in a single row of Table 36, or a sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a pair of dimerization domains comprised in a gene modifying polypeptide or complex as described herein comprise copies of the same coiled-coil dimerization domain (or coiled-coil dimerization domains having at least 90%, 95%, 96%, 97%, 98%, or 99% identity relative to each other).

Table 36. Exemplary coiled coil dimerization domains

In some embodiments, a pair of dimerization domains as described herein bind noncovalently to each other.

In some embodiments, a pair of dimerization domains as described herein bind covalently, e.g., to form a fusion (e g., an intein mediated fusion, e.g., as described herein). In embodiments, a pair of intein dimerization domains comprise a Chain A sequence (or a sequence having at least 75%. 80%. 85%. 90%. 95%, 96%, 97%, 98%, or 99% identity thereto) and a Chain B sequence (or a sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto), as listed in a single row of Table 33.

Localization sequences for gene modifying systems

In certain embodiments, a gene editor system RNA further comprises an intracellular localization sequence, e.g., a nuclear localization sequence (NLS). In some embodiments, a gene modifying polypeptide comprises an NLS as comprised in SEQ ID NO: 4000 and/or SEQ ID NO: 4001, or an NLS having an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

The nuclear localization sequence may be an RNA sequence that promotes the import of tire RNA into the nucleus. In certain embodiments the nuclear localization signal is located on the template RNA. In certain embodiments, the gene modifying polypeptide is encoded on a first RNA, and the template RNA is a second, separate, RNA, and the nuclear localization signal is located on the template RNA and not on an RNA encoding the gene modifying polypeptide. While not wishing to be bound by theory, in some embodiments, the RNA encoding the gene modifying polypeptide is targeted primarily to the cytoplasm to promote its translation, while the template RNA is targeted primarily to the nucleus to promote insertion into the genome. In some embodiments the nuclear localization signal is at the 3' end, 5' end. or in an internal region of the template RNA. In some embodiments the nuclear localization signal is 3' of the heterologous sequence (e.g., is directly 3' of the heterologous sequence) or is 5' of the heterologous sequence (e.g., is directly 5' of the heterologous sequence). In some embodiments the nuclear localization signal is placed outside of tire 5' UTR or outside of the 3' UTR of the template RNA. In some embodiments the nuclear localization signal is placed between the 5' UTR and the 3' UTR, wherein optionally the nuclear localization signal is not transcribed with the transgene (e.g.. the nuclear localization signal is an anti-sense orientation or is downstream of a transcriptional termination signal or polyadenylation signal). In some embodiments the nuclear localization sequence is situated inside of an intron. In some embodiments a plurality of the same or different nuclear localization signals are in the RNA, e.g., in the template RNA. In some embodiments the nuclear localization signal is less than 5, 10, 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900 or 1000 bp in length. Various RNA nuclear localization sequences can be used. For example, Lubelsky and Ulitsky, Nature 555 (107- 111), 2018 describe RNA sequences which drive RNA localization into the nucleus. In some embodiments, the nuclear localization signal is a SINE-derived nuclear RNA localization (SIRLOIN) signal. In some embodiments the nuclear localization signal binds a nuclear-enriched protein. In some embodiments the nuclear localization signal binds the HNRNPK protein. In some embodiments the nuclear localization signal is rich in pyrimidines, e.g., is a C/T rich, C/U rich, C rich, T rich, or U rich region. In some embodiments the nuclear localization signal is derived from a long non-coding RNA. In some embodiments the nuclear localization signal is derived from MALAT 1 long non-coding RNA or is the 600 nucleotide M region of MALAT1 (described in Miyagawa et al., RNA 18. (738-751), 2012). In some embodiments the nuclear localization signal is derived from BORG long non-coding RNA or is a AGCCC motif (described in Zhang et al., Molecular and Cellular Biology 34, 2318-2329 (2014). In some embodiments the nuclear localization sequence is described in Shukla et al., The EMBO Journal e98452 (2018). In some embodiments the nuclear localization signal is derived from a retrovirus.

In some embodiments, a polypeptide described herein comprises one or more (e.g., 2, 3, 4, 5) nuclear targeting sequences, for example a nuclear localization sequence (NLS). In some embodiments, the NLS is a bipartite NLS. In some embodiments, an NLS facilitates the import of a protein comprising an NLS into the cell nucleus. In some embodiments, the NLS is fused to the N-terminus of a gene modifying polypeptide as described herein. In some embodiments, the NLS is fused to the C -terminus of the gene modifying polypeptide. In some embodiments, the NLS is fused to the N-terminus or the C- terminus of a Cas domain. In some embodiments, a linker sequence is disposed between the NLS and the neighboring domain of the gene modifying polypeptide.

In some embodiments, an NLS comprises the amino acid sequence MDSLLMNRRKFLYQFKNVRWAKGRRETYLC (SEQ ID NO: 9), PKKRKVEGADKRTADGSEFESPKKKRKV(SEQ ID NO: 10), RKSGKIAAIWKRPRKPKKKRKV (SEQ ID NO: 11) KRTADGSEFESPKKKRKV(SEQ ID NO: 12), KKTELQTTNAENKTKKL (SEQ ID NO: 13), or KRG1NDRNFWRGENGRKTR (SEQ ID NO: 14), KRPAATKKAGQAKKKK (SEQ ID NO: 15), or a functional fragment or variant thereof. Exemplary NLS sequences are also described in PCT/EP2000/011690, the contents of which are incorporated herein by reference for their disclosure of exemplary nuclear localization sequences. In some embodiments, an NLS comprises an amino acid sequence as disclosed in Table 11. An NLS of this table may be utilized with one or more copies in a polypeptide in one or more locations in a polypeptide, e.g., 1, 2, 3 or more copies of an NLS in an N- terminal domain, between peptide domains, in a C-terminal domain, or in a combination of locations, in order to improve subcellular localization to the nucleus. Multiple unique sequences may be used within a single polypeptide. Sequences may be naturally monopartite or bipartite, e.g., having one or two stretches of basic amino acids, or may be used as chimeric bipartite sequences. Sequence references correspond to

UniProt accession numbers, except where indicated as SeqNLS for sequences mined using a subcellular localization prediction algorithm (Lin et al BMC Bioinformat 13: 157 (2012), incorporated herein by reference in its entirety). Table 11 Exemplary nuclear localization signals for use in gene modifying systems

In some embodiments, the NLS is a bipartite NLS. A bipartite NLS typically comprises two basic amino acid clusters separated by a spacer sequence (which may be, e.g.. about 10 amino acids in length). A monopartite NLS typically lacks a spacer. An example of a bipartite NLS is the nucleoplasmin NLS, having the sequence KR[PAATKKAGQA]KKKK (SEQ ID NO: 15), wherein the spacer is bracketed. Another exemplary bipartite NLS has the sequence PKKKRKVEGADKRTADGSEFESPKKKRKV (SEQ ID NO: 16). Exemplary NLSs arc described in International Application W02020051561, which is herein incorporated by reference in its entirety, including for its disclosures regarding nuclear localization sequences. In some embodiments, the polypeptide comprises (e.g., N-terminal of the Cas domain) a sequence according to PAAKRVKLDGG (SEQ ID NO: 18016) which comprises an NLS. In some embodiments, the polypeptide comprises (e.g., C-terminal of the RT domain) an NLS having a sequence according to KRTADGSEFESPKKKAKVE (SEQ ID NO: 18017).

In certain embodiments, a gene editor system polypeptide (e.g., a gene modifying polypeptide as described herein) further comprises an intracellular localization sequence, e.g., a nuclear localization sequence and/or a nucleolar localization sequence. The nuclear localization sequence and/or nucleolar localization sequence may be amino acid sequences that promote the import of the protein into the nucleus and/or nucleolus, where it can promote integration of heterologous sequence into the genome. In certain embodiments, a gene editor system polypeptide (e.g., (e.g., a gene modifying polypeptide as described herein) further comprises a nucleolar localization sequence. In certain embodiments, the gene modifying polypeptide is encoded on a first RNA, and the template RNA is a second, separate, RNA, and the nucleolar localization signal is encoded on the RNA encoding the gene modify ing polypeptide and not on the template RNA. In some embodiments, the nucleolar localization signal is located at the N- terminus, C-terminus, or in an internal region of the polypeptide. In some embodiments, a plurality of the same or different nucleolar localization signals are used. In some embodiments, the nuclear localization signal is less than 5, 10, 25, 50, 75, or 100 amino acids in length. Various polypeptide nucleolar localization signals can be used. For example, Yang et al., Journal of Biomedical Science 22, 33 (2015), describe a nuclear localization signal that also functions as a nucleolar localization signal. In some embodiments, the nucleolar localization signal may also be a nuclear localization signal. In some embodiments, the nucleolar localization signal may overlap with a nuclear localization signal. In some embodiments, the nucleolar localization signal may comprise a stretch of basic residues. In some embodiments, the nucleolar localization signal may be rich in arginine and lysine residues. In some embodiments, the nucleolar localization signal may be derived from a protein that is enriched in tire nucleolus. In some embodiments, the nucleolar localization signal may be derived from a protein enriched at ribosomal RNA loci. In some embodiments, the nucleolar localization signal may be derived from a protein that binds rRNA. In some embodiments, the nucleolar localization signal may be derived from MSP58. In some embodiments, the nucleolar localization signal may be a monopartite motif. In some embodiments, the nucleolar localization signal may be a bipartite motif. In some embodiments, the nucleolar localization signal may consist of a multiple monopartite or bipartite motifs. In some embodiments, the nucleolar localization signal may consist of a mix of monopartite and bipartite motifs. In some embodiments, tire nucleolar localization signal may be a dual bipartite motif. In some embodiments, the nucleolar localization motif may be a KRASSQALGTIPKRRSSSRFIKRKK (SEQ ID NO: 17). In some embodiments, the nucleolar localization signal may be derived from nuclear factor-KB- inducing kinase. In some embodiments, the nucleolar localization signal may be an RKKRKKK motif (SEQ ID NO: 18) (described in Birbach et al., Journal of Cell Science, 117 (3615-3624), 2004).

Evolved Variants of Gene Modifying Polypeptides and Systems

In some embodiments, the invention provides evolved variants of gene modify ing polypeptides as described herein. Evolved variants can, in some embodiments, be produced by mutagenizing a reference gene modifying polypeptide, or one of the fragments or domains comprised therein. In some embodiments, one or more of the domains (e.g., the reverse transcriptase domain) is evolved. One or more of such evolved variant domains can, in some embodiments, be evolved alone or together with other domains. An evolved variant domain or domains may, in some embodiments, be combined with unevolved cognate component(s) or evolved variants of the cognate component(s), e.g., which may have been evolved in either a parallel or serial manner.

In some embodiments, the process of mutagenizing a reference gene modifying polypeptide, or fragment or domain thereof, comprises mutagenizing the reference gene modifying polypeptide or fragment or domain thereof. In embodiments, the mutagenesis comprises a continuous evolution method (e.g., PACE) or non-continuous evolution method (e.g., PANCE), e.g., as described herein. In some embodiments, the evolved gene modifying polypeptide, or a fragment or domain thereof, comprises one or more amino acid variations introduced into its amino acid sequence relative to the amino acid sequence of the reference gene modifying polypeptide, or fragment or domain thereof. In embodiments, amino acid sequence variations may include one or more mutated residues (e.g., conservative substitutions, nonconservative substitutions, or a combination thereof) within the amino acid sequence of a reference gene modifying polypeptide, e.g., as a result of a change in the nucleotide sequence encoding the gene modifying polypeptide that results in, e.g., a change in the codon at any particular position in the coding sequence, the deletion of one or more amino acids (e.g., a truncated protein), the insertion of one or more amino acids, or any combination of the foregoing. The evolved variant gene modifying polypeptide may include variants in one or more components or domains of the gene modifying polypeptide (e.g., variants introduced into a reverse transcriptase domain).

In some aspects, the disclosure provides gene modifying polypeptides, systems, kits, and methods using or comprising an evolved variant of a gene modifying polypeptide, e.g., employs an evolved variant of a gene modify ing polypeptide or a gene modifying polypeptide produced or producible by PACE or PANCE. In embodiments, the unevolved reference gene modify ing polypeptide is a gene modifying polypeptide as disclosed herein.

The term ‘'phage-assisted continuous evolution (PACE),”as used herein, generally refers to continuous evolution that employs phage as viral vectors. Examples of PACE technology have been described, for example, in International PCT Application No. PCT/US 2009/056194, filed September 8, 2009, published as WO 2010/028347 on March 11, 2010; International PCT Application, PCT/US2011/066747. filed December 22. 2011. published as WO 2012/088381 on June 28. 2012; U.S. Patent No. 9,023,594, issued May 5, 2015; U.S. Patent No. 9,771,574, issued September 26. 2017; U.S. Patent No. 9,394,537, issued July 19, 2016; International PCT Application, PCT/US2015/012022, filed January 20, 2015, published as WO 2015/134121 on September 11, 2015; U.S. Patent No. 10,179,911, issued January 15, 2019; and International PCT Application, PCT/US2016/027795, filed April 15, 2016, published as WO 2016/168631 on October 20, 2016, the entire contents of each of which are incorporated herein by reference.

The term “phage-assisted non-continuous evolution (PANCE),” as used herein, generally refers to non-continuous evolution that employs phage as viral vectors. Examples of PANCE technology have been described, for example, in Suzuki T. et al, Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase, Nat Chem Biol. 13(12): 1261-1266 (2017), incorporated herein by reference in its entirety. Briefly, PANCE is a technique for rapid in vivo directed evolution using serial flask transfers of evolving selection phage (SP), which contain a gene of interest to be evolved, across fresh host cells (e.g., E. coli cells). Genes inside the host cell may be held constant while genes contained in the SP continuously evolve. Following phage growth, an aliquot of infected cells may be used to transfect a subsequent flask containing host E. coli. This process can be repeated and/or continued until the desired phenotype is evolved, e.g.. for as many transfers as desired.

Methods of applying PACE and PANCE to gene modifying polypeptides may be readily appreciated by the skilled artisan by reference to, inter alia, the foregoing references. Additional exemplary methods for directing continuous evolution of genome -modifying proteins or systems, e.g., in a population of host cells, e.g., using phage particles, can be applied to generate evolved variants of gene modifying polypeptides, or fragments or subdomains thereof. Non-limiting examples of such methods are described in International PCT Application, PCT/US2009/056194, fded September 8, 2009, published as WO 2010/028347 on March 11, 2010: International PCT Application, PCT/US2011/066747, filed December 22, 2011, published as WO 2012/088381 on June 28, 2012; U.S. Patent No. 9,023,594, issued May 5, 2015; U.S. Patent No. 9,771,574, issued September 26, 2017; U.S. Patent No. 9,394,537, issued July 19, 2016; International PCT Application, PCT/US2015/012022, filed January 20. 2015, published as WO 2015/134121 on September 11, 2015: U.S. Patent No. 10,179,911, issued January 15, 2019; International Application No. PCT/US2019/37216, filed June 14, 2019, International Patent Publication WO 2019/023680, published January 31, 2019, International PCT Application, PCT/US2016/027795, filed April 15, 2016, published as WO 2016/168631 on October 20, 2016, and International Patent Publication No. PCT/US2019/47996, filed August 23, 2019, each of which is incorporated herein by reference in its entirety.

In some non-limiting illustrative embodiments, a method of evolution of a evolved variant gene modifying polypeptide, of a fragment or domain thereof, comprises: (a) contacting a population of host cells with a population of viral vectors comprising the gene of interest (the starting gene modifying polypeptide or fragment or domain thereof), wherein: (1) the host cell is amenable to infection by the viral vector; (2) tire host cell expresses viral genes required for the generation of viral particles; (3) the expression of at least one viral gene required for the production of an infectious viral particle is dependent on a function of the gene of interest; and/or (4) the viral vector allows for expression of the protein in the host cell, and can be replicated and packaged into a viral particle by the host cell. In some embodiments, the method comprises (b) contacting the host cells with a mutagen, using host cells with mutations that elevate mutation rate (e.g., either by carrying a mutation plasmid or some genome modification — e.g., proofing-impaired DNA polymerase, SOS genes, such as UmuC, UmuD', and/or RecA, which mutations, if plasmid-bound, may be under control of an inducible promoter), or a combination thereof. In some embodiments, the method comprises (c) incubating the population of host cells under conditions allowing for viral replication and the production of viral particles, wherein host cells are removed from the host cell population, and fresh, uninfected host cells are introduced into the population of host cells, thus replenishing the population of host cells and creating a flow of host cells. In some embodiments, the cells are incubated under conditions allowing for the gene of interest to acquire a mutation. In some embodiments, the method further comprises (d) isolating a mutated version of the viral vector, encoding an evolved gene product (e.g., an evolved variant gene modifying polypeptide, or fragment or domain thereof), from the population of host cells.

The skilled artisan will appreciate a variety of features employable within the above-described framework. For example, in some embodiments, the viral vector or the phage is a filamentous phage, for example, an M13 phage, e.g., an M13 selection phage. In certain embodiments, the gene required for the production of infectious viral particles is the M13 gene III (gill). In embodiments, the phage may lack a functional gill, but otherw ise comprise gl, gll, gIV, gV, gVI, gVII, gVIII, glX, and a gX. In some embodiments, the generation of infectious VSV particles involves the envelope protein VSV-G. Various embodiments can use different retroviral vectors, for example, Murine Leukemia Virus vectors, or Lenti viral vectors. In embodiments, the retroviral vectors can efficiently be packaged with VSV-G envelope protein, e.g., as a substitute for the native envelope protein of the virus.

In some embodiments, host cells are incubated according to a suitable number of viral life cycles, e g., at least 10, at least 20, at least 30, at least 40, at least 50, at least 100, at least 200, at least 300, at least 400, at least, 500, at least 600, at least 700, at least 800, at least 900, at least 1000, at least 1250, at least 1500, at least 1750, at least 2000, at least 2500, at least 3000, at least 4000, at least 5000, at least 7500, at least 10000, or more consecutive viral life cycles, which in on illustrative and non-limiting examples of M13 phage is 10-20 minutes per virus life cycle. Similarly, conditions can be modulated to adjust the time a host cell remains in a population of host cells, e.g., about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 70, about 80, about 90, about 100, about 120, about 150, or about 180 minutes. Host cell populations can be controlled in part by density of the host cells, or, in some embodiments, the host cell density in an inflow , e.g., 10 ³ cells/ml, about 10 ⁴ cells/ml, about 10 ⁵ cells/ml, about 5- 10 ⁵ cells/ml, about 10 ⁶ cells/ml, about 5- 10 ⁶ cells/ml, about 10 ⁷ cells/ml, about 5- 10 ⁷ cells/ml, about 10 ⁸ cells/ml, about 5- 10 ⁸ cells/ml, about 10 ⁹ cells/ml, about 5- 10 ⁹ cells/ml, about IO ¹⁰ cells/ml, or about 5- IO ¹⁰ cells/ml.

Inteins

In some embodiments, as described in more detail below, an intein-N (intN) domain may be fused to the N-terminal portion of a first domain of a gene modifying polypeptide described herein, and an intein-C (intC) domain may be fused to the C-terminal portion of a second domain of a gene modify ing polypeptide described herein for the joining of the N-terminal portion to the C-terminal portion, thereby joining the first and second domains. In some embodiments, the first and second domains are each independently chosen from a DNA binding domain, an RNA binding domain, an RT domain, and an endonuclease domain.

Inteins can occur as self-splicing protein intron (e.g., peptide), e.g., which ligates flanking N- terminal and C-terminal exteins (e.g., fragments to be joined). An intein may, in some instances, comprise a fragment of a protein that is able to excise itself and join the remaining fragments (the exteins) with a peptide bond in a process known as protein splicing. Inteins are also referred to as “protein introns.” The process of an intein excising itself and joining the remaining portions of the protein is herein termed “protein splicing” or “intein-mediated protein splicing.”

In some embodiments, an intein of a precursor protein (an intein containing protein prior to intein-mediated protein splicing) comes from two genes. Such intein is referred to herein as a split intein (e.g., split intein-N and split intein-C). Accordingly, an intein-based approach may be used to join a first polypeptide sequence and a second polypeptide sequence together. For example, in cyanobacteria. DnaE, the catalytic subunit a of DNA polymerase III, is encoded by two separate genes, dnaE-n and dnaE-c. An intein-N domain, such as that encoded by the dnaE-n gene, when situated as part of a first polypeptide sequence, may join the first polypeptide sequence with a second polypeptide sequence, wherein the second polypeptide sequence comprises an intein-C domain, such as that encoded by the dnaE-c gene. Accordingly, in some embodiments, a protein can be made by providing nucleic acid encoding the first and second polypeptide sequences (e.g.. wherein a first nucleic acid molecule encodes the first polypeptide sequence and a second nucleic acid molecule encodes the second polypeptide sequence), and the nucleic acid is introduced into the cell under conditions that allow for production of the first and second polypeptide sequences, and for joining of the first to the second polypeptide sequence via an intein-based mechanism. Use of inteins for joining heterologous protein fragments is described, for example, in Wood et al., J. Biol. Chem.289(21); 14512-9 (2014) (incorporated herein by reference in its entirety). For example, when fused to separate protein fragments, the inteins IntN and IntC may recognize each other, splice themselves out, and/or simultaneously ligate the flanking N- and C-terminal exteins of the protein fragments to which they were fused, thereby reconstituting a full-length protein from the two protein fragments.

In some embodiments, a synthetic intein based on the dnaE intein, the Cfa-N (e.g., split intein-N) and Cfa-C (e.g., split intein-C) intein pair, is used. Examples of such inteins have been described, e.g., in Stevens et al., J Am Chem Soc. 2016 Feb. 24; 138(7):2162-5 (incorporated herein by reference in its entirety). Non-limiting examples of intein pairs that may be used in accordance with the present disclosure include: Cfa DnaE intein. Ssp GyrB intein, Ssp DnaX intein, Ter DnaE3 intein. Ter ThyX intein. Rma DnaB intein and Cne Prp8 intein (e.g., as described in U.S. Pat. No. 8,394,604, incorporated herein by reference.

In some embodiments involving a split Cas9, an intein-N domain and an intein-C domain may be fused to the N-tenninal portion of the split Cas9 and the C-terminal portion of a split Cas9, respectively, for the joining of the N-terminal portion of the split Cas9 and the C-terminal portion of the split Cas9. For example, in some embodiments, an intein-N is fused to the C-terminus of the N-terminal portion of the split Cas9, i.e., to form a structure of N — [N-terminal portion of the split Cas9]-[intein-N]~ C. In some embodiments, an intein-C is fused to the N-terminus of the C-terminal portion of the split Cas9, i.e., to form a structure of N- [intein-C] ~ [C-terminal portion of the split Cas9]-C. The mechanism of intein- mediated protein splicing for joining the proteins the inteins are fused to (e.g., split Cas9) is described in Shah et al., Chem Sci. 2014; 5(1):446-461, incorporated herein by reference. Methods for designing and using inteins are known in the art and described, for example by W02020051561. W02014004336, WO2017132580, US20150344549, and US20180127780, each of which is incorporated herein by reference in their entirety.

In some embodiments, a split refers to a division into two or more fragments. In some embodiments, a split Cas9 protein or split Cas9 comprises a Cas9 protein that is provided as an N- terminal fragment and a C-terminal fragment encoded by two separate nucleotide sequences. The polypeptides corresponding to the N-terminal portion and the C-terminal portion of the Cas9 protein may be spliced to form a reconstituted Cas9 protein. In embodiments, the Cas9 protein is divided into two fragments within a disordered region of the protein, e.g., as described in Nishimasu et al., Cell, Volume 156, Issue 5, pp. 935-949, 2014, or as described in Jiang et al. (2016) Science 351: 867-871 and PDB file: 5F9R (each of which is incorporated herein by reference in its entirety ). A disordered region may be determined by one or more protein structure determination techniques known in the art, including, without limitation, X-ray crystallography, NMR spectroscopy, electron microscopy (e.g., cryoEM), and/or in silico protein modeling. In some embodiments, the protein is divided into two fragments at any C, T, A, or S, e.g., within a region of SpCas9 between amino acids A292- G364, F445-K483, or E565- T637, or at corresponding positions in any other Cas9, Cas9 variant (e.g., nCas9, dCas9), or other napDNAbp. In some embodiments, protein is divided into two fragments at SpCas9 T310, T313, A456, S469, or C574. In some embodiments, the process of dividing the protein into two fragments is referred to as splitting the protein.

In some embodiments, a protein fragment ranges from about 2-1000 amino acids (e.g., between 2-10, 10-50, 50-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900- 1000 amino acids) in length. In some embodiments, a protein fragment ranges from about 5-500 amino acids (e.g., between 5-10, 10-50, 50-100, 100-200, 200-300. 300-400, or 400-500 amino acids) in length. In some embodiments, a protein fragment ranges from about 20-200 amino acids (e.g., between 20-30, 30-40, 40-50, 50-100, or 100-200 amino acids) in length.

In some embodiments, a portion or fragment of a gene modifying polypeptide is fused to an intein. The nuclease can be fused to the N-terminus or the C-terminus of the intein. In some embodiments, a portion or fragment of a fusion protein is fused to an intein and fused to an AAV capsid protein. The intein, nuclease and capsid protein can be fused together in any arrangement (e.g.. nuclease -intein-capsid, intein-nuclease-capsid, capsid-intein-nuclease, etc.). In some embodiments, the N-terminus of an intein is fused to the C-terminus of a fusion protein and the C-terminus of the intein is fused to the N-terminus of an AAV capsid protein.

In some embodiments, an endonuclease domain (e.g., a nickase Cas9 domain) is fused to intein-N and a polypeptide comprising an RT domain is fused to an intein-C.

Exemplary nucleotide and amino acid sequences of intein-N domains and compatible intein-C domains are provided below:

DnaE Intein-N DNA: TGCCTGTCATACGAAACCGAGATACTGACAGTAGAATATGGCCTTCTGCCAATCGGGAAG AT TGTGGAGAAACGGATAGAATGCACAGTTTACTCTGTCGATAACAATGGTAACATTTATAC TC AGCCAGTTGCCCAGTGGCACGACCGGGGAGAGCAGGAAGTATTCGAATACTGTCTGGAGG A TGGAAGTCTCATTAGGGCCACTAAGGACCACAAATTTATGACAGTCGATGGCCAGATGCT GC CTATAGACGAAATCTTTGAGCGAGAGTTGGACCTCATGCGAGTTGACAACCTTCCTAAT (SEQ ID NO: 29)

DnaE Intein-N Protein: CLSYETEILTVEYGLLPIGKIVEKRIECTVYSVDNNGNIYTQPVAQWHDRGEQEVFEYCL EDGSLI RATKDHKFMTVDGQMLPIDEIFERELDLMRVDNLPN (SEQ ID NO: 30)

DnaE Intein-C DNA: ATGATCAAGATAGCTACAAGGAAGTATCTTGGCAAACAAAACGTTTATGATATTGGAGTC G

AAAGAGATCACAACTTTGCTCTGAAGAACGGATTCATAGCTTCTAAT (SEQ ID NO: 31)

DnaE Intein-C Protein:

MIKIATRKYLGKQNVYDIGVERDHNFALKNGFIASN (SEQ ID NO: 32)

Cfa-N DNA: TGCCTGTCTTATGATACCGAGATACTTACCGTTGAATATGGCTTCTTGCCTATTGGAAAG ATT GTCGAAGAGAGAATTGAATGCACAGTATATACTGTAGACAAGAATGGTTTCGTTTACACA CA GCCCATTGCTCAATGGCACAATCGCGGCGAACAAGAAGTATTTGAGTACTGTCTCGAGGA TG GAAGCATCATACGAGCAACTAAAGATCATAAATTCATGACCACTGACGGGCAGATGTTGC C AATAGATGAGATATTCGAGCGGGGCTTGGATCTCAAACAAGTGGATGGATTG CCA (SEQ ID NO: 33)

Cfa-N Protein: CLSYDTEILTVEYGFLPIGKIVEERIECTVYTVDKNGFVYTQPIAQWHNRGEQEVFEYCL EDGSIIR ATKDHKFMTTDGQMLPIDEIFERGLDLKQVDGLP (SEQ ID NO: 34)

Cfa-C DNA: ATGAAGAGGACTGCCGATGGATCAGAGTTTGAATCTCCCAAGAAGAAGAGGAAAGTAAAG A TAATATCTCGAAAAAGTCTTGGTACCCAAAATGTCTATGATATTGGAGTGGAGAAAGATC AC AACTTCCTTCTCAAGAACGGTCTCGTAGCCAGCAAC (SEQ ID NO: 35) Cfa-C Protein:

MKRTADGSEFESPKKKRKVKIISRKSLGTQNVYDIGVEKDHNFLLKNGLVASN (SEQ ID NO: 36)

In some embodiments, an RBD of a gene modifying polypeptide as described herein is attached to an RT domain via an intein-based fusion, e.g., via an intein dimerization sequence as listed in Table 33 below (or an intein dimerization sequence comprising an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto). In some embodiments, an RBD of a gene modifying polypeptide as described herein is attached to a DBD (e.g., a Cas domain, e.g., a Cas9 domain, e.g., an nCas9 or dCas9 domain) via an intein-based fusion, e.g., via an intein dimerization sequence as listed in Table 33 below (or an intein dimerization sequence comprising an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto). In some embodiments, an RT domain of a gene modifying polypeptide as described herein is attached to a DBD (e.g., a Cas domain, e.g., a Cas9 domain, e.g., an nCas9 or dCas9 domain) via an intein-based fusion, e.g., via an intein dimerization sequence as listed in Table 33 below (or an intein dimerization sequence comprising an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto). In some embodiments, a DBD (e.g., a Cas domain, e.g., a Cas9 domain, e.g., an nCas9 or dCas9 domain) of a gene modifying polypeptide as described herein is attached to an RBD and to an RT domain via intein-based fusions. In embodiments, the DBD is attached to the RBD and the RT domain via different intein dimerization sequences, e.g., intein dimerization sequences as listed in Table 33 below (or sequences comprising an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto). In embodiments, the DBD is attached to the RBD and the RT domain via the same intein dimerization sequence, e.g., an intein dimerization sequence as listed in Table 33 below (or a sequence comprising an amino acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto). In some embodiments, tire intein dimerization sequences of an RBD and a DBD to be bound to each other comprise a Chain A sequence and a Chain B sequence, respectively, or a Chain B sequence and a Chain A sequence, respectively, as listed in a single row of Table 33 below (or sequences having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto). In some embodiments, the intein dimerization sequences of an RBD and an RT domain to be bound to each other comprise a Chain A sequence and a Chain B sequence, respectively, or a Chain B sequence and a Chain A sequence, respectively, as listed in a single row of Table 33 below (or sequences having at least 75%, 80%, 85%, 90%, 95%, 96%. 97%, 98%, or 99% identity thereto). In some embodiments, the intein dimerization sequences of an RT domain and a DBD to be bound to each other comprise a Chain A sequence and a Chain B sequence, respectively, or a Chain B sequence and a Chain A sequence, respectively, as listed in a single row of Table 33 below (or sequences having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto).

Table 33. Exemplary intein dimerization sequences

Additional domains

The gene modifying polypeptide can bind a target DNA sequence and template nucleic acid (e.g., template RNA), nick the target site, and write (e.g., reverse transcribe) the template into DNA, resulting in a modification of the target site. In some embodiments, additional domains may be added to the polypeptide to enhance the efficiency of the process. In some embodiments, the gene modifying polypeptide may contain an additional DNA ligation domain to join reverse transcribed DNA to the DNA of the target site. In some embodiments, the polypeptide may comprise a heterologous RNA-binding domain. In some embodiments, the polypeptide may comprise a domain having 5' to 3' exonuclease activity (e.g., wherein the 5 ' to 3 ' exonuclease activity increases repair of the alteration of the target site, e.g., in favor of alteration over tire original genomic sequence). In some embodiments, the polypeptide may comprise a domain having 3' to 5' exonuclease activity, e.g., proof-reading activity. In some embodiments, the writing domain, e g., RT domain, has 3 ' to 5' exonuclease activity, e.g., proof-reading activity.

Template nucleic acids

The gene modifying systems described herein can modify a host target DNA site using a template nucleic acid sequence. In some embodiments, the gene modifying systems described herein transcribe an RNA sequence template into host target DNA sites by target-primed reverse transcription (TPRT). By modifying DNA sequence(s) via reverse transcription of the RNA sequence template directly into the host genome, the gene modifying system can insert an object sequence into a target genome without the need for exogenous DNA sequences to be introduced into the host cell (unlike, for example, CRISPR systems), as well as eliminate an exogenous DNA insertion step. The gene modifying system can also delete a sequence from tire target genome or introduce a substitution using an object sequence. Therefore, the gene modify ing system provides a platform for the use of customized RNA sequence templates containing object sequences, e.g.. sequences comprising heterologous gene coding and/or function information.

In some embodiments, the template nucleic acid comprises one or more sequence (e.g., 2 sequences) that binds the gene modifying polypeptide.

In some embodiments, the template RNA comprises a nucleic acid sequence as listed in Table S4, or a nucleic acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, the template RNA comprises a 5’ end block sequence of a template sequence as listed in Table S4, or a nucleic acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%. or 99% identify thereto. In some embodiments, the template RNA comprises a PBS sequence of a template sequence as listed in Table S4, or a nucleic acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, the template RNA comprises a linker sequence of a template sequence as listed in Table S4, or a nucleic acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, the template RNA comprises one or more (e.g., 1, 2, 3, or 4) RRS sequences of a template sequence as listed in Table S4, or nucleic acid sequences having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, the template RNA comprises a 3 ’ end block sequence of a template sequence as listed in Table S4, or a nucleic acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, the template RNA comprises (e.g., in 5' to 3’ order) a 5’ end block sequence, PBS sequence, one or more RRS sequences, and a 3’ end block sequence of a template sequence as listed in Table S4, or nucleic acid sequences having at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto.

In some embodiments a system or method described herein comprises a single template nucleic acid (e.g., template RNA). In some embodiments a system or method described herein comprises a plurality of template nucleic acids (e.g., template RNAs). For example, a system described herein comprises a first RNA comprising (e.g., from 5' to 3') a sequence that binds the gene modifying polypeptide (e.g., the DNA-binding domain and/or the endonuclease domain, e.g.. a gRNA) and a sequence that binds a target site (e.g., a second strand of a site in a target genome), and a second RNA (e.g., a template RNA) comprising (e g., from 5 ' to 3') optionally a sequence that binds the gene modifying polypeptide (e.g., that specifically binds the RT domain), a heterologous object sequence, and a PBS sequence. In some embodiments, when the system comprises a plurality of nucleic acids, each nucleic acid comprises a conjugating domain. In some embodiments, a conjugating domain enables association of nucleic acid molecules, e.g., by hybridization of complementary sequences. For example, in some embodiments a first RNA comprises a first conjugating domain and a second RNA comprises a second conjugating domain, and the first and second conjugating domains are capable of hybridizing to one another, e.g., under stringent conditions. In some embodiments, the stringent conditions for hybridization include hybridization in 4x sodium chloride/sodium citrate (SSC), at about 65 C, followed by a wash in IxSSC, at about 65 C.

In some embodiments, the template nucleic acid comprises RNA. In some embodiments, the template nucleic acid comprises DNA (e.g., single stranded or double stranded DNA). In some embodiments, the template nucleic acid comprises one or more (e.g., 2) homology domains that have homology to the target sequence. In some embodiments, the homology domains are about 10-20, 20-50, or 50-100 nucleotides in length.

In some embodiments, a template RNA can comprise a gRNA sequence, e.g., to direct the gene modifying polypeptide to a target site of interest. In some embodiments, a template RNA comprises (e.g., from 5' to 3') (i) optionally a gRNA spacer that binds a target site (e g., a second strand of a site in a target genome), (ii) optionally a gRNA scaffold that binds a polypeptide described herein (e.g., a gene modifying polypeptide or a Cas polypeptide), (iii) a heterologous object sequence comprising a mutation region (optionally the heterologous object sequence comprises, from 5’ to 3’, a first homology region, a mutation region, and a second homology region), and (iv) a primer binding site (PBS) sequence comprising a 3' target homology domain.

The template nucleic acid (e.g., template RNA) component of a genome editing system described herein typically is able to bind the gene modifying polypeptide of the system. In some embodiments the template nucleic acid (e.g., template RNA) has a 3' region that is capable of binding a gene modifying polypeptide. The binding region, e.g., 3' region, may be a structured RNA region, e.g., having at least 1, 2 or 3 hairpin loops, capable of binding the gene modifying polypeptide of the system. The binding region may associate the template nucleic acid (e g., template RNA) with any of the polypeptide modules. In some embodiments, the binding region of the template nucleic acid (e.g., template RNA) may associate with an RNA-binding domain in the polypeptide. In some embodiments, the binding region of the template nucleic acid (e.g., template RNA) may associate with the reverse transcription domain of the gene modifying polypeptide (e.g., specifically bind to the RT domain). In some embodiments, the template nucleic acid (e.g., template RNA) may associate with the DNA binding domain of the polypeptide, e g., a gRNA associating with a Cas9-derived DNA binding domain. In some embodiments, the binding region may also provide DNA target recognition, e.g.. a gRNA hybridizing to the target DNA sequence and binding the polypeptide, e.g., a Cas9 domain. In some embodiments, the template nucleic acid (e.g., template RNA) may associate with multiple components of the polypeptide, e.g., DNA binding domain and reverse transcription domain.

In some embodiments the template RNA has a poly-A tail at the 3' end. In some embodiments the template RNA does not have a poly-A tail at the 3 ' end.

In some embodiments, a template RNA may be customized to correct a given mutation in the genomic DNA of a target cell (e.g., ex vivo or in vivo, e.g., in a target tissue or organ, e.g., in a subject). For example, the mutation may be a disease-associated mutation relative to the wild-type sequence. Without wishing to be bound by theory, any given target site and edit will have a large number of possible template RNA molecules for use in a gene modifying system that will result in a range of editing efficiencies and fidelities. To partially reduce this screening burden, sets of empirical parameters help ensure optimal initial in silico designs of template RNAs or portions thereof. As a non-limiting illustrative example, for a selected mutation, the following design parameters may be employed. In some embodiments, design is initiated by acquiring approximately 500 bp (e.g., up to 50, 100, 150, 200, 250, 300. 350, 400. 450, 500. 550, 600. 650, or 700 bp. and optionally at least 20, 30, 40. 50. 100, 150. 200, 250, 300, 350, 400, 450, 500, 550, 600, or 650 bp) flanking sequence on either side of the mutation to serve as the target region. In some embodiments, a template nucleic acid comprises a gRNA. In some embodiments, a gRNA comprises a sequence (e.g., a CRISPR spacer) that binds a target site. In some embodiments, tire sequence (e.g., a CRISPR spacer) that binds a target site for use in targeting a template nucleic acid to a target region is selected by considering the particular gene modifying polypeptide (e.g., endonuclease domain or writing domain, e.g., comprising a CRISPR/Cas domain) being used (e.g., for Cas9, a protospacer-adjacent motif (PAM) of NGG immediately 3 ' of a 20 nucleotide gRNA binding region). In some embodiments, the CRISPR spacer is selected by ranking first by whether the PAM will be disrupted by the gene modifying system induced edit. In some embodiments, disruption of the PAM may increase edit efficiency. In some embodiments, the PAM can be disrupted by also introducing (e.g., as part of or in addition to another modification to a target site in genomic DNA) a silent mutation (e.g.. a mutation that does not alter an amino acid residue encoded by the target nucleic acid sequence, if any) in the target site during gene modification. In some embodiments, the CRISPR spacer is selected by ranking sequences by the proximity of their corresponding genomic site to tire desired edit location. In some embodiments, the gRNA comprises a gRNA scaffold. In some embodiments, the gRNA scaffold used may be a standard scaffold (e.g.. for Cas9, 5 -

GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAA AGTGG CACCGAGTCGGTGC-3 ), or may contain one or more nucleotide substitutions. In some embodiments, the heterologous object sequence has at least 90% identify, e.g., at least 90%, 95%, 98%, 99%, or 100% identity, or comprises no more than 1, 2, 3, 4, or 5 positions of non-identity to the target site 3' of the first strand nick (e.g., immediately 3' of the first strand nick or up to 1, 2, 3, 4, or 5 nucleotides 3' of the first strand nick), with tire exception of any insertion, substitution, or deletion that may be written into the target site by tire gene modifying. In some embodiments, the 3' target homology domain contains at least 90% identify, e.g., at least 90%, 95%, 98%, 99%, or 100% identify, or comprises no more than 1, 2, 3, 4, or 5 positions of non-identity to the target site 5' of the first strand nick (e.g., immediately 5' ofthe first strand nick or up to 1, 2, 3, 4, or 5 nucleotides 3' of the first strand nick).

In some embodiments, the template nucleic acid is a template RNA. In some embodiments, the template RNA comprises one or more modified nucleotides. For example, in some embodiments, the template RNA comprises one or more deoxyribonucleotides. In some embodiments, regions of the template RNA are replaced by DNA nucleotides, e.g., to enhance stability of the molecule. For example, the 3 ' end of the template may comprise DNA nucleotides, while the rest of the template comprises RNA nucleotides that can be reverse transcribed. For instance, in some embodiments, the heterologous object sequence is primarily or wholly made up of RNA nucleotides (e.g., at least 90%, 95%, 98%, or 99% RNA nucleotides). In some embodiments, the PBS sequence is primarily or wholly made up of DNA nucleotides (e.g., at least 90%, 95%, 98%, or 99% DNA nucleotides). In other embodiments, the heterologous object sequence for writing into the genome may comprise DNA nucleotides. In some embodiments, the DNA nucleotides in the template are copied into the genome by a domain capable of DNA-dependent DNA polymerase activity. In some embodiments, the DNA-dependent DNA polymerase activity is provided by a DNA polymerase domain in the polypeptide. In some embodiments, the DNA- dependent DNA polymerase activity is provided by a reverse transcriptase domain that is also capable of DNA-dependent DNA polymerization, e.g., second strand synthesis. In some embodiments, the template molecule is composed of only DNA nucleotides.

In some embodiments, a system described herein comprises two nucleic acids which together comprise the sequences of a template RNA described herein. In some embodiments, the two nucleic acids are associated with each other non-covalently, e.g., directly associated with each other (e.g., via base pairing), or indirectly associated as part of a complex comprising one or more additional molecule.

A template RNA described herein may comprise, from 5’ to 3’: (1) a gRNA spacer; (2) a gRNA scaffold; (3) heterologous object sequence (4) a primer binding site (PBS) sequence. Each of these components is now described in more detail. gRNA spacer and gRNA scaffold

A template RNA described herein may comprise a gRNA spacer that directs the gene modifying system to a target nucleic acid, and a gRNA scaffold that promotes association of the template RNA with the Cas domain of tire gene modify ing polypeptide. The systems described herein can also comprise a gRNA that is not part of a template nucleic acid. For example, a gRNA that comprises a gRNA spacer and gRNA scaffold, but not a heterologous object sequence or a PBS sequence, can be used, e.g., to promote unwinding of the target nucleic acid or to reduce MMR reversal of a desired edit by the host cell (e.g., as described in the End Block Sequences and Additional Guide RNA sections herein), or to induce second strand nicking, e.g., as described in the section herein entitled “Second Strand Nicking”.

In some embodiments, the gRNA is a short synthetic RNA composed of a scaffold sequence that participates in CRISPR-associated protein binding and a user-defined ~20 nucleotide targeting sequence for a genomic target. The structure of a complete gRNA was described by Nishimasu et al. Cell 156, P935-949 (2014). The gRNA (also referred to as sgRNA for single-guide RNA) consists of crRNA- and tracrRNA -derived sequences connected by an artificial tetraloop. The crRNA sequence can be divided into guide (20 nt) and repeat (12 nt) regions, whereas the tracrRNA sequence can be divided into antirepeat (14 nt) and three tracrRNA stem loops (Nishimasu et al. Cell 156, P935-949 (2014)). In practice, guide RNA sequences are generally designed to have a length of between 17 - 24 nucleotides (e.g., 19, 20, or 21 nucleotides) and be complementary to a targeted nucleic acid sequence. Custom gRNA generators and algorithms are available commercially for use in the design of effective guide RNAs. In some embodiments, the gRNA comprises two RNA components from the native CRISPR system, e.g. crRNA and tracrRNA. As is well known in the art, the gRNA may also comprise a chimeric, single guide RNA (sgRNA) containing sequence from both a tracrRNA (for binding tire nuclease) and at least one crRNA (to guide the nuclease to the sequence targeted for editing/binding). Chemically modified sgRNAs have also been demonstrated to be effective for use with CRISPR-associated proteins; see. for example, Hendel et al. (2015) Nature Biotechnol., 985 - 991. In some embodiments, a gRNA spacer comprises a nucleic acid sequence that is complementary to a DNA sequence associated with a target gene.

In some embodiments, the region of the template nucleic acid, e.g., template RNA, comprising the gRNA adopts an underwound ribbon-like structure of gRNA bound to target DNA (e.g.. as described in Mulepati et al. Science 19 Sep 2014:Vol. 345, Issue 6203, pp. 1479-1484). Without wishing to be bound by theory, this non-canonical structure is thought to be facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid. Thus, in some embodiments, the region of the template nucleic acid, e.g., template RNA, comprising the gRNA may tolerate increased mismatching with the target site at some interval, e.g., every sixth base. In some embodiments, the region of the template nucleic acid, e.g.. template RNA, comprising the gRNA comprising homology to the target site may possess wobble positions at a regular interval, e.g., every sixth base, that do not need to base pair with the target site.

In some embodiments, the template nucleic acid (e.g., template RNA) has at least 15, 16, 17, 18, 19, 20, 21. 22, 23, or 24 bases of at least 80%, 85%, 90%, 95%, 99%, or 100% homology to the target site, e.g., at the 5’ end, e.g., comprising a gRNA spacer sequence of length appropriate to the Cas9 domain of the gene modifying polypeptide (Table 8).

Table 12 provides parameters to define components for designing gRNA and/or Template RNAs to apply Cas variants listed in Table 8 for gene modifying. The cut site indicates the validated or predicted protospaccr adjacent motif (PAM) requirements, validated or predicted location of cut site (relative to the most upstream base of the PAM site). The gRNA for a given enzyme can be assembled by concatenating the crRNA, Tetraloop, and tracrRNA sequences, and further adding a 5' spacer of a length within Spacer (min) and Spacer (max) that matches a protospacer at a target site. Further, the predicted location of the ssDNA nick at the target is important for designing a PBS sequence of a Template RNA that can anneal to the sequence immediately 5' of the nick in order to initiate target primed reverse transcription. In some embodiments, a gRNA scaffold described herein comprises a nucleic acid sequence comprising, in the 5 ’ to 3’ direction, a crRNA of Table 12, a tetraloop from the same row of Table 12, and a tracrRNA from tire same row of Table 12. or a sequence having at least 70%, 80%, 85%, 90%, 95%, or 99% identity thereto. In some embodiments, tire gRNA or template RNA comprising the scaffold further comprises a gRNA spacer having a length within the Spacer (min) and Spacer (max) indicated in the same row of Table 12. In some embodiments, the gRNA or template RNA having a sequence according to Table 12 is comprised by a system that further comprises a gene modifying polypeptide, wherein the gene modifying polypeptide comprises a Cas domain described in the same row of Table 12.

Table 12. Parameters to define components for designing gRNA and/or Template RNAs to apply

Cas variants listed in Table 8 in gene modifying systems

Herein, when an RNA sequence (e.g., a template RNA sequence) is said to comprise a particular sequence (e.g., a sequence of Table 12 or a portion thereof) that comprises thymine (T), it is of course understood that the RNA sequence may (and frequently does) comprise uracil (U) in place of T. For instance, the RNA sequence may comprise U at every position shown as T in the sequence in Table 12. More specifically, the present disclosure provides an RNA sequence according to every gRNA scaffold sequence of Table 12, wherein the RNA sequence has a U in place of each T in the sequence in Table 12. Additionally, it is understood that terminal Us and Ts may optionally be added or removed from tracrRNA sequences and may be modified or unmodified when provided as RNA. Without wishing to be bound by example, versions of gRNA scaffold sequences alternative to those exemplified in Table 12 may also function with the different Cas9 enzymes or derivatives thereof exemplified in Table 8, e.g., alternate gRNA scaffold sequences with nucleotide additions, substitutions, or deletions, e.g., sequences with stem-loop structures added or removed. It is contemplated herein that the gRNA scaffold sequences represent a component of gene modifying systems that can be similarly optimized for a given system, Cas-RT fusion polypeptide, indication, target mutation, template RNA, or delivery vehicle.

RNA binding domain recruitment sites (RRS)

In some embodiments, a template RNA described herein comprises an RNA binding domain (RBD) recruitment site (RRS), capable of binding to an RBD as described herein. In some embodiments, an RRS binds to the RBD of a gene modifying polypeptide or complex as described herein. In some embodiments, tire RRS is located at the 5’ end of the template RNA. In some embodiments, the RRS is located within 5, 10, 15, 20, 25, or 30 nucleotides of the 5’ end of the template RNA. In some embodiments, the RRS comprises one or more (e.g.. 1 or 2) stem-loop sequences.

In some embodiments, a template nucleic acid comprises a plurality of RRS sequences (e.g., a plurality of the same RRS sequence, or a plurality of different RRS sequences). In some embodiments, the RRS sequence is repeated at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 times. In some embodiments, the plurality of RRS sequences is separated by one or more linker sequences. In some embodiments, the plurality of RRS sequences are positioned adjacent to each other (e.g., without an intervening linker sequence).

In some embodiments, the RRS is not located between a PBS and a heterologous object sequence. In some embodiments, the RRS is located between a PBS and a heterologous object sequence. In some embodiments, an RRS comprises tire nucleic acid sequence of an RRS as listed in Table

40, or a nucleic acid sequence having at least 75%, 80%, 85%, 90%, 95%. 96%. 97%, 98%, or 99% identity thereto. In some embodiments, an RRS comprises the nucleic acid sequence of an RRS as listed in Table 40, or a nucleic acid sequence having no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotide differences therefrom. Herein, when an RNA sequence (e.g., an RRS) is said to comprise a particular sequence (e.g., a sequence of Table 40 or a portion thereof) that comprises thymine (T), it is of course understood that the RNA sequence may (and frequently does) comprise uracil (U) in place of T. For instance, the RNA sequence may comprise U at every position shown as T in the sequence in Table 40. More specifically, the present disclosure provides an RNA sequence according to every RRS sequence of Table 40, wherein the RNA sequence has a U in place of each T in the sequence in Table 40.

Table 40. Exemplary RNA binding domain recruitment sites (RRS)

End block sequences In some embodiments, a template RNA as described herein comprises one or more end block sequences. In some instances, an end block sequence or end protection sequence, as described herein, may protect the template RNA from exonuclease degradation (e.g., reduces exonuclease degradation of the template RNA by at least 25%, 50%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% relative to an otherwise similar template RNA lacking the end block sequence). In some instances, an end block sequence or end protection sequence, as described herein, may act to terminate a reverse transcriptase reaction. In some embodiments, an end block sequence is positioned adjacent to, or within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, or 30 nucleotides of a gRNA spacer sequence (e.g., which pairs with the nicked target nucleic acid strand). In embodiments, the gRNA spacer sequence has 100% complementarity to the nicked target nucleic acid strand and/or directs nicking activity by a Cas domain (e.g., a Cas9 domain, e.g., an nCas9). In embodiments, the gRNA spacer sequence has greater than or equal to 18 nucleotides of complementarity (e.g., about 18, 19, or 20 nucleotides of complementarity) to the target nucleic acid strand, e.g., and promotes unwinding of the target nucleic acid without nicking. In some embodiments, an end block sequence (e.g., a 5’ end blocksequence) comprises a gRNA scaffold as described herein. In some embodiments, a gRNA spacer within or adjacent to a 5' end block as described herein has a length suitable for limited nicking, e.g., the spacer induces less nicking activity than the activity of a Cas domain paired with a spacer having the preferred spacer length for that Cas domain. In some embodiments, a gRNA spacer as described herein has a length suitable for full nicking.

In some embodiments, an end block sequence comprises the nucleic acid sequence of an end block sequence as listed in Table 41, or a nucleic acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto, or the reverse complement thereof. In some embodiments, an end block sequence comprises the nucleic acid sequence of an end block sequence as listed in Table 41, or a nucleic acid sequence having no more than 1, 2. 3, 4, 5, 6. 7, 8, 9, or 10 nucleotide differences therefrom, or the reverse complement thereof. Herein, when an RNA sequence (e.g., a end block sequence) is said to comprise a particular sequence (e.g., a sequence of Table 41 or a portion thereof) that comprises thymine (T), it is of course understood that the RNA sequence may (and frequently does) comprise uracil (U) in place of T. For instance, the RNA sequence may comprise U at every position shown as T in the sequence in Table 41. More specifically, the present disclosure provides an RNA sequence according to every end block sequence of Table 41, wherein the RNA sequence has a U in place of each T in the sequence in Table 41.

Table 41. Exemplary end block sequences

In some embodiments, an end block comprises a gRNA spacer sequence, e.g., as described herein. In certain embodiments, the gRNA spacer sequence has greater than or equal to 18 nucleotides of complementarity (e.g., about 18, 19, 20, 21, 22, or 23 nucleotides of complementarity) to the target nucleic acid strand. In certain embodiments, the gRNA spacer sequence promotes unwinding and nicking of the target nucleic acid.

Heterologous object sequence

A template RNA described herein may comprise a heterologous object sequence that the gene modifying polypeptide can use as a template for reverse transcription, to write a desired sequence into the target nucleic acid. In some embodiments, the heterologous object sequence comprises, from 5’ to 3’, a post-edit homology region, the mutation region, and a pre-edit homology region. Without wishing to be bound by theory, an RT performing reverse transcription on tire template RNA first reverse transcribes the pre-edit homology region, then the mutation region, and then tire post-edit homology region, thereby creating a DNA strand comprising the desired mutation with a homology region on either side.

In some embodiments, the heterologous object sequence is at least 32, 33. 34. 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 120, 140, 160, 180, 200, 500, or 1,000 nucleotides (nts) in length, or at least 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, or 10 kilobases in length. In some embodiments, the heterologous object sequence is no more than 33, 34, 35, 36, 37, 38. 39, 40, 41, 42, 43, 44, 45, 46. 47, 48, 49, 50, 51. 52. 53. 54, 55, 56, 57, 58, 59, 60. 61. 62. 63, 64, 65, 66, 67, 68, 69. 70. 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 120, 140, 160, 180, 200, 500, 1,000, or 2000 nucleotides (nts) in length, or no more than 20, 15, 10, 9, 8, 7, 6, 5, 4, or 3 kilobases in length. In some embodiments, the heterologous object sequence is 30-1000, 40-1000, 50- 1000, 60-1000, 70-1000, 74-1000, 75-1000, 76-1000, 77-1000, 78-1000, 79-1000, 80-1000, 85-1000, 90- 1000, 100-1000. 120-1000, 140-1000. 160-1000, 180-1000, 200-1000, 500-1000, 30-500, 40-500. 50- 500. 60-500, 70-500, 74-500, 75-500, 76-500. 77-500. 78-500, 79-500, 80-500, 85-500. 90-500. 100-500. 120-500, 140-500, 160-500, 180-500, 200-500, 30-200, 40-200, 50-200, 60-200, 70-200, 74-200, 75-200, 76-200, 77-200, 78-200, 79-200, 80-200, 85-200, 90-200, 100-200, 120-200, 140-200, 160-200, 180-200, 30-100, 40-100, 50-100, 60-100, 70-100, 74-100, 75-100, 76-100, 77-100, 78-100, 79-100, 80-100, 85- 100, or 90-100 nucleotides (nts) in length, or 1-20, 1-15, 1-10. 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, 1-2, 2-20, 2-15, 2-10, 2-9, 2-8, 2-7, 2-6, 2-5, 2-4, 2-3, 3-20, 3-15, 3-10, 3-9, 3-8, 3-7, 3-6, 3-5, 3-4. 4-20. 4-15, 4-10, 4-9. 4-8. 4-7, 4-6, 4-5. 5-20. 5-15. 5-10. 5-9. 5-8, 5-7. 5-6. 6-20. 6-15. 6-10. 6-9. 6-8, 6-7. 7-20, 7-15, 7- 10, 7-9, 7-8, 8-20, 8-15, 8-10, 8-9, 9-20, 9-15, 9-10, 10-15, 10-20, or 15-20 kilobases in length. In some embodiments, the heterologous object sequence is 10-100, 10-90, 10-80, 10-70, 10-60, 10-50, 10-40, 10- 30, or 10-20 nt in length, e.g., 10-80, 10-50, or 10-20 nt in length, e.g., aboutl0-20 nt in length. In some embodiments, the heterologous object sequence is 8-30, 9-25, 10-20, 11-16, or 12-15 nucleotides in length, e.g., is 11-16 nt in length. Without wishing to be bound by theory, in some embodiments, a larger insertion size, larger region of editing (e.g., the distance between a first edit/substitution and a second edit/substitution in the target region), and/or greater number of desired edits (e.g., mismatches of the heterologous object sequence to the target genome), may result in a longer optimal heterologous object sequence.

In certain embodiments, the template nucleic acid comprises a customized RNA sequence template which can be identified, designed, engineered and constructed to contain sequences altering or specifying host genome function, for example by introducing a heterologous coding region into a genome; affecting or causing exon structure/altemative splicing, e.g., leading to exon skipping of one or more exons; causing disruption of an endogenous gene, e.g., creating a genetic knockout; causing transcriptional activation of an endogenous gene; causing epigenetic regulation of an endogenous DNA; causing up-regulation of one or more operably linked genes, e.g., leading to gene activation or overexpression; causing down-regulation of one or more operably linked genes, e.g., creating a genetic knock-down; etc. In certain embodiments, a customized RNA sequence template can be engineered to contain sequences coding for exons and/or transgenes, provide binding sites for transcription factor activators, repressors, enhancers, etc., and combinations thereof. In some embodiments, a customized template can be engineered to encode a nucleic acid or peptide tag to be expressed in an endogenous RNA transcript or endogenous protein operably linked to the target site. In other embodiments, the coding sequence can be further customized with splice donor sites, splice acceptor sites, or poly-A tails.

The template nucleic acid (e.g., template RNA) of the system typically comprises an object sequence (e.g., a heterologous object sequence) for writing a desired sequence into a target DNA. The object sequence may be coding or non-coding. The template nucleic acid (e.g., template RNA) can be designed to result in insertions, mutations, or deletions at the target DNA locus. In some embodiments, the template nucleic acid (e.g., template RNA) may be designed to cause an insertion in the target DNA. For example, the template nucleic acid (e.g., template RNA) may contain a heterologous sequence, wherein the reverse transcription will result in insertion of the heterologous sequence into the target DNA. In other embodiments, the RNA template may be designed to introduce a deletion into the target DNA. For example, the template nucleic acid (e.g.. template RNA) may match the target DNA upstream and downstream of the desired deletion, wherein the reverse transcription will result in the copying of the upstream and downstream sequences from the template nucleic acid (e.g., template RNA) without the intervening sequence, e.g., causing deletion of the intervening sequence. In other embodiments, the template nucleic acid (e.g., template RNA) may be designed to introduce an edit into the target DNA. For example, the template RNA may match the target DNA sequence with the exception of one or more nucleotides, wherein the reverse transcription will result in the copying of these edits into the target DNA, e.g., resulting in mutations, e.g., transition or transversion mutations.

In some embodiments, writing of an object sequence into a target site results in the substitution of nucleotides, e.g., where the full length of the object sequence corresponds to a matching length of the target site with one or more mismatched bases. In some embodiments, a heterologous object sequence may be designed such that a combination of sequence alterations may occur, e.g., a simultaneous addition and deletion, addition and substitution, or deletion and substitution.

In some embodiments, the heterologous object sequence may contain an open reading frame or a fragment of an open reading frame. In some embodiments the heterologous object sequence has a Kozak sequence. In some embodiments the heterologous object sequence has an internal ribosome entry site. In some embodiments the heterologous object sequence has a self-cleaving peptide such as a T2A or P2A site. In some embodiments the heterologous object sequence has a start codon. In some embodiments the template RNA has a splice acceptor site. In some embodiments the template RNA has a splice donor site. Exemplary splice acceptor and splice donor sites are described in WO2016044416, incorporated herein by reference in its entirety. Exemplary splice acceptor site sequences are known to those of skill in the art. In some embodiments the template RNA has a microRNA binding site downstream of the stop codon. In some embodiments the template RNA has a polyA tail downstream of the stop codon of an open reading frame. In some embodiments the template RNA comprises one or more exons. In some embodiments the template RNA comprises one or more introns. In some embodiments the template RNA comprises a eukaryotic transcriptional terminator. In some embodiments the template RNA comprises an enhanced translation element or a translation enhancing element. In some embodiments the RNA comprises the human T-cell leukemia vims (HTLV-1) R region. In some embodiments the RNA comprises a posttranscriptional regulatory element that enhances nuclear export, such as that of Hepatitis B Vims (HPRE) or Woodchuck Hepatitis Vims (WPRE).

In some embodiments, the heterologous object sequence may contain a non -coding sequence. For example, the template nucleic acid (e.g., template RNA) may comprise a regulatory element, e.g., a promoter or enhancer sequence or miRNA binding site. In some embodiments, integration of the object sequence at a target site will result in upregulation of an endogenous gene. In some embodiments, integration of the object sequence at a target site will result in downregulation of an endogenous gene. In some embodiments the template nucleic acid (e.g., template RNA) comprises a tissue specific promoter or enhancer, each of which may be unidirectional or bidirectional. In some embodiments the promoter is an RNA polymerase I promoter, RNA polymerase II promoter, or RNA polymerase III promoter. In some embodiments the promoter comprises a TATA element. In some embodiments the promoter comprises a B recognition element. In some embodiments the promoter has one or more binding sites for transcription factors.

In some embodiments, the template nucleic acid (e.g., template RNA) comprises a site that coordinates epigenetic modification. In some embodiments, tire template nucleic acid (e.g., template RNA) comprises a chromatin insulator. For example, the template nucleic acid (e.g., template RNA) comprises a CTCF site or a site targeted for DNA methylation.

In some embodiments, the template nucleic acid (e.g., template RNA) comprises a gene expression unit composed of at least one regulatory region operably linked to an effector sequence. The effector sequence may be a sequence that is transcribed into RNA (e.g., a coding sequence or a noncoding sequence such as a sequence encoding a micro RNA).

In some embodiments, the heterologous object sequence of the template nucleic acid (e.g., template RNA) is inserted into a target genome in an endogenous intron. In some embodiments, the heterologous object sequence of the template nucleic acid (e.g., template RNA) is inserted into a target genome and thereby acts as a new exon. In some embodiments, the insertion of the heterologous object sequence into the target genome results in replacement of a natural exon or the skipping of a natural exon.

In some embodiments, the heterologous object sequence of the template nucleic acid (e.g., template RNA) is inserted into tire target genome in a genomic safe harbor site, such as AAVS1, CCR5. ROSA26, or albumin locus. In some embodiments, a gene modifying is used to integrate a CAR into the T-cell receptor a constant (TRAC) locus (Eyquem et al Nature 543, 113-117 (2017)). In some embodiments, a gene modifying system is used to integrate a CAR into a T-cell receptor fl constant (TRBC) locus. Many other safe harbors have been identified by computational approaches (Pellenz et al Hum Gen Ther 30, 814-828 (2019)) and could be used for gene modifying system-mediated integration. In some embodiments, tire heterologous object sequence of the template nucleic acid (e.g., template RNA) is added to the genome in an intergenic or intragenic region. In some embodiments, the heterologous object sequence of the template nucleic acid (e.g., template RNA) is added to the genome 5' or 3' within 0.1 kb, 0.25 kb, 0.5 kb, 0.75, kb, 1 kb, 2 kb, 3 kb, 4 kb, 5 kb, 7.5 kb, 10 kb, 15 kb, 20 kb, 25 kb, 50, 75 kb, or 100 kb of an endogenous active gene. In some embodiments, the heterologous object sequence of the template nucleic acid (e.g., template RNA) is added to the genome 5' or 3' within 0.1 kb, 0.25 kb, 0.5 kb, 0.75, kb, 1 kb. 2 kb, 3 kb, 4 kb, 5 kb, 7.5 kb. 10 kb, 15 kb. 20 kb, 25 kb, 50, 75 kb, or 100 kb of an endogenous promoter or enhancer. In some embodiments, the heterologous object sequence of the template nucleic acid (e.g., template RNA) can be, e.g., 50-50,000 base pairs (e.g., between 50-40,000 bp, between 500-30,000 bp between 500-20,000 bp, between 100-15,000 bp, between 500-10,000 bp, between 50-10,000 bp, between 50-5,000 bp. The template nucleic acid (e.g., template RNA) can be designed to result in insertions, mutations, or deletions at the target DNA locus. In some embodiments, the template nucleic acid (e.g., template RNA) may be designed to cause an insertion in the target DNA. For example, the template nucleic acid (e.g., template RNA) may contain a heterologous object sequence, wherein the reverse transcription will result in insertion of the heterologous object sequence into the target DNA. In other embodiments, the RNA template may be designed to write a deletion into the target DNA. For example, the template nucleic acid (e.g., template RNA) may match the target DNA upstream and downstream of the desired deletion, wherein the reverse transcription will result in the copying of the upstream and downstream sequences from the template nucleic acid (e.g., template RNA) without the intervening sequence, e.g., causing deletion of the intervening sequence. In other embodiments, the template nucleic acid (e.g., template RNA) may be designed to write an edit into the target DNA. For example, the template RNA may match the target DNA sequence with the exception of one or more nucleotides, wherein the reverse transcription will result in the copying of these edits into the target DNA, e.g., resulting in mutations, e.g., transition or transversion mutations.

In some embodiments, the pre-edit homology domain comprises a nucleic acid sequence having 100% sequence identity with a nucleic acid sequence comprised in a target nucleic acid molecule.

In some embodiments, the post-edit homology domain comprises a nucleic acid sequence having 100% sequence identity with a nucleic acid sequence comprised in a target nucleic acid molecule.

The template RNA (e.g., trans template RNA) sequences may be customized. For example, in some embodiments it is desired to inactivate a PAM sequence upon editing (e.g., using a ‘'PAM-kill” modification) to decrease the potential for further gene editing (e.g., by Cas retargeting) following the initial edit. Consequently, certain template RNAs are designed to install a mutation (e.g., a substitution) into the PAM of the target nucleic acid, such that upon editing, the PAM site will be mutated to a sequence no longer recognized by the gene modifying polypeptide. Tirus, a mutation region within the heterologous object sequence of the template RNA may comprise a PAM-kill sequence. Without wishing to be bound by theory, in some embodiments, a PAM-kill sequence prevents re-engagement of the gene modifying polypeptide upon completion of a genetic modification, or decreases re-engagement relative to a template RNA lacking a PAM-kill sequence. In some embodiments, a PAM-kill sequence does not alter the amino acid sequence encoded by a gene, e.g., the PAM-kill sequence results in a silent mutation. In some embodiments, the PAM edited by the PAM-kill trans template RNA is the PAM used to direct the first strand nick. In other embodiments, it is desired to leave the PAM sequence intact (no PAM-kill).

In some embodiments, a homology domain (e.g., a pre-edit homology domain) comprises the nucleic acid sequence of a homology 1 sequence as listed in Table 38 below, or a nucleic acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a homology domain (e.g., a pre-edit homology domain) comprises the nucleic acid sequence of a homology 1 sequence as listed in Table 38 below, or a nucleic acid sequence having no more than 1, 2, 3, 4, or 5 nucleotide differences relative thereto. In some embodiments, a homology domain has a length of 0-30 nucleotides (e.g., about 0-10, 10-20, or 20-30 nucleotides). Herein, when an RNA sequence (e.g., a homology domain sequence) is said to comprise a particular sequence (e.g., a sequence of Table 38 or a portion thereof) that comprises thymine (T), it is of course understood that the RNA sequence may (and frequently does) comprise uracil (U) in place of T. For instance, the RNA sequence may comprise U at even' position shown as T in the sequence in Table 38. More specifically, the present disclosure provides an RNA sequence according to even’ homology domain sequence of Table 38, wherein the RNA sequence has a U in place of each T in tire sequence in Table 38. In certain embodiments, the homology domain has a length between 0-5, 5-10, 10-15, 15-20, 20-25. 25-30, 30-35. 35-40, 40-45, or 45-50 nucleotides. In certain embodiments, the homology domain has a length between 50-100, 100-150, 150-200, 200-250, 250-300, 300-350, 350-400, 400-450, or 450-550 nucleotides. In certain embodiments, the homology domain has a length of about 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 50, 60. 70, 80, 90, 100, 150, 200, 250, 300. 350, 400. 450, or 500 nucleotides.

Table 38. Exemplary homology 1 sequences

In some embodiments, a homology domain (e.g., a post-edit homology domain) comprises the nucleic acid sequence of a homology 2 sequence as listed in Table 39 below, or a nucleic acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, a homology domain (e.g.. a post-edit homology domain) comprises the nucleic acid sequence of a homology 2 sequence as listed in Table 39 below, or a nucleic acid sequence having no more than 1, 2, 3, 4, or 5 nucleotide differences relative thereto. In some embodiments, a homology domain has a length of 0-1000 nucleotides (e.g., about 0-5, 5-10, 10-50, 50-100, 100-500, or 500-1000 nucleotides). Herein, when an RNA sequence (e.g., a homology domain sequence) is said to comprise a particular sequence (e.g., a sequence of Table 39 or a portion thereof) that comprises thymine (T), it is of course understood that the RNA sequence may (and frequently does) comprise uracil (U) in place of T. For instance, the RNA sequence may comprise U at every position shown as T in the sequence in Table 39. More specifically, the present disclosure provides an RNA sequence according to every homology domain sequence of Table 39, wherein the RNA sequence has a U in place of each T in the sequence in Table 39.

Table 39. Exempla ry homology 2 sequences

PBS sequence

In some embodiments, a template nucleic acid (e.g., template RNA) comprises a PBS sequence. In some embodiments, a PBS sequence is disposed 3 ' of the heterologous object sequence and is complementary to a sequence adjacent to a site to be modified by a system described herein, or comprises no more than 1, 2, 3, 4, or 5 mismatches to a sequence complementary to the sequence adjacent to a site to be modified by the system/gene modifying polypeptide. In some embodiments, the PBS sequence binds within 1, 2, 3, 4. 5, 6, 7, 8. 9, or 10 nucleotides of a nick site in tire target nucleic acid molecule. In some embodiments, binding of the PBS sequence to the target nucleic acid molecule permits initiation of target-primed reverse transcription (TPRT), e.g., with the 3 ' homology domain acting as a primer for TPRT. In some embodiments, the PBS sequence is 3-5, 5-10, 10-30, 10-25, 10-20, 10-19, 10-18, 10-17,

10-16, 10-15, 10-14, 10-13, 10-12, 10-11, 11-30, 11-25, 11-20, 11-19, 11-18, 11-17, 11-16, 11-15, 11-14,

11-13, 11-12, 12-30. 12-25, 12-20, 12-19, 12-18, 12-17, 12-16, 12-15. 12-14, 12-13, 13-30, 13-25, 13-20,

13-19. 13-18, 13-17, 13-16, 13-15, 13-14, 14-30, 14-25. 14-20, 14-19. 14-18, 14-17, 14-16, 14-15, 15-30,

15-25, 15-20, 15-19, 15-18, 15-17, 15-16, 16-30, 16-25, 16-20, 16-19, 16-18, 16-17, 17-30, 17-25, 17-20,

17-19, 17-18, 18-30, 18-25, 18-20, 18-19, 19-30, 19-25, 19-20, 20-30, 20-25, or 25-30 nucleotides in length, e.g., 10-17, 12-16, or 12-14 nucleotides in length. In some embodiments, the PBS sequence is 5- 20, 8-16, 8-14, 8-13, 9-13, 9-12, or 10-12 nucleotides in length, e.g., 9-12 nucleotides in length.

The template nucleic acid (e.g., template RNA) may have some homology to the target DNA. In some embodiments, the template nucleic acid (e.g., template RNA) PBS sequence domain may serve as an annealing region to the target DNA, such that the target DNA is positioned to prime the reverse transcription of the template nucleic acid (e.g., template RNA). In some embodiments the template nucleic acid (e.g., template RNA) has at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 175, 200 or more bases of exact homology to the target DNA at the 3' end of the RNA. In some embodiments the template nucleic acid (e.g., template RNA) has at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15. 20, 25, 30, 35, 40, 45, 50, 60. 70. 80, 90, 100. 110, 120. 130, 140. 150, 175. 200 or more bases of at least 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% homology to the target DNA, e.g., at the 5' end of the template nucleic acid (e.g., template RNA). In some embodiments, a PBS sequence comprises a nucleic acid sequence as listed in Table 37, or a nucleic acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity thereto. In some embodiments, a PBS sequence comprises a nucleic acid sequence as listed in Table 37, or a nucleic acid sequence having no more than 1, 2, 3, 4, or 5 nucleotide differences thereto. Herein, when an RNA sequence (e.g., in a PBS sequence) is said to comprise a particular sequence (e.g., a sequence of Table 37 or a portion thereof) that comprises thymine (T), it is of course understood that the RNA sequence may (and frequently does) comprise uracil (U) in place of T. For instance, tire RNA sequence may comprise U at every position shown as T in the sequence in Table 37. More specifically, the present disclosure provides an RNA sequence according to every PBS sequence of Table 37, wherein the RNA sequence has a U in place of each T in the sequence in Table 37. In certain embodiments, the PBS has a length between 1-3, 3-5, 5-8, 8-10, 10-12, 12-15, 15-17, 17-20, 20-25, 25-30. or 30-40 nucleotides. In certain embodiments, the PBS has a length of about 1. 2, 3, 4. 5. 6, 7, 8. 9, 10. 11. 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides.

Table 37. Exemplary PBS sequences. The below sequences are listed 5' to 3' direction. gRNAs with inducible activity

In some embodiments, a gRNA described herein (e.g., a gRNA that is part of a template RNA or a gRNA used for second strand nicking) has inducible activity. Inducible activity may be achieved by tire template nucleic acid, e.g., template RNA, further comprising (in addition to the gRNA) a blocking domain, wherein the sequence of a portion of or all of the blocking domain is at least partially complementary to a portion or all of the gRNA. The blocking domain is thus capable of hybridizing or substantially hybridizing to a portion of or all of the gRNA. In some embodiments, the blocking domain and inducibly active gRNA are disposed on the template nucleic acid, e.g., template RNA, such that the gRNA can adopt a first confonnation where the blocking domain is hybridized or substantially hybridized to the gRNA, and a second conformation where the blocking domain is not hybridized or not substantially hybridized to the gRNA. In some embodiments, in the first conformation the gRNA is unable to bind to the gene modifying polypeptide (e.g., the template nucleic acid binding domain, DNA binding domain, or endonuclease domain (e.g., a CRISPR/Cas protein)) or binds with substantially decreased affinity compared to an otherwise similar template RNA lacking the blocking domain. In some embodiments, in the second conformation the gRNA is able to bind to tire gene modifying polypeptide (e.g., the template nucleic acid binding domain, DNA binding domain, or endonuclease domain (e.g., a CRISPR/Cas protein)). In some embodiments, whether the gRNA is in the first or second conformation can influence whether the DNA binding or endonuclease activities of the gene modifying polypeptide (e.g., of tire CRISPR/Cas protein the gene modifying polypeptide comprises) are active.

In some embodiments, the gRNA that coordinates the second nick has inducible activity. In some embodiments, the gRNA that coordinates the second nick is induced after the template is reverse transcribed. In some embodiments, hybridization of the gRNA to the blocking domain can be disrupted using an opener molecule. In some embodiments, an opener molecule comprises an agent that binds to a portion or all of the gRNA or blocking domain and inhibits hybridization of the gRNA to the blocking domain. In some embodiments, tire opener molecule comprises a nucleic acid, e.g., comprising a sequence that is partially or wholly complementary to the gRNA, blocking domain, or both. By choosing or designing an appropriate opener molecule, providing the opener molecule can promote a change in the conformation of the gRNA such that it can associate with a CRISPR/Cas protein and provide the associated functions of the CRISPR/Cas protein (e.g., DNA binding and/or endonuclease activity). Without wishing to be bound by theory, providing the opener molecule at a selected time and/or location may allow for spatial and temporal control of the activity of the gRNA, CRISPR/Cas protein, or gene modifying system comprising the same. In some embodiments, the opener molecule is exogenous to the cell comprising the gene modifying polypeptide and or template nucleic acid. In some embodiments, the opener molecule comprises an endogenous agent (e.g., endogenous to the cell comprising the gene modifying polypeptide and or template nucleic acid comprising the gRNA and blocking domain). For example, an inducible gRNA, blocking domain, and opener molecule may be chosen such that the opener molecule is an endogenous agent expressed in a target cell or tissue, e.g., thereby ensuring activity of a gene modifying system in the target cell or tissue. As a further example, an inducible gRNA, blocking domain, and opener molecule may be chosen such that the opener molecule is absent or not substantially expressed in one or more non-target cells or tissues, e.g., thereby ensuring that activity of a gene modifying system does not occur or substantially occur in the one or more non-target cells or tissues, or occurs at a reduced level compared to a target cell or tissue. Exemplary blocking domains, opener molecules, and uses thereof are described in PCT App. Publication W02020044039A1, which is incorporated herein by reference in its entirety. In some embodiments, tire template nucleic acid, e.g., template RNA, may comprise one or more sequences or structures for binding by one or more components of a gene modifying polypeptide, e.g., by a reverse transcriptase or RNA binding domain, and a gRNA. In some embodiments, the gRNA facilitates interaction with the template nucleic acid binding domain (e.g., RNA binding domain) of the gene modifying polypeptide. In some embodiments, the gRNA directs the gene modifying polypeptide to the matching target sequence, e.g., in a target cell genome.

Additional Guide RNAs

In some embodiments, a gene modifying system as described herein comprises an additional guide RNA (gRNA), e.g., for unwinding or nicking of the target nucleic acid (e.g., nicking of the opposite strand of that recognized by a PBS sequence of the template RNA). In embodiments, a gene modifying system as described herein comprises 1, 2. 3, 4, or 5 additional distinct gRNAs. In certain embodiments, the additional guide RNA is a separate molecule from the template RNA. In other embodiments, the additional guide RNA is attached to or incorporated into the template RNA (e.g., at the 3’ end of the template RNA). In embodiments, the additional guide RNA is attached to the remainder of the template RNA by a linker region. In some embodiments, the additional guide RNA comprises a stem-loop sequence, e.g., as noted in Table 44.

In some embodiments, the additional gRNA comprises a gRNA spacer, e.g., attached to an end block sequence of the template RNA (e.g., as described herein). In some embodiments, the gRNA spacer is 18 nucleotides or longer (e.g., at least about 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, or 40 nucleotides). In embodiments, the gRNA spacer directs nicking of the target nucleic acid by a Cas domain (e.g., a Cas9 domain, e.g., an nCas9 domain). In embodiments, the gRNA spacer directs unwinding of the target nucleic acid (e.g., by a Cas domain, e.g., a Cas9 domain, e.g., a dCas9 domain). In some embodiments, the additional gRNA comprises a scaffold sequence as listed in Table 44, or a nucleic acid sequence having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto. In some embodiments, the additional gRNA comprises a scaffold sequence as listed in Table 44, or a nucleic acid sequence having no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, or 50 nucleotide differences therefrom.

Herein, when an RNA sequence (e.g.. a gRNA sequence) is said to comprise a particular sequence (e.g., a sequence of Table 44 or a portion thereof) that comprises thymine (T), it is of course understood that the RNA sequence may (and frequently does) comprise uracil (U) in place of T. For instance, the RNA sequence may comprise U at every position shown as T in the sequence in Table 44. More specifically, the present disclosure provides an RNA sequence according to every gRNA sequence of Table 44, wherein tire RNA sequence has a U in place of each T in the sequence in Table 44.

Table 44. Exemplary additional guide RNA (gRNA) sequences

Circular RNAs and Ribozymes in Gene Modifying Systems

It is contemplated that it may be useful to employ circular and/or linear RNA states during the formulation, delivery, or gene modifying reaction within the target cell. Thus, in some embodiments of any of the aspects described herein, a gene modifying system comprises one or more circular RNAs (circRNAs). In some embodiments of any of the aspects described herein, a gene modifying system comprises one or more linear RNAs. In some embodiments, a nucleic acid as described herein (e.g., a template nucleic acid, a nucleic acid molecule encoding a gene modifying polypeptide, or both) is a circRNA. In some embodiments, a circular RNA molecule encodes the gene modifying polypeptide. In some embodiments, the circRNA molecule encoding the gene modifying polypeptide is delivered to a host cell. In some embodiments, a circular RNA molecule encodes a recombinase, e.g., as described herein. In some embodiments, the circRNA molecule encoding the recombinase is delivered to a host cell. In some embodiments, the circRNA molecule encoding the gene modifying polypeptide is linearized (e.g., in the host cell, e.g., in the nucleus of the host cell) prior to translation.

Circular RNAs (circRNAs) have been found to occur naturally in cells and have been found to have diverse functions, including both non-coding and protein coding roles in human cells. It has been shown that a circRNA can be engineered by incorporating a self-splicing intron into an RNA molecule (or DNA encoding the RNA molecule) that results in circularization of the RNA, and that an engineered circRNA can have enhanced protein production and stability (Wesselhoeft et al. Nature Communications 2018). In some embodiments, the gene modifying polypeptide is encoded as circRNA. In certain embodiments, the template nucleic acid is a DNA, such as a dsDNA or ssDNA. In certain embodiments, the circDNA comprises a template RNA.

In some embodiments, the circRNA comprises one or more ribozyme sequences. In some embodiments, the ribozyme sequence is activated for autocleavage, e.g.. in a host cell, e.g., thereby resulting in linearization of the circRNA. In some embodiments, the ribozyme is activated when the concentration of magnesium reaches a sufficient level for cleavage, e.g.. in a host cell. In some embodiments the circRNA is maintained in a low magnesium environment prior to delivery to the host cell. In some embodiments, the ribozyme is a protein-responsive ribozyme. In some embodiments, the ribozyme is a nucleic acid-responsive ribozyme. In some embodiments, the circRNA comprises a cleavage site. In some embodiments, the circRNA comprises a second cleavage site.

In some embodiments, the circRNA is linearized in the nucleus of a target cell. In some embodiments, linearization of a circRNA in the nucleus of a cell involves components present in the nucleus of the cell, e.g., to activate a cleavage event. In some embodiments, a ribozyme, e.g., a ribozyme from a B2 or ALU element, that is responsive to a nuclear element, e.g., a nuclear protein, e.g., a genomeinteracting protein, e.g., an epigenetic modifier, e.g., EZH2, is incorporated into a circRNA, e.g., of a gene modifying system. In some embodiments, nuclear localization of the circRNA results in an increase in autocatalytic activity of the ribozyme and linearization of the circRNA.

In some embodiments, the ribozyme is heterologous to one or more of the other components of the gene modifying system. In some embodiments, an inducible ribozyme (e.g., in a circRNA as described herein) is created synthetically, for example, by utilizing a protein ligand-responsive aptamer design. A system for utilizing the satellite RNA of tobacco ringspot virus hammerhead ribozyme with an MS2 coat protein aptamer has been described (Kennedy et al. Nucleic Acids Res 42(19): 12306-12321 (2014), incorporated herein by reference in its entirety) that results in activation of the ribozyme activity in the presence of the MS2 coat protein. In embodiments, such a system responds to protein ligand localized to the cytoplasm or the nucleus. In some embodiments the protein ligand is not MS2. Methods for generating RNA aptamers to target ligands have been described, for example, based on the systematic evolution of ligands by exponential enrichment (SELEX) (Tuerk and Gold, Science 249(4968):505-510 (1990); Ellington and Szostak, Nature 346(6287): 818-822 (1990); tire methods of each of which are incorporated herein by reference) and have, in some instances, been aided by in silico design (Bell et al. PNAS 117( 15): 8486-8493, the methods of which are incorporated herein by reference). Thus, in some embodiments, an aptamer for a target ligand is generated and incorporated into a synthetic ribozyme system, e.g., to trigger ribozyme-mediated cleavage and circRNA linearization, e.g., in the presence of the protein ligand. In some embodiments, circRNA linearization is triggered in the cytoplasm, e.g., using an aptamer that associates with a ligand in the cytoplasm. In some embodiments, circRNA linearization is triggered in the nucleus, e.g., using an aptamer that associates with a ligand in tire nucleus. In embodiments, the ligand in the nucleus comprises an epigenetic modifier or a transcription factor. In some embodiments the ligand that triggers linearization is present at higher levels in on-target cells than off-target cells.

It is further contemplated that a nucleic acid-responsive ribozyme system can be employed for circRNA linearization. For example, biosensors that sense defined target nucleic acid molecules to trigger ribozyme activation are described, e.g., in Penchovsky (Biotechnology Advances 32(5): 1015-1027 (2014), incorporated herein by reference). By these methods, a ribozyme naturally folds into an inactive state and is only activated in the presence of a defined target nucleic acid molecule (e.g., an RNA molecule). In some embodiments, a circRNA of a gene modifying system comprises a nucleic acid- responsive ribozyme that is activated in the presence of a defined target nucleic acid, e.g., an RNA, e.g., an mRNA, miRNA, guide RNA, gRNA, sgRNA, ncRNA, IncRNA, tRNA, snRNA, or mtRNA. In some embodiments the nucleic acid that triggers linearization is present at higher levels in on-target cells than off-target cells.

In some embodiments of any of the aspects herein, a gene modifying system incorporates one or more ribozymes with inducible specificity to a target tissue or target cell of interest, e.g., a ribozyme that is activated by a ligand or nucleic acid present at higher levels in a target tissue or target cell of interest. In some embodiments, the gene modifying system incorporates a ribozyme with inducible specificity to a subcellular compartment, e.g., the nucleus, nucleolus, cytoplasm, or mitochondria. In some embodiments, the ribozyme that is activated by a ligand or nucleic acid present at higher levels in the target subcellular compartment. In some embodiments, an RNA component of a gene modifying system is provided as circRNA, e.g., that is activated by linearization. In some embodiments, linearization of a circRNA encoding a gene modifying polypeptide activates the molecule for translation. In some embodiments, a signal that activates a circRNA component of a gene modifying system is present at higher levels in on-target cells or tissues, e.g., such that the system is specifically activated in these cells.

In some embodiments, an RNA component of a gene modifying system is provided as a circRNA that is inactivated by linearization. In some embodiments, a circRNA encoding the gene modifying polypeptide is inactivated by cleavage and degradation. In some embodiments, a circRNA encoding the gene modifying polypeptide is inactivated by cleavage that separates a translation signal from the coding sequence of the polypeptide. In some embodiments, a signal that inactivates a circRNA component of a gene modifying system is present at higher levels in off-target cells or tissues, such that the system is specifically inactivated in these cells.

Target Nucleic Acid Site

In some embodiments, after gene modification, the target site surrounding the edited sequence contains a limited number of insertions or deletions, for example, in less than about 50% or 10% of editing events, e.g., as determined by long-read amplicon sequencing of the target site, e.g., as described in Karst et al. (2020) bioRxiv doi.org/10.1101/645903 (incorporated by reference herein in its entirety). In some embodiments, the target site does not show multiple consecutive editing events, e.g., head-to-tail or head-to-head duplications, e.g., as detennined by long -read amplicon sequencing of the target site, e.g., as described in Karst et al. bioRxiv doi.org/10.1101/645903 (2020) (incorporated herein by reference in its entirety). In some embodiments, the target site contains an integrated sequence corresponding to the template RNA. In some embodiments, the target site does not contain insertions resulting from endogenous RNA in more than about 1% or 10% of events, e.g., as determined by long-read amplicon sequencing of the target site, e.g., as described in Karst et al. bioRxiv doi.org/10.1101/645903 (2020) (incorporated herein by reference in its entirety). In some embodiments, the target site contains the integrated sequence corresponding to the template RNA.

In certain aspects of the present invention, the host DNA-binding site integrated into by the gene modify ing system can be in a gene, in an intron, in an exon, an ORF, outside of a coding region of any gene, in a regulatory region of a gene, or outside of a regulatory region of a gene. In other aspects, the polypeptide may bind to one or more than one host DNA sequence.

In some embodiments, a gene modifying system is used to edit a target locus in multiple alleles. In some embodiments, a gene modifying system is designed to edit a specific allele. For example, a gene modifying polypeptide may be directed to a specific sequence that is only present on one allele, e.g., comprises a template RNA with homology to a target allele, e.g., a gRNA or annealing domain, but not to a second cognate allele. In some embodiments, a gene modifying system can alter a haplotype-specific allele. In some embodiments, a gene modifying system that targets a specific allele preferentially targets that allele, e.g., has at least a 2, 4, 6, 8, or 10-fold preference for a target allele.

Second Strand Nicking

In some embodiments, a gene modifying system described herein comprises a nickase activity (e.g., in the gene modifying polypeptide) that nicks the first strand, and a nickase activity (e.g., in a polypeptide separate from the gene modifying polypeptide) that nicks the second strand of target DNA. As discussed herein, without wishing to be bound by theory, nicking of the first strand of the target site DNA is thought to provide a 3 ' OH that can be used by an RT domain to reverse transcribe a sequence of a template RNA, e.g., a heterologous object sequence. Without wishing to be bound by theory, it is thought that introducing an additional nick to the second strand may bias the cellular DNA repair machinery to adopt the heterologous object sequence -based sequence more frequently than the original genomic sequence. In some embodiments, the additional nick to the second strand is made by the same endonuclease domain (e g., nickase domain) as the nick to the first strand. In some embodiments, the same gene modifying polypeptide performs both the nick to the first strand and the nick to the second strand. In some embodiments, the gene modifying polypeptide comprises a CRISPR/Cas domain and the additional nick to the second strand is directed by an additional nucleic acid, e.g., comprising a second gRNA directing the CRISPR/Cas domain to nick the second strand. In other embodiments, the additional second strand nick is made by a different endonuclease domain (e.g., nickase domain) than the nick to tire first strand. In some embodiments, that different endonuclease domain is situated in an additional polypeptide (e.g., a system of the invention further comprises the additional polypeptide), separate from the gene modifying polypeptide. In some embodiments, the additional polypeptide comprises an endonuclease domain (e.g., nickase domain) described herein. In some embodiments, the additional polypeptide comprises a DNA binding domain, e.g., described herein.

It is contemplated herein that the position at which the second strand nick occurs relative to tire first strand nick may influence the extent to which one or more of: desired gene modifying DNA modifications are obtained, undesired double-strand breaks (DSBs) occur, undesired insertions occur, or undesired deletions occur. Without wishing to be bound by theory, second strand nicking may occur in two general orientations: inward nicks and outward nicks.

In some embodiments, in the inward nick orientation, the RT domain polymerizes (e.g., using the template RNA (e.g., the heterologous object sequence)) away from the second strand nick. In some embodiments, in the inward nick orientation, tire location of the nick to the first strand and the location of the nick to the second strand are positioned between the first PAM site and second PAM site (e.g., in a scenario wherein both nicks are made by a polypeptide (e.g., a gene modifying polypeptide) comprising a CRISPR/Cas domain). When there are two PAMs on the outside and two nicks on the inside, this inward nick orientation can also be referred to as “PAM-out”. In some embodiments, in tire inward nick orientation, the location of the nick to the first strand and the location of the nick to the second strand are between the sites where the polypeptide and the additional polypeptide bind to tire target DNA. In some embodiments, in the inward nick orientation, the location of the nick to the second strand is positioned between the binding sites of the polypeptide and additional polypeptide, and the nick to the first strand is also located between the binding sites of tire polypeptide and additional polypeptide. In some embodiments, in tire inward nick orientation, the location of tire nick to the first strand and the location of the nick to the second strand are positioned between the PAM site and the binding site of the second polypeptide which is at a distance from the target site.

An example of a gene modifying system that provides an inward nick orientation comprises a gene modifying polypeptide comprising a CRISPR/Cas domain, a template RNA comprising a gRNA that directs nicking of the target site DNA on the first strand, and an additional nucleic acid comprising an additional gRNA that directs nicking at a site a distance from the location of the first nick, wherein the location of the first nick and the location of the second nick are between the PAM sites of the sites to which the two gRNAs direct the gene modifying polypeptide. As a further example, another gene modifying system that provides an inward nick orientation comprises a gene modify ing polypeptide comprising a zinc finger molecule and a first nickase domain wherein tire zinc finger molecule binds to the target DNA in a manner that directs the first nickase domain to nick the first strand of the target site; an additional polypeptide comprising a CRISPR/Cas domain, and an additional nucleic acid comprising a gRNA that directs the additional polypeptide to nick a site a distance from the target site DNA on the second strand, wherein the location of the first nick and the location of the second nick are between the PAM site and the site to which the zinc finger molecule binds. As a further example, another gene modifying system that provides an inward nick orientation comprises a gene modifying polypeptide comprising a zinc finger molecule and a first nickase domain wherein the zinc finger molecule binds to the target DNA in a manner that directs the first nickase domain to nick the first strand of the target site; an additional polypeptide comprising a TAL effector molecule and a second nickase domain wherein the TAL effector molecule binds to a site a distance from the target site in a manner that directs the additional polypeptide to nick the second strand, wherein the location of the first nick and the location of tire second nick are between the site to which the TAL effector molecule binds and the site to which the zinc finger molecule binds.

In some embodiments, in the outward nick orientation, the RT domain polymerizes (e.g., using the template RNA (e.g., the heterologous object sequence)) toward the second strand nick. In some embodiments, in the outward nick orientation when both the first and second nicks are made by a polypeptide comprising a CRISPR/Cas domain (e.g., a gene modifying polypeptide), the first PAM site and second PAM site are positioned between the location of the nick to the first strand and the location of the nick to the second strand. When there are two PAMs on the inside and two nicks on the outside, this outward nick orientation also can be referred to as "PAM-in". In some embodiments, in the outward nick orientation, the polypeptide (e.g., the gene modifying polypeptide) and the additional polypeptide bind to sites on the target DNA between the location of the nick to the first strand and the location of the nick to the second. In some embodiments, in the outward nick orientation, the location of the nick to the second strand is positioned on the opposite side of the binding sites of the polypeptide and additional polypeptide relative to the location of the nick to the first strand. In some embodiments, in the outward orientation, the PAM site and the binding site of the second polypeptide which is at a distance from the target site are positioned between the location of the nick to the first strand and the location of tire nick to the second strand.

An example of a gene modifying system that provides an outward nick orientation comprises a gene modifying polypeptide comprising a CRISPR/Cas domain, a template RNA comprising a gRNA that directs nicking of the target site DNA on the first strand, and an additional nucleic acid comprising an additional gRNA that directs nicking at a site a distance from the location of the first nick, wherein the location of the first nick and tire location of the second nick are outside of the PAM sites of the sites to which tire two gRNAs direct the gene modifying polypeptide (i.e., the PAM sites are between the location of the first nick and the location of tire second nick). As a further example, another gene modifying system that provides an outward nick orientation comprises a gene modifying polypeptide comprising a zinc finger molecule and a first nickase domain wherein the zinc finger molecule binds to the target DNA in a manner that directs the first nickase domain to nick the first strand of the target site; an additional polypeptide comprising a CRISPR/Cas domain, and an additional nucleic acid comprising a gRNA that directs tire additional polypeptide to nick a site a distance from the target site DNA on tire second strand, wherein the location of the first nick and the location of the second nick are outside the PAM site and the site to which the zinc finger molecule binds (i.e., the PAM site and the site to which the zinc finger molecule binds are between the location of the first nick and the location of the second nick). As a further example, another gene modifying system that provides an outward nick orientation comprises a gene modifying polypeptide comprising a zinc finger molecule and a first nickase domain wherein the zinc finger molecule binds to the target DNA in a manner that directs the first nickase domain to nick the first strand of the target site; an additional polypeptide comprising a TAL effector molecule and a second nickase domain wherein the TAL effector molecule binds to a site a distance from the target site in a manner that directs the additional polypeptide to nick the second strand, wherein the location of the first nick and the location of the second nick are outside the site to which the TAL effector molecule binds and the site to which the zinc finger molecule binds (i.e., the site to which the TAL effector molecule binds and the site to which the zinc finger molecule binds are between the location of the first nick and the location of the second nick).

Without wishing to be bound by theory, it is thought that, for gene modifying systems where a second strand nick is provided, an outward nick orientation is preferred in some embodiments. As is described herein, an inward nick may produce a higher number of double-strand breaks (DSBs) than an outward nick orientation. DSBs may be recognized by the DSB repair pathways in the nucleus of a cell, which can result in undesired insertions and deletions. An outward nick orientation may provide a decreased risk of DSB formation, and a corresponding lower amount of undesired insertions and deletions. In some embodiments, undesired insertions and deletions are insertions and deletions not encoded by the heterologous object sequence, e.g., an insertion or deletion produced by the double-strand break repair pathway unrelated to the modification encoded by the heterologous object sequence. In some embodiments, a desired gene modification comprises a change to the target DNA (e g., a substitution, insertion, or deletion) encoded by the heterologous object sequence (e.g., and achieved by the gene modifying writing the heterologous object sequence into the target site). In some embodiments, the first strand nick and the second strand nick are in an outward orientation.

In addition, the distance between the first strand nick and second strand nick may influence the extent to which one or more of: desired gene modifying system DNA modifications are obtained, undesired double-strand breaks (DSBs) occur, undesired insertions occur, or undesired deletions occur. Without wishing to be bound by theory, it is thought tire second strand nick benefit, the biasing of DNA repair toward incorporation of the heterologous object sequence into the target DNA, increases as the distance between the first strand nick and second strand nick decreases. However, it is thought that the risk of DSB formation also increases as the distance between the first strand nick and second strand nick decreases. Correspondingly, it is thought that the number of undesired insertions and/or deletions mayincrease as the distance between the first strand nick and second strand nick decreases. In some embodiments, the distance between the first strand nick and second strand nick is chosen to balance the benefit of biasing DNA repair toward incorporation of the heterologous object sequence into the target DNA and the risk of DSB formation and of undesired deletions and/or insertions. In some embodiments, a system where the first strand nick and the second strand nick are at least a threshold distance apart has an increased level of desired gene modifying system modification outcomes, a decreased level of undesired deletions, and/or a decreased level of undesired insertions relative to an otherwise similar inward nick orientation system where the first nick and the second nick are less than the a threshold distance apart. In some embodiments the threshold distance(s) is given below.

In some embodiments, the first nick and the second nick are at least 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 nucleotides apart. In some embodiments, the first nick and the second nick are no more than 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75. 80. 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, or 250 nucleotides apart. In some embodiments, the first nick and the second nick are 20-200, 30-200, 40-200, 50-200, 60-200, 70- 200, 80-200, 90-200, 100-200, 1 10-200, 120-200, 130-200, 140-200, 150-200, 160-200, 170-200, 180- 200, 190-200, 20-190, 30-190, 40-190, 50-190, 60-190, 70-190, 80-190, 90-190, 100-190, 110-190, 120- 190, 130-190, 140-190, 150-190, 160-190, 170-190, 180-190, 20-180, 30-180, 40-180, 50-180, 60-180, 70-180, 80-180, 90-180, 100-180, 110-180, 120-180, 130-180, 140-180, 150-180, 160-180, 170-180, 20- 170, 30-170, 40-170, 50-170, 60-170, 70-170, 80-170, 90-170, 100-170, 110-170, 120-170, 130-170, 140- 170, 150-170, 160-170, 20-160, 30-160, 40-160, 50-160, 60-160, 70-160, 80-160, 90-160, 100-160, 110- 160, 120-160, 130-160, 140-160, 150-160, 20-150, 30-150, 40-150, 50-150, 60-150, 70-150, 80-150, 90- 150, 100-150, 110-150, 120-150, 130-150, 140-150, 20-140, 30-140, 40-140, 50-140, 60-140, 70-140, 80- 140, 90-140, 100-140, 110-140, 120-140, 130-140, 20-130, 30-130, 40-130. 50-130, 60-130, 70-130, 80- 130. 90-130, 100-130. 110-130, 120-130, 20-120, 30-120. 40-120, 50-120, 60-120, 70-120, 80-120. 90- 120, 100-120, 110-120, 20-110, 30-110, 40-110, 50-110, 60-110, 70-110, 80-110, 90-110, 100-110, 20- 100, 30-100, 40-100, 50-100, 60-100, 70-100, 80-100, 90-100, 20-90, 30-90, 40-90, 50-90, 60-90, 70-90, 80-90, 20-80, 30-80, 40-80, 50-80, 60-80, 70-80, 20-70, 30-70, 40-70, 50-70, 60-70, 20-60, 30-60, 40-60, 50-60, 20-50, 30-50, 40-50, 20-40, 30-40, or 20-30 nucleotides apart. In some embodiments, the first nick and the second nick are 40-100 nucleotides apart.

Without wishing to be bound by theory, it is thought that, for gene modify ing systems where a second strand nick is provided and an inward nick orientation is selected, increasing the distance between the first strand nick and second strand nick may be preferred. As is described herein, an inward nick orientation may produce a higher number of DSBs than an outward nick orientation, and may result in a higher amount of undesired insertions and deletions than an outward nick orientation, but increasing the distance between the nicks may mitigate that increase in DSBs, undesired deletions, and/or undesired insertions. In some embodiments, an inward nick orientation wherein the first nick and the second nick are at least a threshold distance apart has an increased level of desired gene modifying system modification outcomes, a decreased level of undesired deletions, and/or a decreased level of undesired insertions relative to an otherwise similar inward nick orientation system where the first nick and the second nick are less than the a threshold distance apart. In some embodiments the threshold distance is given below.

In some embodiments, the first strand nick and the second strand nick are in an inward orientation. In some embodiments, the first strand nick and the second strand nick are in an inward orientation and the first strand nick and second strand nick are at least 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 220, 240, 260, 280, 300, 350, 400, 450, or 500 nucleotides apart, e.g., at least 100 nucleotides apart, (and optionally no more than 500, 400, 300. 200, 190, 180, 170, 160, 150, 140, 130, or 120 nucleotides apart). In some embodiments, the first strand nick and the second strand nick are in an inward orientation and the first strand nick and second strand nick are 100-200, 110-200, 120-200, 130- 200, 140-200, 150-200, 160-200, 170-200, 180-200, 190-200, 100-190, 1 10-190, 120-190, 130- 190, 140-

190, 150-190, 160-190, 170-190, 180-190, 100-180, 110-180, 120-180, 130-180, 140-180, 150-180, 160-

180, 170-180, 100-170, 110-170, 120-170, 130-170, 140-170, 150-170, 160-170, 100-160, 110-160, 120- 160, 130-160, 140-160, 150-160, 100-150, 110-150, 120-150, 130-150, 140-150, 100-140, 110-140, 120- 140, 130-140, 100-130, 110-130, 120-130, 100-120, 110-120, or 100-110 nucleotides apart.

Chemically modified nucleic acids and nucleic acid end features

A nucleic acid described herein (e.g., a template nucleic acid, e.g., a template RNA; or a nucleic acid (e.g., mRNA) encoding a gene modifying polypeptide; or a gRNA) can comprise unmodified or modified nucleobases. Naturally occurring RNAs are synthesized from four basic ribonucleotides: ATP, CTP, UTP and GTP, but may contain post-transcriptionally modified nucleotides. Further, approximately one hundred different nucleoside modifications have been identified in RNA (Rozenski, J, Crain, P, and McCloskey, J. (1999). The RNA Modification Database: 1999 update. Nucl Acids Res 27: 196-197). An RNA can also comprise wholly synthetic nucleotides that do not occur in nature.

In some embodiments, the chemical modification is one provided in WO/2016/183482, US Pat. Pub. No. 20090286852, of International Application No. WO/2012/019168, WO/2012/045075, WO/2012/135805, WO/2012/158736, WO/2013/039857, WO/2013/039861, WO/2013/052523. WO/2013/090648, WO/2013/096709, WO/2013/101690, WO/2013/106496, WO/2013/130161, WO/2013/151669, WO/2013/151736, WO/2013/151672, WO/2013/151664, WO/2013/151665, WO/2013/151668, WO/2013/151671, WO/2013/151667, WO/2013/151670, WO/2013/151666, WO/2013/151663, WO/2014/028429, WO/2014/081507, WO/2014/093924, WO/2014/093574, WO/2014/113089, WO/2014/144711, WO/2014/ 144767, WO/2014/144039, WO/2014/152540, WO/2014/152030, WO/2014/ 152031, WO/2014/152027, WO/2014/152211, WO/2014/158795. WO/2014/159813, WO/2014/ 164253, WO/2015/006747, WO/2015/034928, WO/2015/034925, WO/2015/038892, WO/2015/048744, WO/2015/051214, WO/2015/051173, WO/2015/051169, WO/2015/058069, WO/2015/085318, WO/2015/089511, WO/2015/105926, WO/2015/164674, WO/2015/ 196130, WO/2015/196128, WO/2015/196118, WO/2016/011226, WO/2016/011222, WO/2016/011306, WO/2016/014846, WO/2016/022914, WO/2016/036902, WO/2016/077125, or WO/2016/077123, each of which is herein incorporated by reference in its entirety. It is understood that incorporation of a chemically modified nucleotide into a polynucleotide can result in the modification being incorporated into a nucleobase, the backbone, or both, depending on the location of the modification in the nucleotide. In some embodiments, the backbone modification is one provided in EP 2813570, which is herein incorporated by reference in its entirety. In some embodiments, the modified cap is one provided in US Pat. Pub. No. 20050287539, which is herein incorporated by reference in its entirety.

In some embodiments, the chemically modified nucleic acid (e.g., RNA, e.g., mRNA) comprises one or more of ARCA: anti-reverse cap analog (m27.3'-OGP3G), GP3G (Unmethylated Cap Analog), m7GP3G (Monomethylated Cap Analog), m32.2.7GP3G (Trimethylated Cap Analog), m5CTP (5 - methyl-cytidine triphosphate), m6ATP (N6-methyl-adenosine-5 '-triphosphate), s2UTP (2-thio-uridine triphosphate), and Ψ (pseudouridine triphosphate).

In some embodiments, the chemically modified nucleic acid comprises a 5' cap, e.g.: a 7- methylguanosine cap (e.g., a 0-Me-m7G cap); a hypermethylated cap analog; an NAD+-derived cap analog (e.g., as described in Kiledjian. Trends in Cell Biology 28, 454-464 (2018)); or a modified, e.g., biotinylated, cap analog (e.g., as described in Bednarek et al., Phil Trans R Soc B 373, 20180167 (2018)).

In some embodiments, the chemically modified nucleic acid comprises a 3 ' feature selected from one or more of: a polyA tail; a 16-nucleotide long stem-loop structure flanked by unpaired 5 nucleotides (e.g., as described by Mannironi et al., Nucleic Acid Research 17, 9113-9126 (1989)); a triple-helical structure (e.g., as described by Brown et al., PNAS 109, 19202-19207 (2012)); a tRNA, Y RNA, or vault RNA structure (e.g.. as described by Labno et al., Biochemica et Biophysica Acta 1863. 3125-3147 (2016)); incorporation of one or more deoxyribonucleotide triphosphates (dNTPs), 2’O-Methylated NTPs, or phosphorothioate-NTPs; a single nucleotide chemical modification (e.g., oxidation of the 3' terminal ribose to a reactive aldehyde followed by conjugation of the aldehyde-reactive modified nucleotide); or chemical ligation to another nucleic acid molecule.

In some embodiments, the nucleic acid (e.g., template nucleic acid) comprises one or more modified nucleotides, e.g.. selected from dihydrouridine, inosine, 7-methylguanosine, 5 -methylcytidine (5mC), 5' Phosphate ribothymidine, 2'-O-methyl ribothymidine, 2'-O-ethyl ribothymidine, 2'-fluoro ribothymidine, C-5 propynyl-deoxycytidine (pdC), C-5 propynyl-deoxyuridine (pdU), C-5 propynyl- cytidine (pC), C-5 propynyl -uridine (pU), 5-methyl cytidine, 5-methyl uridine, 5-methyl deoxycytidine, 5-methyl deoxyuridine methoxy, 2,6-diaminopurine, 5 '-Dimethoxytrityl -N4-ethyl -2 '-deoxy cytidine, C-5 propynyl-f-cytidine (pfC), C-5 propynyl-f-uridine (pfU), 5-methyl f-cytidinc. 5-methyl f-uridine, C-5 propynyl-m-cytidinc (pmC). C-5 propynyl-f-uridine (pmU), 5-methyl m-cytidine, 5-methyl m-uridine, LNA (locked nucleic acid), MGB (minor groove binder) pseudouridine (Ψ). 1-N-methylpseudouridine (1- Me- Ψ), or 5 -methoxyuridine (5-MO-U).

In some embodiments, the nucleic acid comprises a backbone modification, e.g., a modification to a sugar or phosphate group in the backbone. In some embodiments, the nucleic acid comprises a nucleobase modification.

In some embodiments, the nucleic acid comprises one or more chemically modified nucleotides of Table 13, one or more chemical backbone modifications of Table 14, one or more chemically modified caps of Table 15. For instance, in some embodiments, the nucleic acid comprises two or more (e.g., 3, 4, 5, 6, 7, 8, 9, or 10 or more) different types of chemical modifications. As an example, the nucleic acid may comprise two or more (e.g., 3, 4, 5, 6, 7, 8, 9, or 10 or more) different types of modified nucleobases, e.g., as described herein, e.g., in Table 13. Alternatively or in combination, the nucleic acid may comprise two or more (e.g., 3, 4, 5, 6, 7, 8, 9, or 10 or more) different types of backbone modifications, e.g., as described herein, e.g., in Table 14. Alternatively or in combination, the nucleic acid may comprise one or more modified cap, e.g., as described herein, e.g., in Table 15. For instance, in some embodiments, the nucleic acid comprises one or more type of modified nucleobase and one or more type of backbone modification: one or more type of modified nucleobase and one or more modified cap; one or more type of modified cap and one or more type of backbone modification: or one or more type of modified nucleobase, one or more type of backbone modification, and one or more type of modified cap.

In some embodiments, the nucleic acid comprises one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, or more) modified nucleobases. In some embodiments, all nucleobases of the nucleic acid are modified. In some embodiments, the nucleic acid is modified at one or more (e.g., 2, 3. 4, 5, 6, 7. 8, 9, 10, 20, 30, 40, 50. 60, 70, 80, 90. 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000. or more) positions in the backbone. In some embodiments, all backbone positions of the nucleic acid are modified. Table 13. Modified nucleotides

Table 14. Backbone modifications

Table 15. Modified caps

The nucleotides comprising the template of the gene modifying system can be natural or modified bases, or a combination thereof. For example, the template may contain pseudouridine, dihydrouridine, inosine, 7-methylguanosine, or other modified bases. In some embodiments, the template may contain locked nucleic acid nucleotides. In some embodiments, the modified bases used in the template do not inhibit the reverse transcription of the template. In some embodiments, the modified bases used in tire template may improve reverse transcription, e.g., specificity or fidelity.

In some embodiments, an RNA component of the system (e.g., a template RNA or a gRNA) comprises one or more nucleotide modifications. In some embodiments, the modification pattern of a gRNA can significantly affect in vivo activity compared to unmodified or cnd-modificd guides (e.g., as shown in Figure ID from Finn et al. Cell Rep 22(9):2227 -2235 (2018); incorporated herein by reference in its entirety). Without wishing to be bound by theory, this process may be due, at least in part, to a stabilization of the RNA conferred by the modifications. Non-limiting examples of such modifications may include 2'-O-methyl (2'-O-Me), 2'-0-(2-methoxyethyl) (2’-0-MOE), 2'- fluoro (2’-F), phosphorothioate (PS) bond between nucleotides, G-C substitutions, and inverted abasic linkages between nucleotides and equivalents thereof.

In some embodiments, the template RNA (e.g., at the portion thereof that binds a target site) or the guide RNA comprises a 5' terminus region. In some embodiments, the template RNA or the guide RNA does not comprise a 5' terminus region. In some embodiments, the 5' terminus region comprises a gRNA spacer region, e g., as described with respect to sgRNA in Briner AE et al, Molecular Cell 56: 333- 339 (2014) (incorporated herein by reference in its entirety; applicable herein, e.g., to all guide RNAs). In some embodiments, the 5' terminus region comprises a 5' end modification. In some embodiments, a 5' terminus region with or without a spacer region may be associated with a crRNA, trRNA, sgRNA and/or dgRNA. The gRNA spacer region can, in some instances, comprise a guide region, guide domain, or targeting domain. In some embodiments, the template RNAs (e.g., at the portion thereof that binds a target site) or guide RNAs described herein comprises any of the sequences shown in Table 4 of W02018107028A1, incorporated herein by reference in its entirety. In some embodiments, where a sequence shows a guide and/or spacer region, the composition may comprise this region or not. In some embodiments, a guide RNA comprises one or more of the modifications of any of the sequences shown in Table 4 of W02018107028A1. e.g., as identified therein by a SEQ ID NO. In embodiments, the nucleotides may be the same or different, and/or the modification pattern shown may be the same or similar to a modification pattern of a guide sequence as shown in Table 4 of W02018107028A1. In some embodiments, a modification pattern includes the relative position and identity of modifications of the gRNA or a region of tire gRNA (e.g. 5' terminus region, lower stem region, bulge region, upper stem region, nexus region, hairpin 1 region, hairpin 2 region, 3' terminus region). In some embodiments, the modification pattern contains at least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%. 97%. 98%. 99%. or 100% of the modifications of any one of the sequences shown in the sequence column of Table 4 of W02018107028A1, and/or over one or more regions of the sequence. In some embodiments, the modification pattern is at least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to tire modification pattern of any one of the sequences shown in the sequence column of Table 4 ofW02018107028Al. In some embodiments, the modification pattern is at least 50%, 55%, 60%, 70%, 75%, 80%, 85%. 90%. 95%. 96%. 97%. 98%, 99%, or 100% identical over one or more regions of the sequence shown in Table 4 of W020I8107028AI, e g., in a 5 ¹ terminus region, lower stem region, bulge region, upper stem region, nexus region, hairpin 1 region, hairpin 2 region, and/or 3' terminus region. In some embodiments, the modification pattern is least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%. 97%, 98%, 99%, or 100% identical to the modification pattern of a sequence over the 5 ^' terminus region. In some embodiments, the modification pattern is least 50%. 55%. 60%, 70%, 75%, 80%, 85%, 90%. 95%, 96%, 97%, 98%, 99%, or 100% identical over the lower stem. In some embodiments, the modification pattern is least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical over the bulge. In some embodiments, the modification pattern is least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical over the upper stem. In some embodiments, the modification pattern is least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%. 97%. 98%. 99%, or 100% identical over the nexus. In some embodiments, the modification pattern is least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical over the hairpin 1 . In some embodiments, the modification pattern is least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical over the hairpin 2. In some embodiments, the modification pattern is least 50%, 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical over the 3 ^' terminus. In some embodiments, tire modification pattern differs from the modification pattern of a sequence of Table 4 of W02018107028A1, or a region (e.g. 5' terminus, lower stem, bulge, upper stem, nexus, hairpin 1, hairpin 2, 3' terminus) of such a sequence, e.g., at 0, 1, 2, 3, 4, 5, 6, or more nucleotides. In some embodiments, the gRNA comprises modifications that differ from the modifications of a sequence of Table 4 of W02018107028A1, e.g., at 0, 1, 2, 3, 4, 5, 6, or more nucleotides. In some embodiments, the gRNA comprises modifications that differ from modifications of a region (e.g. 5 ^' terminus, lower stem, bulge, upper stem, nexus, hairpin 1, hairpin 2, 3' terminus) of a sequence of Table 4 of W020I8107028AI, e.g., at 0, 1, 2, 3, 4, 5, 6, or more nucleotides.

In some embodiments, the template RNAs (e.g., at the portion thereof that binds a target site) or the gRNA comprises a 2'-O-methyl (2'-O-Me) modified nucleotide. In some embodiments, the gRNA comprises a 2'-O-(2 -methoxy ethyl) (2'-O-moe) modified nucleotide. In some embodiments, the gRNA comprises a 2'-fluoro (2'- F) modified nucleotide. In some embodiments, the gRNA comprises a phosphorothioate (PS) bond between nucleotides. In some embodiments, the gRNA comprises a 5' end modification, a 3' end modification, or 5' and 3' end modifications. In some embodiments, the 5' end modification comprises a phosphorothioate (PS) bond between nucleotides. In some embodiments, the 5' end modification comprises a 2'-O-mcthyl (2'-O-Mc), 2'-O-(2-mcthoxy ethyl) (2'-0-M0E), and/or 2'- fluoro (2'-F) modified nucleotide. In some embodiments, the 5' end modification comprises at least one phosphorothioate (PS) bond and one or more of a 2'-O-methyl (2'-O- Me). 2'-O-(2-methoxyethyl) (2'-O- MOE), and/or 2'-fluoro (2'-F) modified nucleotide. The end modification may comprise a phosphorothioate (PS), 2'-O-methyl (2'-O-Me), 2'-O-(2- methoxyethyl) (2 -O-MOE), and/or 2'-fluoro (2 - F) modification. Equivalent end modifications are also encompassed by embodiments described herein. In some embodiments, the template RNA or gRNA comprises an end modification in combination with a modification of one or more regions of the template RNA or gRNA. Additional exemplary modifications and methods for protecting RNA, e.g.. gRNA. and fonnulae thereof, are described in WO2018126176A1. which is incorporated herein by reference in its entirety.

In some embodiments, structure-guided and systematic approaches are used to introduce modifications (e.g., 2'-OMe-RNA, 2'-F-RNA, and PS modifications) to a template RNA or guide RNA, for example, as described in Mir et al. Nat Commun 9:2641 (2018) (incorporated by reference herein in its entirety). In some embodiments, tire incorporation of 2'-F-RNAs increases thermal and nuclease stability of RNA:RNA or RNA:DNA duplexes, e.g., while minimally interfering with C3'-endo sugar puckering. In some embodiments, 2'-F may be better tolerated than 2'-OMe at positions where the 2'-OH is important for RNA:DNA duplex stability. In some embodiments, a crRNA comprises one or more modifications that do not reduce Cas9 activity, e.g., C10, C20, or C21 (fully modified), e.g., as described in Supplementary Table 1 of Mir et al. Nat Commun 9:2641 (2018), incorporated herein by reference in its entirety. In some embodiments, a tracrRNA comprises one or more modifications that do not reduce Cas9 activity, e.g., T2, T6, T7, or T8 (fully modified) of Supplementary Table 1 of Mir et al. Nat Commun 9:2641 (2018). In some embodiments, a crRNA comprises one or more modifications (e.g., as described herein) may be paired with a tracrRNA comprising one or more modifications, e.g., C20 and T2. In some embodiments, a gRNA comprises a chimera, e.g.. of a crRNA and a tracrRNA (e.g., Jinek et al. Science 337(6096): 816-821 (2012)). In embodiments, modifications from the crRNA and tracrRNA are mapped onto the single-guide chimera, e.g., to produce a modified gRNA with enhanced stability.

In some embodiments, gRNA molecules may be modified by the addition or subtraction of the naturally occurring structural components, e.g., hairpins. In some embodiments, a gRNA may comprise a gRNA with one or more 3' hairpin elements deleted, e.g., as described in WO2018106727, incorporated herein by reference in its entirety. In some embodiments, a gRNA may contain an added hairpin structure, e.g., an added hairpin structure in the spacer region, which was shown to increase specificity of a CRISPR-Cas system in the teachings of Kocak et al. Nat Biotechno] 37(6):657-666 (2019). Additional modifications, including examples of shortened gRNA and specific modifications improving in vivo activity, can be found in US20190316121, incorporated herein by reference in its entirety.

In some embodiments, structure-guided and systematic approaches (e g., as described in Mir et al. Nat Commun 9:2641 (2018); incorporated herein by reference in its entirety) are employed to find modifications for the template RNA. In embodiments, the modifications are identified with the inclusion or exclusion of a guide region of the template RNA. In some embodiments, a structure of polypeptide bound to template RNA is used to determine non-protein-contacted nucleotides of the RNA that may then be selected for modifications, e.g., with lower risk of disrupting the association of tire RNA with the polypeptide. Secondary structures in a template RNA can also be predicted in silico by software tools, e.g., the RNAstructure tool available at ma.urmc.rochester.edu/RNAstructureWeb (Bellaousov et al. Nucleic Acids Res 41:W471-W474 (2013); incorporated by reference herein in its entirety), e.g., to determine secondary structures for selecting modifications, e g., hairpins, stems, and/or bulges.

Production of Compositions and Systems

As will be appreciated by one of skill, methods of designing and constructing nucleic acid constructs and proteins or polypeptides (such as the systems, constructs and polypeptides described herein) are routine in the art. Generally, recombinant methods may be used. See, in general, Smales & James (Eds.), Therapeutic Proteins: Methods and Protocols (Methods in Molecular Biology), Humana Press (2005); and Crommelin, Sindelar & Meibohm (Eds.), Pharmaceutical Biotechnology: Fundamentals and Applications , Springer (2013). Methods of designing, preparing, evaluating, purifying and manipulating nucleic acid compositions are described in Green and Sambrook (Eds.), Molecular Cloning: A Laboratory Manual (Fourth Edition), Cold Spring Harbor Laboratory Press (2012).

The disclosure provides, in part, a nucleic acid, e.g., vector, encoding a gene modifying polypeptide described herein, a template nucleic acid described herein, or both. In some embodiments, a vector comprises a selective marker, e.g., an antibiotic resistance marker. In some embodiments, tire antibiotic resistance marker is a kanamycin resistance marker. In some embodiments, the antibiotic resistance marker does not confer resistance to beta-lactam antibiotics. In some embodiments, the vector does not comprise an ampicillin resistance marker. In some embodiments, the vector comprises a kanamycin resistance marker and does not comprise an ampicillin resistance marker. In some embodiments, a vector encoding a gene modifying polypeptide is integrated into a target cell genome (e.g., upon administration to a target cell, tissue, organ, or subject). In some embodiments, a vector encoding a gene modifying polypeptide is not integrated into a target cell genome (e.g., upon administration to a target cell, tissue, organ, or subject). In some embodiments, a vector encoding a template nucleic acid (e.g., template RNA) is not integrated into atarget cell genome (e.g., upon administration to a target cell, tissue, organ, or subject). In some embodiments, if a vector is integrated into a target site in a target cell genome, tire selective marker is not integrated into the genome. In some embodiments, if a vector is integrated into a target site in a target cell genome, genes or sequences involved in vector maintenance (e.g., plasmid maintenance genes) are not integrated into the genome. In some embodiments, if a vector is integrated into a target site in a target cell genome, transfer regulating sequences (e.g., inverted terminal repeats, e.g., from an AAV) are not integrated into the genome. In some embodiments, administration of a vector (e.g., encoding a gene modifying polypeptide described herein, a template nucleic acid described herein, or both) to atarget cell, tissue, organ, or subject results in integration of a portion of the vector into one or more target sites in the genome(s) of said target cell, tissue, organ, or subject. In some embodiments, less than 99, 95, 90, 80, 70, 60, 50, 40, 30, 20, 10, 5, 4, 3, 2, or 1% of target sites (e g ., no target sites) comprising integrated material comprise a selective marker (e.g., an antibiotic resistance gene), a transfer regulating sequence (e.g., an inverted terminal repeat, e.g., from an AAV), or both from tire vector.

Exemplary methods for producing a therapeutic pharmaceutical protein or polypeptide described herein involve expression in mammalian cells, although recombinant proteins can also be produced using insect cells, yeast, bacteria, or other cells under control of appropriate promoters. Mammalian expression vectors may comprise non-transcribed elements such as an origin of replication, a suitable promoter, and other 5' or 3' flanking non-transcribed sequences, and 5' or 3' non-translated sequences such as necessary ribosome binding sites, a polyadenylation site, splice donor and acceptor sites, and termination sequences. DNA sequences derived from the SV40 viral genome, for example, SV40 origin, early promoter, splice. and polyadenylation sites may be used to provide other genetic elements required for expression of a heterologous DNA sequence. Appropriate cloning and expression vectors for use with bacterial, fungal, yeast, and mammalian cellular hosts are described in Green & Sambrook, Molecular Cloning: A Laboratory Manual (Fourth Edition), Cold Spring Harbor Laboratory Press (2012).

Various mammalian cell culture systems can be employed to express and manufacture recombinant protein. Examples of mammalian expression systems include CHO, COS, HEK293. HeLA, and BHK cell lines. Processes of host cell culture for production of protein therapeutics are described in Zhou and Kantardjieff (Eds.), Mammalian Cell Cultures for Biologies Manufacturing (Advances in Biochemical Engineering/Biotechnology) , Springer (2014). Compositions described herein may include a vector, such as a viral vector, e.g., a lentiviral vector, encoding a recombinant protein. In some embodiments, a vector, e.g., a viral vector, may comprise a nucleic acid encoding a recombinant protein.

Purification of protein therapeutics is described in Franks. Protein Biotechnology: Isolation. Characterization, and Stabilization, Humana Press (2013); and in Cutler, Protein Purification Protocols (Methods in Molecular Biology), Humana Press (2010).

The disclosure also provides compositions and methods for the production of template nucleic acid molecules (e.g., template RNAs) with specificity for a gene modifying polypeptide and/or a genomic target site. In an aspect, the method comprises production of RNA segments including an upstream homology segment, a heterologous object sequence segment, a gene modifying polypeptide binding motif, and a gRNA segment.

Therapeutic Applications

In some embodiments, a gene modifying system as described herein can be used to modify a cell (e.g., an animal cell, plant cell, or fungal cell). In some embodiments, a gene modifying system as described herein can be used to modify a mammalian cell (e.g., a human cell). In some embodiments, a gene modifying system as described herein can be used to modify a cell from a livestock animal (e.g.. a cow, horse, sheep, goat, pig, llama, alpaca, camel, yak, chicken, duck, goose, or ostrich). In some embodiments, a gene modifying system as described herein can be used as a laboratory tool or a research tool, or used in a laboratory method or research method, e.g., to modify an animal cell, e.g., a mammalian cell (e g., a human cell), a plant cell, or a fungal cell.

By integrating coding genes into a RNA sequence template, the gene modifying system can address therapeutic needs, for example, by providing expression of a therapeutic transgene in individuals with loss-of-fiinction mutations, by replacing gain-of-function mutations with normal transgenes, by providing regulatory sequences to eliminate gain-of-function mutation expression, and/or by controlling the expression of operably linked genes, transgenes and systems thereof. In certain embodiments, the RNA sequence template encodes a promotor region specific to the therapeutic needs of the host cell, for example a tissue specific promotor or enhancer. In still other embodiments, a promotor can be operably linked to a coding sequence.

In some embodiments, an insertion, deletion, substitution, or combination thereof, increases or decreases expression (e.g. transcription or translation) of a target gene. In some embodiments, an insertion, deletion, substitution, or combination thereof, increases or decreases expression (e.g. transcription or translation) of a target gene by altering, adding, or deleting sequences in a promoter or enhancer, e.g. sequences that bind transcription factors. In some embodiments, an insertion, deletion, substitution, or combination thereof alters translation of a target gene (e.g. alters an amino acid sequence), inserts or deletes a start or stop codon, alters or fixes the translation frame of a gene. In some embodiments, an insertion, deletion, substitution, or combination thereof alters splicing of a target gene, e.g. by inserting, deleting, or altering a splice acceptor or donor site. In some embodiments, an insertion, deletion, substitution, or combination thereof alters transcript or protein half-life. In some embodiments, an insertion, deletion, substitution, or combination thereof, alters, increases, decreases the activity of a target gene, e.g. a protein encoded by tire target gene.

Compensatory edits

In some embodiments, the systems or methods provided herein can be used to introduce a compensatory edit. In some embodiments, the compensatory edit is at a position of a gene associated with a disease or disorder, which is different from the position of a disease-causing mutation. In some embodiments, the compensatory mutation is not in the gene containing the causative mutation. In some embodiments, the compensatory edit can negate or compensate for a disease-causing mutation. In some embodiments, tire compensatory edit can be introduced by tire systems or methods provided herein to suppress or reverse the mutant effect of a disease-causing mutation.

Regulatory edits

In some embodiments, the systems or methods provided herein can be used to introduce a regulatory edit. In some embodiments, the regulatory' edit is introduced to a regulatory sequence of a gene, for example, a gene promoter, gene enhancer, gene repressor, or a sequence that regulates gene splicing. In some embodiments, the regulatory edit increases or decreases the expression level of a target gene. In some embodiments, the target gene is the same as the gene containing a disease-causing mutation. In some embodiments, the target gene is different from the gene containing a disease-causing mutation.

Repeat expansion diseases

In some embodiments, the systems or methods provided herein can be used to treat a repeat expansion disease. In some embodiments, the systems or methods provided herein, for example, those comprising gene modifying polypeptides, can be used to treat repeat expansion diseases by resetting tire number of repeats at the locus according to a customized RNA template.

Administration and Delivery

The compositions and systems described herein may be used in vitro or in vivo. In some embodiments the system or components of the system are delivered to cells (e.g., mammalian cells, e.g., human cells), e.g., in vitro or in vivo. In some embodiments, the cells are eukaryotic cells, e.g., cells of a multicellular organism, e.g., an animal, e.g., a mammal (e g., human, swine, bovine), a bird (e.g., poultry, such as chicken, turkey, or duck), or a fish. In some embodiments, the cells are non-human animal cells (e.g., a laboratory animal, a livestock animal, or a companion animal). In some embodiments, the cell is a stem cell (e.g., a hematopoietic stem cell), a fibroblast, or a T cell. In some embodiments, the cell is an immune cell, e.g., a T cell (e.g., a Treg, CD4, CD8, y8, or memory T cell), B cell (e.g., memory B cell or plasma cell), or NK cell. In some embodiments, the cell is a non-dividing cell, e.g., a non-dividing fibroblast or non-dividing T cell. In some embodiments, the cell is an HSC and p53 is not upregulated or is upregulated by less than 10%. 5%, 2%, or 1%, e.g., as detennined according to the method described in Example 30 of PCT/US2019/048607. The skilled artisan will understand that the components of the gene modifying system may be delivered in the form of polypeptide, nucleic acid (e.g., DNA, RNA), and combinations thereof.

In one embodiment the system and/or components of the system are delivered as nucleic acid. For example, the gene modifying polypeptide may be delivered in tire form of a DNA or RNA encoding the polypeptide, and the template RNA may be delivered in the form of RNA or its complementary DNA to be transcribed into RNA. In some embodiments the system or components of the system are delivered on 1, 2, 3, 4, or more distinct nucleic acid molecules. In some embodiments the system or components of the system are delivered as a combination of DNA and RNA. In some embodiments the system or components of the system are delivered as a combination of DNA and protein. In some embodiments the system or components of the system are delivered as a combination of RNA and protein. In some embodiments the gene modifying polypeptide is delivered as a protein. In some embodiments the system or components of the system are delivered to cells, e.g. mammalian cells or human cells, using a vector. The vector may be, e.g., a plasmid or a vims. In some embodiments, delivery is in vivo, in vitro, ex vivo, or in situ. In some embodiments the virus is an adeno associated virus (AAV), a lentivirus, or an adenovirus. In some embodiments the system or components of the system are delivered to cells with a viral-like particle or a virosome. In some embodiments the delivery uses more than one vims, viral-like particle or virosome.

In one embodiment, the compositions and systems described herein can be formulated in liposomes or other similar vesicles. Liposomes are spherical vesicle structures composed of a uni- or multilamellar lipid bilayer surrounding internal aqueous compartments and a relatively impermeable outer lipophilic phospholipid bilayer. Liposomes may be anionic, neutral or cationic. Liposomes are biocompatible, nontoxic, can deliver both hydrophilic and lipophilic drug molecules, protect their cargo from degradation by plasma enzymes, and transport their load across biological membranes and the blood brain barrier (BBB) (see, e.g., Spuch and Navarro, Journal of Drug Delivery, vol. 2011, Article ID 469679, 12 pages, 2011. doi: 10.1155/2011/469679 for review).

Vesicles can be made from several different types of lipids; however, phospholipids are most commonly used to generate liposomes as drug carriers. Methods for preparation of multilamellar vesicle lipids are known in the art (see for example U.S. Pat. No. 6,693,086, the teachings of which relating to multilamellar vesicle lipid preparation are incorporated herein by reference). Although vesicle formation can be spontaneous when a lipid film is mixed with an aqueous solution, it can also be expedited by applying force in the form of shaking by using a homogenizer, sonicator, or an extrusion apparatus (see, e.g., Spuch and Navarro, Journal of Drug Delivery, vol. 2011, Article ID 469679, 12 pages, 2011. doi: 10. 1155/2011/469679 for review). Extruded lipids can be prepared by extruding through filters of decreasing size, as described in Templeton et al., Nature Biotech, 15:647-652, 1997, the teachings of which relating to extruded lipid preparation are incorporated herein by reference.

A variety of nanoparticles can be used for delivery, such as a liposome, a lipid nanoparticle, a cationic lipid nanoparticle, an ionizable lipid nanoparticle, a polymeric nanoparticle, a gold nanoparticle, a dendrimer, a cyclodextrin nanoparticle, a micelle, or a combination of the foregoing.

Lipid nanoparticles are an example of a carrier that provides a biocompatible and biodegradable delivery system for the pharmaceutical compositions described herein. Nanostructured lipid carriers (NLCs) are modified solid lipid nanoparticles (SLNs) that retain the characteristics of the SLN, improve drug stability and loading capacity, and prevent drug leakage. Polymer nanoparticles (PNPs) are an important component of drug deli very. These nanoparticles can effectively direct drug delivery to specific targets and improve drug stability and controlled drag release. Lipid-polymer nanoparticles (PLNs), a type of carrier that combines liposomes and polymers, may also be employed. These nanoparticles possess the complementary advantages of PNPs and liposomes. A PLN is composed of a core-shell structure; the polymer core provides a stable structure, and the phospholipid shell offers good biocompatibility. As such, the two components increase the drug encapsulation efficiency rate, facilitate surface modification, and prevent leakage of water-soluble drugs. For a review , see, e.g., Li et al. 2017, Nanomaterials 7, 122; doi: 10.3390/nano7060122.

Exosomes can also be used as drug delivery vehicles for the compositions and systems described herein. For a review, see Ha et al. July 2016. Acta Pharmaceutica Sinica B. Volume 6, Issue 4, Pages 287-296; doi.org/10.1016/j.apsb.2016.02.001.

Fusosomes interact and fuse with target cells, and thus can be used as deli ven vehicles for a variety of molecules. They generally consist of a bilayer of amphipathic lipids enclosing a lumen or cavity and a fusogen that interacts with the amphipathic lipid bilayer. The fusogen component has been shown to be engineerable in order to confer target cell specificity for the fusion and payload delivery, allowing the creation of delivery vehicles with programmable cell specificity (see for example Patent Application W02020014209, the teachings of which relating to fusosome design, preparation, and usage are incorporated herein by reference).

In some embodiments, the protein component(s) of the gene modifying system may be preassociated with the template nucleic acid (e.g., template RNA). For example, in some embodiments, the gene modifying polypeptide may be first combined with the template nucleic acid (e.g., template RNA) to form a ribonucleoprotein (RNP) complex. In some embodiments, the RNP may be delivered to cells via, e.g., transfection, nucleofection, virus, vesicle, LNP, exosome, fusosome.

A gene modifying system can be introduced into cells, tissues and multicellular organisms. In some embodiments the system or components of the system are delivered to the cells via mechanical means or physical means.

Formulation of protein therapeutics is described in Meyer (Ed.), Therapeutic Protein Drug Products : Practical Approaches to formulation in the Laboratory, Manufacturing, and the Clinic, Woodhead Publishing Series (2012).

Tissue Speci fic Activity/ Administration

In some embodiments, a system described herein can make use of one or more feature (e.g.. a promoter or microRNA binding site) to limit activity in off-target cells or tissues.

In some embodiments, a nucleic acid described herein (e.g., a template RNA or a DNA encoding a template RNA) comprises a promoter sequence, e.g., a tissue specific promoter sequence. In some embodiments, the tissue-specific promoter is used to increase tire target-cell specificity of a gene modifying system. For instance, the promoter can be chosen on the basis that it is active in a target cell type but not active in (or active at a lower level in) a non-target cell type. Thus, even if the promoter integrated into the genome of a non-target cell, it would not drive expression (or only drive low level expression) of an integrated gene. A system having a tissue-specific promoter sequence in the template RNA may also be used in combination with a microRNA binding site, e.g., in tire template RNA or a nucleic acid encoding a gene modifying protein, e.g., as described herein. A system having a tissuespecific promoter sequence in the template RNA may also be used in combination with a DNA encoding a gene modifying polypeptide, driven by a tissue-specific promoter, e.g., to achieve higher levels of gene modifying protein in target cells than in non-target cells. In some embodiments, e.g., for liver indications, a tissue-specific promoter is selected from Table 3 of W02020014209, incorporated herein by reference.

In some embodiments, a nucleic acid described herein (e.g., a template RNA or a DNA encoding a template RNA) comprises a microRNA binding site. In some embodiments, the microRNA binding site is used to increase the target-cell specificity of a gene modifying system. For instance, the microRNA binding site can be chosen on the basis that is recognized by a miRNA that is present in a non-target cell type, but that is not present (or is present at a reduced level relative to the non-target cell) in a target cell type. Tirus, when the template RNA is present in a non-target cell, it would be bound by the miRNA, and when the template RNA is present in a target cell, it would not be bound by tire miRNA (or bound but at reduced levels relative to the non-target cell). While not wishing to be bound by theory, binding of the miRNA to the template RNA may interfere with its activity, e.g., may interfere with insertion of the heterologous object sequence into the genome. Accordingly, the system would edit the genome of target cells more efficiently than it edits the genome of non-target cells, e.g., the heterologous object sequence would be inserted into the genome of target cells more efficiently than into the genome of non-target cells, or an insertion or deletion is produced more efficiently in target cells than in non-target cells. A system having a microRNA binding site in the template RNA (or DNA encoding it) may also be used in combination with a nucleic acid encoding a gene modifying polypeptide, wherein expression of the gene modifying polypeptide is regulated by a second microRNA binding site, e.g., as described herein. In some embodiments, e.g., for liver indications, a miRNA is selected from Table 4 of W02020014209, incorporated herein by reference.

In some embodiments, the template RNA comprises a microRNA sequence, an siRNA sequence, a guide RNA sequence, or a piwi RNA sequence.

Promoters

In some embodiments, one or more promoter or enhancer elements are operably linked to a nucleic acid encoding a gene modify ing protein or a template nucleic acid, e.g., that controls expression of the heterologous object sequence. In certain embodiments, the one or more promoter or enhancer elements comprise cell-type or tissue specific elements. In some embodiments, the promoter or enhancer is the same or derived from the promoter or enhancer that naturally controls expression of tire heterologous object sequence. For example, the ornithine transcarbomylase promoter and enhancer may be used to control expression of the ornithine transcarbomylase gene in a system or method provided by the invention for correcting ornithine transcarbomylase deficiencies. In some embodiments, the promoter is a promoter of Table 16 or 17 or a functional fragment or variant thereof.

Exemplary tissue specific promoters that are commercially available can be found, for example, at a uniform resource locator (e.g., invivogen.com/tissue-specific-promoters). In some embodiments, a promoter is a native promoter or a minimal promoter, e.g., which consists of a single fragment from the 5 ' region of a given gene. In some embodiments, a native promoter comprises a core promoter and its natural 5' UTR. In some embodiments, the 5' UTR comprises an intron. In other embodiments, these include composite promoters, which combine promoter elements of different origins or were generated by assembling a distal enhancer with a minimal promoter of the same origin.

Exemplar}' cell or tissue specific promoters are provided in the tables, below, and exemplar}' nucleic acid sequences encoding them are known in the art and can be readily accessed using a variety of resources, such as the NCBI database, including RefSeq, as well as the Eukary otic Promoter Database (//epd.epfl.ch//index.php).

Table 16. Exemplary’ cell or tissue-specific promoters

Table 17. Additional exemplary cell or tissue-specific promoters

Depending on the host/vector system utilized, any of a number of suitable transcription and translation control elements, including constitutive and inducible promoters, transcription enhancer elements, transcription tenninators, etc. may be used in the expression vector (see e.g., Bitter et al. (1987) Methods in Enzymology. 153:516-544; incorporated herein by reference in its entirety).

In some embodiments, a nucleic acid encoding a gene modifying protein or template nucleic acid is operably linked to a control element, e.g., a transcriptional control element, such as a promoter. The transcriptional control element may, in some embodiment, be functional in either a eukaryotic cell, e.g., a mammalian cell; or a prokaryotic cell (e.g., bacterial or archaeal cell). In some embodiments, a nucleotide sequence encoding a polypeptide is operably linked to multiple control elements, e.g., that allow expression of the nucleotide sequence encoding the polypeptide in both prokaryotic and eukaryotic cells.

For illustration purposes, examples of spatially restricted promoters include, but are not limited to, neuron-specific promoters, adipocyte-specific promoters, cardiomyocyte-specific promoters, smooth muscle-specific promoters, photoreceptor-specific promoters, etc. Neuron-specific spatially restricted promoters include, but are not limited to, a neuron-specific enolase (NSE) promoter (see, e.g.. EMBL HSENO2, X51956); an aromatic amino acid decarboxylase (AADC) promoter, a neurofilament promoter (see, e.g., GenBank HUMNFL, L04147); a synapsin promoter (see, e.g., GenBank HUMSYNIB, M55301); a thy-1 promoter (see, e.g., Chen et al. (1987) Cell 51:7-19; and Llewellyn, et al. (2010) Nat. Med. 16(10): 1161-1166); a serotonin receptor promoter (see, e.g., GenBank S62283); a tyrosine hydroxylase promoter (TH) (see, e.g., Oh et al. (2009) Gene Ther 16:437; Sasaoka et al. (1992) Mol. Brain Res. 16:274; Boundy et al. (1998) J. Neurosci. 18:9989: and Kaneda et al. (1991) Neuron 6:583- 594); a GnRH promoter (see, e.g., Radovick et al. (1991) Proc. Natl. Acad. Sci. USA 88:3402-3406); an L7 promoter (see, e.g., Oberdick et al. (1990) Science 248:223-226); a DNMT promoter (see, e.g., Bartge et al. (1988) Proc. Natl. Acad. Sci. USA 85:3648-3652); an enkephalin promoter (see, e.g., Comb et al. (1988) EMBO J. 17:3793-3805); a myelin basic protein (MBP) promoter; a Ca2+-calmodulin-dependent protein kinase II-alpha (CamKIIa) promoter (see, e.g., Mayford et al. (1996) Proc. Natl. Acad. Sci. USA 93: 13250; and Casanova et al. (2001) Genesis 31:37); a CMV enhancer/platelet-derived growth factor-0 promoter (see, e g., Liu et al. (2004) Gene Therapy 11:52-60); and the like.

Adipocyte-specific spatially restricted promoters include, but are not limited to. the aP2 gene promoter/enhancer, e.g., a region from -5.4 kb to +21 bp of a human aP2 gene (see, e.g., Tozzo et al. (1997) Endocrinol. 138: 1604; Ross et al. (1990) Proc. Natl. Acad. Sci. USA 87:9590; and Pavjani et al. (2005) Nat. Med. 11 :797); a glucose transporter-4 (GLUT4) promoter (see, e.g., Knight et al. (2003) Proc. Natl. Acad. Sci. USA 100: 14725); a fatty acid translocase (FAT/CD36) promoter (see, e.g., Kuriki et al. (2002) Biol. Pharm. Bull. 25: 1476; and Sato et al. (2002) J. Biol. Chem. 277: 15703); a stearoyl-CoA desaturase-1 (SCD1) promoter (Tabor et al. (1999) J. Biol. Chem. 274:20603); a leptin promoter (see. e.g., Mason et al. (1998) Endocrinol. 139: 1013; and Chen et al. (1999) Biochem. Biophys. Res. Comm. 262:187); an adiponectin promoter (see, e.g., Kita et al. (2005) Biochem. Biophys. Res. Comm. 331:484; and Chakrabarti (2010) Endocrinol. 151:2408); an adipsin promoter (see, e.g., Platt et al. (1989) Proc. Natl. Acad. Sci. USA 86:7490); a resistin promoter (see, e.g., Seo et al. (2003) Molec. Endocrinol. 17: 1522); and the like.

Cardiomyocyte-specific spatially restricted promoters include, but are not limited to, control sequences derived from the following genes: myosin light chain-2, a-myosin heavy chain, AE3, cardiac troponin C, cardiac actin, and the like. Franz et al. (1997) Cardiovasc. Res. 35:560-566; Robbins et al. (1995) Ann. N.Y. Acad. Sci. 752:492-505; Linn et al. (1995) Circ. Res. 76:584-591; Parmacek et al. (1994) Mol. Cell. Biol. 14: 1870-1885; Hunter et al. (1993) Hypertension 22:608-617; and Sartorelli et al. (1992) Proc. Natl. Acad. Sci. USA 89:4047-4051.

Smooth muscle-specific spatially restricted promoters include, but are not limited to, an SM22a promoter (see, e g., Akyiirek et al. (2000) Mol. Med. 6:983; and U.S. Pat. No. 7,169,874); a smoothelin promoter (see, e.g., WO 2001/018048); an a-smooth muscle actin promoter; and the like. For example, a 0.4 kb region of the SM22a promoter, within which lie two CArG elements, has been shown to mediate vascular smooth muscle cell-specific expression (see, e.g.. Kim, et al. (1997) Mol. Cell. Biol. 17, 2266- 2278; Li, et al., (1996) J. Cell Biol. 132. 849-859; and Moessler, et al. (1996) Development 122, 2415- 2425).

Photoreceptor-specific spatially restricted promoters include, but are not limited to, a rhodopsin promoter; a rhodopsin kinase promoter (Young et al. (2003) Ophthalmol. Vis. Sci. 44:4076); a beta phosphodiesterase gene promoter (Nicoud et al. (2007) J. Gene Med. 9: 1015); a retinitis pigmentosa gene promoter (Nicoud et al. (2007) supra); an interphotoreceptor retinoid-binding protein (IRBP) gene enhancer (Nicoud et al. (2007) supra); an IRBP gene promoter (Yokoyama et al. (1992) Exp Eye Res. 55:225); and the like.

In some embodiments, a gene modifying system, e.g., DNA encoding a gene modifying polypeptide. DNA encoding a template RNA, or DNA or RNA encoding a heterologous object sequence, is designed such that one or more elements is operably linked to a tissue-specific promoter, e.g., a promoter that is active in T-cells. In further embodiments, the T-cell active promoter is inactive in other cell types, e.g., B-cells, NK cells. In some embodiments, the T-cell active promoter is derived from a promoter for a gene encoding a component of the T-cell receptor, e.g., TRAC, TRBC, TRGC, TRDC. In some embodiments, the T-cell active promoter is derived from a promoter for a gene encoding a component of a T-cell-specific cluster of differentiation protein, e.g., CD3, e.g.. CD3D, CD3E, CD3G, CD3Z. In some embodiments, T-cell-specific promoters in gene modifying systems are discovered by comparing publicly available gene expression data across cell types and selecting promoters from the genes with enhanced expression in T-cells. In some embodiments, promoters may be selecting depending on the desired expression breadth, e.g., promoters that are active in T-cells only, promoters that are active in NK cells only, promoters that are active in both T-cells and NK cells.

Cell-specific promoters known in the art may be used to direct expression of a gene modifying protein, e.g., as described herein. Nonlimiting exemplary mammalian cell-specific promoters have been characterized and used in mice expressing Cre recombinase in a cell-specific manner. Certain nonlimiting exemplary' mammalian cell-specific promoters are listed in Table 1 of US9845481, incorporated herein by reference.

In some embodiments, a vector as described herein comprises an expression cassette. Typically, an expression cassette comprises the nucleic acid molecule of the instant invention operatively linked to a promoter sequence. For example, a promoter is operatively linked with a coding sequence when it is capable of affecting the expression of that coding sequence (e.g., the coding sequence is under the transcriptional control of the promoter). Encoding sequences can be operatively linked to regulatory’ sequences in sense or antisense orientation. In certain embodiments, the promoter is a heterologous promoter. In certain embodiments, an expression cassette may comprise additional elements, for example, an intron, an enhancer, a polyadenylation site, a woodchuck response element (WRE), and/or other elements known to affect expression levels of the encoding sequence. A promoter typically controls the expression of a coding sequence or functional RNA. In certain embodiments, a promoter sequence comprises proximal and more distal upstream elements and can further comprise an enhancer clement. An enhancer can typically stimulate promoter activity and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue-specificity of a promoter. In certain embodiments, the promoter is derived in its entirety from a native gene. In certain embodiments, the promoter is composed of different elements derived from different naturally occurring promoters. In certain embodiments, the promoter comprises a synthetic nucleotide sequence. It will be understood by those skilled in the art that different promoters will direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions or to the presence or the absence of a drug or transcriptional co-factor. Ubiquitous, cell-type-specific, tissuespecific, developmental stage-specific, and conditional promoters, for example, drug-responsive promoters (e.g., tetracycline-responsive promoters) are well known to those of skill in the art. Exemplary promoters include, but are not limited to, the phosphoglycerate kinase (PKG) promoter, CAG (composite of tire CMV enhancer the chicken beta actin promoter (CBA) and the rabbit beta globin intron), NSE (neuronal specific enolase), synapsin or NeuN promoters, the SV40 early promoter, mouse mammary tumor virus LTR promoter; adenovirus major late promoter (Ad MLP), a herpes simplex virus (HSV) promoter, a cytomegalovirus (CMV) promoter such as tire CMV immediate early promoter region (CMVIE), SFFV promoter, rous sarcoma virus (RSV) promoter, synthetic promoters, hybrid promoters, and the like. Other promoters can be of human origin or from other species, including from mice.

Common promoters include, e.g., the human cytomegalovirus (CMV) immediate early gene promoter, the SV40 early promoter, the Rous sarcoma virus long tenninal repeat, [beta]- actin, rat insulin promoter, the phosphoglycerate kinase promoter, the human alpha- 1 antitrypsin (hAAT) promoter, the transthyretin promoter, the TBG promoter and other liver-specific promoters, the desmin promoter and similar musclespecific promoters, the EFl -alpha promoter, hybrid promoters with multi -tissue specificity, promoters specific for neurons like synapsin and glyceraldehyde-3 -phosphate dehydrogenase promoter, all of which are promoters well known and readily available to those of skill in the art, can be used to obtain high-level expression of the coding sequence of interest. In addition, sequences derived from non-viral genes, such as the murine metallothionein gene, will also find use herein. Such promoter sequences are commercially available from, e g., Stratagene (San Diego, CA). Additional exemplary promoter sequences are described, for example, in WO2018213786A1 (incorporated by reference herein in its entirety).

In some embodiments, the apolipoprotein E enhancer (ApoE) or a functional fragment thereof is used, e.g., to drive expression in the liver. In some embodiments, two copies of the ApoE enhancer or a functional fragment thereof are used. In some embodiments, the ApoE enhancer or functional fragment thereof is used in combination with a promoter, e.g., the human alpha- 1 antitrypsin (hAAT) promoter.

In some embodiments, the regulatory sequences impart tissue-specific gene expression capabilities. In some cases, the tissue-specific regulatory sequences bind tissue-specific transcription factors that induce transcription in a tissue specific manner. Various tissue-specific regulatory sequences (e.g., promoters, enhancers, etc.) are known in the art. Exemplary tissue-specific regulatory sequences include, but are not limited to, the following tissue-specific promoters: a liver-specific thyroxin binding globulin (TBG) promoter, a insulin promoter, a glucagon promoter, a somatostatin promoter, a pancreatic polypeptide (PPY) promoter, a synapsin-1 (Syn) promoter, a creatine kinase (MCK) promoter, a mammalian desmin (DES) promoter, a a-myosin heavy chain (a-MHC) promoter, or a cardiac Troponin T (cTnT) promoter. Other exemplary promoters include Beta-actin promoter, hepatitis B virus core promoter, Sandig et al., Gene Ther.. 3: 1002-9 (1996); alpha-fetoprotein (AFP) promoter, Arbuthnot et al.. Hum. Gene Ther., 7: 1503-14 (1996)), bone osteocalcin promoter (Stein et al., Mol. Biol. Rep., 24: 185-96 (1997)); bone sialoprotein promoter (Chen et al., J. Bone Miner. Res., 11:654-64 (1996)), CD2 promoter (Hansal et al., J. Immunol., 161: 1063-8 (1998); immunoglobulin heavy chain promoter; T cell receptor a- chain promoter, neuronal such as neuron-specific enolase (NSE) promoter (Andersen et al., Cell. Mol. Neurobiol., 13:503-15 (1993)), neurofilament light-chain gene promoter (Piccioli et al., Proc. Natl. Acad. Sci. USA, 88:5611-5 (1991)), and the neuron-specific vgf gene promoter (Piccioli et al.. Neuron, 15:373- 84 (1995)), and others. Additional exemplary promoter sequences are described, for example, in U.S. Patent No. 10300146 (incorporated herein by reference in its entirety). In some embodiments, a tissuespecific regulatory element, e.g., a tissue-specific promoter, is selected from one known to be operably linked to a gene that is highly expressed in a given tissue, e.g., as measured by RNA-seq or protein expression data, or a combination thereof. Methods for analyzing tissue specificity by expression are taught in Fagerberg et al. Mol Cell Proteomics 13(2):397-406 (2014), which is incorporated herein by reference in its entirety.

In some embodiments, a vector described herein is a multicistronic expression construct. Multicistronic expression constructs include, for example, constructs harboring a first expression cassette, e.g. comprising a first promoter and a first encoding nucleic acid sequence, and a second expression cassette, e.g. comprising a second promoter and a second encoding nucleic acid sequence. Such multicistronic expression constructs may, in some instances, be particularly useful in the delivery of nontranslated gene products, such as hairpin RNAs, together with a polypeptide, for example, a gene modifying polypeptide and gene modifying template. In some embodiments, multicistronic expression constructs may exhibit reduced expression levels of one or more of the included transgenes, for example, because of promoter interference or the presence of incompatible nucleic acid elements in close proximity. If a multicistronic expression construct is part of a viral vector, the presence of a self- complementary nucleic acid sequence may, in some instances, interfere with the formation of structures necessary for viral reproduction or packaging.

In some embodiments, the sequence encodes an RNA with a hairpin. In some embodiments, the hairpin RNA is a guide RNA, a template RNA, a shRNA, or a microRNA. In some embodiments, the first promoter is an RNA polymerase I promoter. In some embodiments, the first promoter is an RNA polymerase II promoter. In some embodiments, the second promoter is an RNA polymerase III promoter. In some embodiments, the second promoter is a U6 or Hl promoter.

Without wishing to be bound by theory, multicistronic expression constructs may not achieve optimal expression levels as compared to expression systems containing only one cistron. One of the suggested causes of lower expression levels achieved with multicistronic expression constructs comprising two or more promoter elements is the phenomenon of promoter interference (see, e.g.. Curtin J A, Dane A P, Swanson A, Alexander I E, Ginn S L. Bidirectional promoter interference between two widely used internal heterologous promoters in a late-generation lentiviral construct. Gene Ther. 2008 March; 15(5):384-90; and Martin-Duque P, Jezzard S, Kaftansis L, Vassaux G. Direct comparison of the insulating properties of two genetic elements in an adenoviral vector containing two different expression cassettes. Hum Gene Ther. 2004 October; 15(10):995-1002: both references incorporated herein by reference for disclosure of promoter interference phenomenon). In some embodiments, the problem of promoter interference may be overcome, e.g., by producing multicistronic expression constructs comprising only one promoter driving transcription of multiple encoding nucleic acid sequences separated by internal ribosomal entry sites, or by separating cistrons comprising their own promoter with transcriptional insulator elements. In some embodiments, single -promoter driven expression of multiple cistrons may result in uneven expression levels of the cistrons. In some embodiments, a promoter cannot efficiently be isolated and isolation elements may not be compatible with some gene transfer vectors, for example, some retroviral vectors.

MicroRNAs

MicroRNAs (miRNAs) and other small interfering nucleic acids generally regulate gene expression via target RNA transcript cleavage/degradation or translational repression of the target messenger RNA (mRNA). miRNAs may, in some instances, be natively expressed, typically as final 19- 25 non-translatcd RNA products. miRNAs generally exhibit their activity through scqucncc-spccific interactions with the 3' untranslated regions (UTR) of target mRNAs. These endogenously expressed miRNAs may form hairpin precursors that are subsequently processed into an miRNA duplex, and further into a mature single stranded miRNA molecule This mature miRNA generally guides a multiprotein complex, miRISC, which identifies target 3' UTR regions of target mRNAs based upon their complementarity to the mature miRNA. Useful transgene products may include, for example, miRNAs or miRNA binding sites that regulate the expression of a linked polypeptide. A non-limiting list of miRNA genes; the products of these genes and their homologues are useful as transgenes or as targets for small interfering nucleic acids (e.g., miRNA sponges, antisense oligonucleotides), e.g., in methods such as those listed in US10300146, 22:25-25:48, are herein incorporated by reference. In some embodiments, one or more binding sites for one or more of the foregoing rniRNAs are incorporated in a transgene, e.g., a transgene delivered by a rAAV vector, e.g., to inhibit the expression of the transgene in one or more tissues of an animal harboring the transgene. In some embodiments, a binding site may be selected to control the expression of a transgene in a tissue specific manner. For example, binding sites for the liverspecific miR-122 may be incorporated into a transgene to inhibit expression of that transgene in the liver. Additional exemplary miRNA sequences are described, for example, in U.S. Patent No. 10,300,146 (incorporated herein by reference in its entirety).

An miR inhibitor or miRNA inhibitor is generally an agent that blocks miRNA expression and/or processing. Examples of such agents include, but are not limited to, microRNA antagonists, microRNA specific antisense, microRNA sponges, and microRNA oligonucleotides (double-stranded, hairpin, short oligonucleotides) that inhibit miRNA interaction with a Drosha complex. MicroRNA inhibitors, e.g.. miRNA sponges, can be expressed in cells from transgenes (e.g., as described in Ebert, M. S. Nature Methods, Epub Aug. 12, 2007; incorporated by reference herein in its entirety). In some embodiments, microRNA sponges, or other miR inhibitors, are used with the AAVs. microRNA sponges generally specifically inhibit rniRNAs through a complementary heptameric seed sequence. In some embodiments, an entire family of rniRNAs can be silenced using a single sponge sequence. Other methods for silencing miRNA function (derepression of miRNA targets) in cells will be apparent to one of ordinary skill in the art.

In some embodiments, a gene modifying system, template RNA, or polypeptide described herein is administered to or is active in (e.g., is more active in) a target tissue, e.g., a first tissue. In some embodiments, the gene modifying system, template RNA, or polypeptide is not administered to or is less active in (e.g., not active in) a non-target tissue. In some embodiments, a gene modifying system, template RNA, or polypeptide described herein is useful for modifying DNA in a target tissue, e.g., a first tissue, (e.g., and not modifying DNA in a non-target tissue).

In some embodiments, a gene modifying system comprises (a) a polypeptide described herein or a nucleic acid encoding the same, (b) a template nucleic acid (e.g., template RNA) described herein, and (c) one or more first tissue-specific expression-control sequences specific to the target tissue, wherein the one or more first tissue-specific expression-control sequences specific to tire target tissue are in operative association with (a), (b), or (a) and (b), wherein, when associated with (a), (a) comprises a nucleic acid encoding the polypeptide.

In some embodiments, the nucleic acid in (b) comprises RNA.

In some embodiments, the nucleic acid in (b) comprises DNA. In some embodiments, the nucleic acid in (b): (i) is single-stranded or comprises a single-stranded segment, e.g., is single-stranded DNA or comprises a single-stranded segment and one or more double stranded segments; (ii) has inverted terminal repeats; or (iii) both (i) and (ii).

In some embodiments, the nucleic acid in (b) is double -stranded or comprises a double-stranded segment.

In some embodiments, (a) comprises a nucleic acid encoding the polypeptide.

In some embodiments, the nucleic acid in (a) comprises RNA.

In some embodiments, the nucleic acid in (a) comprises DNA.

In some embodiments, the nucleic acid in (a): (i) is single-stranded or comprises a single -stranded segment, e.g., is single-stranded DNA or comprises a single-stranded segment and one or more double stranded segments; (ii) has inverted terminal repeats; or (iii) both (i) and (ii).

In some embodiments, the nucleic acid in (a) is double -stranded or comprises a double-stranded segment.

In some embodiments, the nucleic acid in (a), (b), or (a) and (b) is linear.

In some embodiments, the nucleic acid in (a), (b), or (a) and (b) is circular, e.g., a plasmid or minicircle.

In some embodiments, tire heterologous object sequence is in operative association with a first promoter.

In some embodiments, the one or more first tissue-specific expression-control sequences comprises a tissue specific promoter.

In some embodiments, the tissue-specific promoter comprises a first promoter in operative association with: (i) the heterologous object sequence, (ii) a nucleic acid encoding the retroviral RT. or (iii) (i) and (ii).

In some embodiments, the one or more first tissue-specific expression-control sequences comprises a tissue-specific microRNA recognition sequence in operative association with: (i) the heterologous object sequence, (ii) a nucleic acid encoding the retroviral RT domain, or (iii) (i) and (ii).

In some embodiments, a system comprises a tissue-specific promoter, and the system further comprises one or more tissue-specific microRNA recognition sequences, wherein: (i) the tissue specific promoter is in operative association with: (I) the heterologous object sequence, (II) a nucleic acid encoding the retroviral RT domain, or (111) (I) and (II); and/or (ii) the one or more tissue-specific microRNA recognition sequences are in operative association with: (I) the heterologous object sequence, (II) a nucleic acid encoding the retroviral RT, or (III) (I) and (II).

In some embodiments, wherein (a) comprises a nucleic acid encoding the polypeptide, the nucleic acid comprises a promoter in operative association with the nucleic acid encoding the polypeptide. In some embodiments, the nucleic acid encoding the polypeptide comprises one or more second tissue-specific expression-control sequences specific to the target tissue in operative association with the polypeptide coding sequence.

In some embodiments, the one or more second tissue-specific expression-control sequences comprises a tissue specific promoter.

In some embodiments, the tissue-specific promoter is the promoter in operative association with the nucleic acid encoding the polypeptide.

In some embodiments, the one or more second tissue-specific expression-control sequences comprises a tissue-specific microRNA recognition sequence.

In some embodiments, the promoter in operative association with the nucleic acid encoding the polypeptide is a tissue-specific promoter, the system further comprising one or more tissue-specific microRNA recognition sequences.

In some embodiments, a nucleic acid component of a system provided by the invention is a sequence (e.g., encoding the polypeptide or comprising a heterologous object sequence) flanked by untranslated regions (UTRs) that modify protein expression levels. Various 5' and 3' UTRs can affect protein expression. For example, in some embodiments, the coding sequence may be preceded by a 5 ' UTR that modifies RNA stability or protein translation. In some embodiments, the sequence may be followed by a 3' UTR that modifies RNA stability or translation. In some embodiments, the sequence may be preceded by a 5 ' UTR and followed by a 3 ' UTR that modify RNA stability or translation. In some embodiments, the 5 ' and/or 3 ' UTR may be selected from the 5 ' and 3 ' UTRs of complement factor 3 (C3) (CACTCCTCCCCATCCTCTCCCTCTGTCCCTCTGTCCCTCTGACCCTGCACTGTCCCAGC ACC) or orosomucoid 1 (0RM1) (CAGGACACAGCCTTGGATCAGGACAGAGACTTGGGGGCCATCCTGCCCCTCCAACCCGA CA TGTGTACCTCAGCTTTTTCCCTCACTTGCATCAATAAAGCTTCTGTGTTTGGAACAGCTA A) (Asrani et al. RNA Biology 2018). In certain embodiments, the 5' UTR is the 5' UTR from C3 and the 3' UTR is the 3' UTR from 0RM1. In certain embodiments, a 5' UTR and 3' UTR for protein expression, e.g., mRNA (or DNA encoding the RNA) for a gene modifying polypeptide or heterologous object sequence, comprise optimized expression sequences. In some embodiments, the 5' UTR comprises GGGAAAUAAGAGAGAAAAGAAGAGUAAGAAGAAAUAUAAGAGCCACC and/or the 3' UTR comprising UGAUAAUAGGCUGGAGCCUCGGUGGCCAUGCUUCUUGCCCCUUGGGCCUCCCCCCAGCCC CUCCUCCCCUUCCUGCACCCGUACCCCCGUGGUCUUUGAAUAAAGUCUGA, e.g., as described in Richner et al. Cell 168(6): Pl 114-1125 (2017), the sequences of which are incorporated herein by reference.

In some embodiments, a 5' and/or 3' UTR may be selected to enhance protein expression. In some embodiments, a 5 ' and/or 3 ' UTR may be selected to modify protein expression such that overproduction inhibition is minimized. In some embodiments, UTRs are around a coding sequence, e.g.. outside the coding sequence and in other embodiments proximal to the coding sequence, In some embodiments, additional regulatory elements (e.g., miRNA binding sites, cis-regulatory sites) are included in the UTRs.

In some embodiments, an open reading frame of a gene modifying system, e.g., an ORF of an mRNA (or DNA encoding an mRNA) encoding a gene modify ing polypeptide or one or more ORFs of an mRNA (or DNA encoding an mRNA) of a heterologous object sequence, is flanked by a 5 ' and/or 3 ' untranslated region (UTR) that enhances the expression thereof. In some embodiments, the 5' UTR of an mRNA component (or transcript produced from a DNA component) of the system comprises the sequence 5 -GGGAAAUAAGAGAGAAAAGAAGAGUAAGAAGAAAUAUAAGAGCCACC-3 ' . In some embodiments, the 3 ' UTR of an mRNA component (or transcript produced from a DNA component) of the system comprises the sequence 5 - UGAUAAUAGGCUGGAGCCUCGGUGGCCAUGCUUCUUGCCCCUUGGGCCUCCCCCCAGCCC CUCCUCCCCUUCCUGCACCCGUACCCCCGUGGUCUUUGAAUAAAGUCUGA-3 This combination of 5 ' UTR and 3 ' UTR has been shown to result in desirable expression of an operably linked ORF by Richner et al. Cell 168(6): Pl 114-1125 (2017), the teachings and sequences of which are incorporated herein by reference. In some embodiments, a system described herein comprises a DNA encoding a transcript, wherein the DNA comprises the corresponding 5 ' UTR and 3 ' UTR sequences, with T substituting for U in the above-listed sequence). In some embodiments, a DNA vector used to produce an RNA component of the system further comprises a promoter upstream of the 5 ' UTR for initiating in vitro transcription, e.g, a T7, T3, or SP6 promoter. The 5' UTR above begins with GGG, which is a suitable start for optimizing transcription using T7 RNA polymerase. For tuning transcription levels and altering tire transcription start site nucleotides to fit alternative 5 ' UTRs, the teachings of Davidson et al. Pac Symp Biocomput 433-443 (2010) describe T7 promoter variants, and tire methods of discovery thereof, that fulfill both of these traits.

Viral vectors and components thereof

Viruses are a useful source of delivery vehicles for the systems described herein, in addition to a source of relevant enzymes or domains as described herein, e.g.. as sources of polymerases and polymerase functions used herein, e g., DNA-dependent DNA polymerase, RNA-dependent RNA polymerase, RNA-dependent DNA polymerase, DNA-dependent RNA polymerase, reverse transcriptase. Some enzymes, e.g., reverse transcriptases, may have multiple activities, e.g., be capable of both RNA- dependent DNA polymerization and DNA-dependent DNA polymerization, e.g., first and second strand synthesis. In some embodiments, the vims used as a gene modifying delivery system or a source of components thereof may be selected from a group as described by Baltimore Bacterial Rev 35(3):235-241 (1971).

In some embodiments, the vims is selected from a Group I vims, e.g., is a DNA vims and packages dsDNA into virions. In some embodiments, the Group I vims is selected from, e.g., Adenovimses, Herpesviruses, Poxvimses.

In some embodiments, the vims is selected from a Group II vims, e.g., is a DNA vims and packages ssDNA into virions. In some embodiments, the Group II vims is selected from, e.g., Parvoviruses. In some embodiments, the parvovirus is a dependoparvovims, e.g.. an adeno-associated vims (AAV).

In some embodiments, the vims is selected from a Group III vims, e.g., is an RNA vims and packages dsRNA into virions. In some embodiments, the Group III vims is selected from, e.g., Reovimses. In some embodiments, one or both strands of the dsRNA contained in such virions is a coding molecule able to serve directly as mRNA upon transduction into a host cell, e.g.. can be directly translated into protein upon transduction into a host cell without requiring any intervening nucleic acid replication or polymerization steps.

In some embodiments, the vims is selected from a Group IV vims, e.g., is an RNA vims and packages ssRNA(+) into virions. In some embodiments, the Group IV vims is selected from, e.g., Coronaviruses, Picomavimses, Togavimses. In some embodiments, the ssRNA(+) contained in such virions is a coding molecule able to serve directly as mRNA upon transduction into a host cell, e.g., can be directly translated into protein upon transduction into a host cell without requiring any intervening nucleic acid replication or polymerization steps.

In some embodiments, the vims is selected from a Group V vims, e.g., is an RNA vims and packages ssRNA(-) into virions. In some embodiments, tire Group V vims is selected from, e.g., Orthomyxoviruses, Rhabdovimses. In some embodiments, an RNA vims with an ssRNA(-) genome also carries an enzyme inside tire virion that is transduced to host cells with tire viral genome, e.g., an RNA- dependent RNA polymerase, capable of copying tire ssRNA(-) into ssRNA(+) that can be translated directly by the host.

In some embodiments, the vims is selected from a Group VI vims, e.g., is a retrovirus and packages ssRNA(+) into virions. In some embodiments, the Group VI vims is selected from, e.g., retrovimses. In some embodiments, the retrovims is a lentivims, e.g., HIV-1, HIV-2, SIV, BIV. In some embodiments, the retrovirus is a spumavirus, e.g., a foamy virus, e.g., HFV, SFV, BFV. In some embodiments, the ssRNA(+) contained in such virions is a coding molecule able to serve directly as mRNA upon transduction into a host cell, e.g., can be directly translated into protein upon transduction into a host cell without requiring any intervening nucleic acid replication or polymerization steps. In some embodiments, the ssRNA(+) is first reverse transcribed and copied to generate a dsDNA genome intermediate from which mRNA can be transcribed in the host cell. In some embodiments, an RNA virus with an ssRNA(+) genome also carries an enzyme inside the virion that is transduced to host cells with the viral genome, e.g., an RNA-dependent DNA polymerase, capable of copying the ssRNA(+) into dsDNA that can be transcribed into mRNA and translated by the host. In some embodiments, the reverse transcriptase from a Group VI retrovirus is incorporated as the reverse transcriptase domain of a gene modifying polypeptide.

In some embodiments, the virus is selected from a Group VII virus, e.g., is a retrovirus and packages dsRNA into virions. In some embodiments, the Group VII virus is selected from, e.g., Hepadnaviruses. In some embodiments, one or both strands of the dsRNA contained in such virions is a coding molecule able to serve directly as mRNA upon transduction into a host cell, e.g., can be directly translated into protein upon transduction into a host cell without requiring any intervening nucleic acid replication or polymerization steps. In some embodiments, one or both strands of the dsRNA contained in such virions is first reverse transcribed and copied to generate a dsDNA genome intermediate from which mRNA can be transcribed in the host cell. In some embodiments, an RNA virus with a dsRNA genome also carries an enzyme inside the virion that is transduced to host cells with the viral genome, e.g., an RNA-dependent DNA polymerase, capable of copying the dsRNA into dsDNA that can be transcribed into mRNA and translated by tire host. In some embodiments, the reverse transcriptase from a Group VII retrovirus is incorporated as the reverse transcriptase domain of a gene modifying polypeptide.

In some embodiments, virions used to deliver nucleic acid in this invention may also carry enzymes involved in the process of gene modification. For example, a retroviral virion may contain a reverse transcriptase domain that is delivered into a host cell along with the nucleic acid. In some embodiments, an RNA template may be associated with a gene modifying polypeptide within a virion, such that both are co-delivered to a target cell upon transduction of the nucleic acid from the viral particle. In some embodiments, the nucleic acid in a virion may comprise DNA, e.g., linear ssDNA, linear dsDNA. circular ssDNA, circular dsDNA, minicircle DNA, dbDNA, ceDNA. In some embodiments, the nucleic acid in a virion may comprise RNA, e.g., linear ssRNA, linear dsRNA, circular ssRNA, circular dsRNA. In some embodiments, a viral genome may circularize upon transduction into a host cell, e.g., a linear ssRNA molecule may undergo a covalent linkage to form a circular ssRNA, a linear dsRNA molecule may undergo a covalent linkage to fonn a circular dsRNA or one or more circular ssRNA. In some embodiments, a viral genome may replicate by rolling circle replication in a host cell.

In some embodiments, a viral genome may comprise a single nucleic acid molecule, e.g., comprise a nonsegmented genome. In some embodiments, a viral genome may comprise two or more nucleic acid molecules, e.g., comprise a segmented genome. In some embodiments, a nucleic acid in a virion may be associated with one or proteins. In some embodiments, one or more proteins in a virion may be delivered to a host cell upon transduction. In some embodiments, a natural virus may be adapted for nucleic acid delivery by the addition of virion packaging signals to the target nucleic acid, wherein a host cell is used to package the target nucleic acid containing the packaging signals.

In some embodiments, a virion used as a delivery vehicle may comprise a commensal human virus. In some embodiments, a virion used as a delivery vehicle may comprise an anellovirus, the use of which is described in WO2018232017A1, which is incorporated herein by reference in its entirety.

A A V Administration

In some embodiments, an adeno-associated virus (AAV) is used in conjunction with the system, template nucleic acid, and/or polypeptide described herein. In some embodiments, an AAV is used to deliver, administer, or package tire system, template nucleic acid, and/or polypeptide described herein. In some embodiments, the AAV is a recombinant AAV (rAAV).

In some embodiments, a system comprises (a) a polypeptide described herein or a nucleic acid encoding the same, (b) a template nucleic acid (e.g., template RNA) described herein, and (c) one or more first tissue-specific expression-control sequences specific to the target tissue, wherein the one or more first tissue-specific expression-control sequences specific to the target tissue are in operative association with (a), (b). or (a) and (b), wherein, when associated with (a), (a) comprises a nucleic acid encoding the polypeptide.

In some embodiments, a system described herein further comprises a first recombinant adeno- associated virus (rAAV) capsid protein; wherein the at least one of (a) or (b) is associated with the first rAAV capsid protein, wherein at least one of (a) or (b) is flanked by AAV inverted terminal repeats (ITRs).

In some embodiments, (a) and (b) are associated with the first rAAV capsid protein.

In some embodiments, (a) and (b) are on a single nucleic acid.

In some embodiments, the system further comprises a second rAAV capsid protein, wherein at least one of (a) or (b) is associated with the second rAAV capsid protein, and wherein the at least one of (a) or (b) associated with the second rAAV capsid protein is different from the at least one of (a) or (b) is associated with the first rAAV capsid protein. In some embodiments, the at least one of (a) or (b) is associated with the first or second rAAV capsid protein is dispersed in the interior of the first or second rAAV capsid protein, which first or second rAAV capsid protein is in the form of an AAV capsid particle.

In some embodiments, the system further comprises a nanoparticle, wherein the nanoparticle is associated with at least one of (a) or (b).

In some embodiments, (a) and (b), respectively are associated with: a) a first rAAV capsid protein and a second rAAV capsid protein: b) a nanoparticle and a first rAAV capsid protein; c) a first rAAV capsid protein; d) a first adenovirus capsid protein; e) a first nanoparticle and a second nanoparticle; or f) a first nanoparticle.

Viral vectors are useful for delivering all or part of a system provided by the invention, e.g., for use in methods provided by the invention. Systems derived from different viruses have been employed for the delivery of polypeptides or nucleic acids; for example: integrase -deficient lentivirus, adenovirus, adeno-associated virus (AAV), herpes simplex virus, and baculovirus (reviewed in Hodge et al. Hum Gene Ther 2017; Narayanavari et al. Crit Rev Biochem Mol Biol 2017; Boehme et al. Curr Gene Ther 2015).

Adenoviruses are common viruses that have been used as gene delivery vehicles given well- defined biology, genetic stability, high transduction efficiency, and ease of large-scale production (see, for example, review by Lee et al. Genes & Diseases 2017). They possess linear dsDNA genomes and come in a variety of serotypes that differ in tissue and cell tropisms. In order to prevent replication of infectious virus in recipient cells, adenovirus genomes used for packaging are deleted of some or all endogenous viral proteins, which are provided in trans in viral production cells. This renders the genomes helper-dependent, meaning they can only be replicated and packaged into viral particles in the presence of the missing components provided by so-called helper functions. A helper-dependent adenovirus system with all viral ORFs removed may be compatible with packaging foreign DNA of up to ~37 kb (Parks et al. J Virol 1997). In some embodiments, an adenoviral vector is used to deliver DNA corresponding to the polypeptide or template component of the gene modifying system, or both are contained on separate or the same adenoviral vector. In some embodiments, the adenovirus is a helper-dependent adenovirus (HD- AdV) that is incapable of self-packaging. In some embodiments, the adenovirus is a high-capacity adenovirus (HC-AdV) that has had all or a substantial portion of endogenous viral ORFs deleted, while retaining the necessary sequence components for packaging into adenoviral particles. For this type of vector, the only adenoviral sequences required for genome packaging are noncoding sequences: the inverted terminal repeats (ITRs) at both ends and the packaging signal at the 5'-end (Jager et al. Nat Protoc 2009). In some embodiments, tire adenoviral genome also comprises stuffer DNA to meet a minimal genome size for optimal production and stability (see, for example, Hausl et al. Mol Ther 2010). In some embodiments, an adenovirus is used to deliver a gene modifying system to the liver.

In some embodiments, an adenovirus is used to deliver a gene modifying system to HSCs, e.g., HDAd5/35++. HDAd5/35++ is an adenovirus with modified serotype 35 fibers that de-target the vector from the liver (Wang et al. Blood Adv 2019). In some embodiments, the adenovirus that delivers a gene modifying system to HSCs utilizes a receptor that is expressed specifically on primitive HSCs, e.g.. CD46.

Adeno-associated viruses (AAV) belong to the parvoviridae family and more specifically constitute the dependoparvovirus genus. The AAV genome is composed of a linear single-stranded DNA molecule which contains approximately 4.7 kilobases (kb) and consists of two major open reading frames (ORFs) encoding tire non-structural Rep (replication) and structural Cap (capsid) proteins. A second ORF within the cap gene was identified that encodes the assembly-activating protein (AAP). The DNAs flanking the AAV coding regions are two cis-acting inverted terminal repeat (ITR) sequences, approximately 145 nucleotides in length, with interrupted palindromic sequences that can be folded into energetically stable hairpin structures that function as primers of DNA replication. In addition to their role in DNA replication, tire ITR sequences have been shown to be involved in viral DNA integration into tire cellular genome, rescue from the host genome or plasmid, and encapsidation of viral nucleic acid into mature virions (Muzyczka, (1992) Curr. Top. Micro. Immunol. 158:97-129). In some embodiments, one or more gene modifying nucleic acid components is flanked by ITRs derived from AAV for viral packaging. See, e.g., W02019113310.

In some embodiments, one or more components of the gene modifying system are carried via at least one AAV vector. In some embodiments, the at least one AAV vector is selected for tropism to a particular cell, tissue, organism. In some embodiments, the AAV vector is pseudotyped, e.g., AAV2/8, wherein AAV2 describes the design of the construct but the capsid protein is replaced by that from AAV8. It is understood that any of the described vectors could be pseudotype derivatives, wherein the capsid protein used to package the AAV genome is derived from that of a different AAV serotype. Without wishing to be limited in vector choice, a list of exemplary' AAV seroty pes can be found in Table 18. In some embodiments, an AAV to be employed for gene modifying may be evolved for novel cell or tissue tropism as has been demonstrated in the literature (e.g., Davidsson et al. Proc Natl Acad Sci U S A 2019).

In some embodiments, the AAV delivery vector is a vector which has two AAV inverted terminal repeats (ITRs) and a nucleotide sequence of interest (for example, a sequence coding for a gene modifying polypeptideor a DNA template, or both), each of said ITRs having an interrupted (or noncontiguous) palindromic sequence, i.e., a sequence composed of three segments: a first segment and a last segment that are identical when read 5'— > 3' but hybridize when placed against each other, and a segment that is different that separates tire identical segments. See, for example, WO2012123430.

Conventionally, AAV virions with capsids are produced by introducing a plasmid or plasmids encoding the rAAV or scAAV genome, Rep proteins, and Cap proteins (Grimm et al, 1998). Upon introduction of these helper plasmids in trans, the AAV genome is ‘“rescued" (i.e., released and subsequently recovered) from the host genome, and is further encapsidated to produce infectious AAV. In some embodiments, one or more gene modifying nucleic acids are packaged into AAV particles by introducing the ITR-flanked nucleic acids into a packaging cell in conjunction with the helper functions.

In some embodiments, the AAV genome is a so called self-complementary genome (referred to as scAAV), such that the sequence located between the ITRs contains both the desired nucleic acid sequence (e.g., DNA encoding the gene modifying polypeptide or template, or both) in addition to the reverse complement of the desired nucleic acid sequence, such that these two components can fold over and self-hybridize. In some embodiments, the self-complementary modules are separated by an intervening sequence that permits the DNA to fold back on itself, e.g., forms a stem-loop. An scAAV has the advantage of being poised fortranscription upon entering the nucleus, rather than being first dependent on ITR priming and second-strand synthesis to form dsDNA. In some embodiments, one or more gene modifying components is designed as an scAAV, wherein the sequence between the AAV ITRs contains two reverse complementing modules that can self-hybridize to create dsDNA.

In some embodiments, nucleic acid (e.g., encoding a polypeptide, or a template, or both) delivered to cells is closed-ended, linear duplex DNA (CELiD DNA or ceDNA). In some embodiments, ceDNA is derived from the replicative form of the AAV genome (Li et al. PLoS One 2013). In some embodiments, the nucleic acid (e.g., encoding a polypeptide, or a template DNA, or both) is flanked by ITRs, e.g., AAV ITRs, wherein at least one of the ITRs comprises a terminal resolution site and a replication protein binding site (sometimes referred to as a replicative protein binding site). In some embodiments, the ITRs are derived from an adeno-associated virus, e.g., AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, or a combination thereof. In some embodiments, the ITRs are symmetric. In some embodiments, the ITRs are asymmetric. In some embodiments, at least one Rep protein is provided to enable replication of the construct. In some embodiments, the at least one Rep protein is derived from an adeno-associated virus, e.g., AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV 10, AAV 1 1, AAV 12, or a combination thereof. In some embodiments, ceDNA is generated by providing a production cell with (i) DNA flanked by ITRs, e.g., AAV ITRs, and (ii) components required for ITR-dependent replication, e.g., AAV proteins Rep78 and Rep52 (or nucleic acid encoding the proteins). In some embodiments, ceDNA is free of any capsid protein, e.g., is not packaged into an infectious AAV particle. In some embodiments, ceDNA is formulated into LNPs (see, for example, WO2019051289A1).

In some embodiments, the ceDNA vector consists of two self-complementary sequences, e.g., asymmetrical or symmetrical or substantially symmetrical ITRs as defined herein, flanking said expression cassette, wherein the ceDNA vector is not associated with a capsid protein. In some embodiments, the ceDNA vector comprises two self-complementary sequences found in an AAV genome, where at least one ITR comprises an operative Rep-binding element (RBE) (also sometimes referred to herein as “RBS”) and a terminal resolution site (trs) of AAV or a functional variant of the RBE. See, for example, WO2019113310.

In some embodiments, the AAV genome comprises two genes that encode four replication proteins and three capsid proteins, respectively. In some embodiments, the genes are flanked on either side by 145-bp inverted terminal repeats (ITRs). In some embodiments, the virion comprises up to three capsid proteins (Vpl, Vp2, and/or Vp3), e.g., produced in a 1: 1: 10 ratio. In some embodiments, the capsid proteins are produced from the same open reading frame and/or from differential splicing (Vpl) and alternative translational start sites (Vp2 and Vp3, respectively). Generally, Vp3 is the most abundant subunit in the virion and participates in receptor recognition at the cell surface defining the tropism of tire vims. In some embodiments, Vpl comprises a phospholipase domain, e.g., which functions in viral infectivity, in the N-terminus of Vpl.

In some embodiments, packaging capacity of the viral vectors limits the size of the gene modifying system that can be packaged into the vector. For example, the packaging capacity of the AAVs can be about 4.5 kb (e.g., about 3.0, 3.5, 4.0, 4.5, 5.0, 5.5, or 6.0 kb), e.g., including one or two inverted terminal repeats (ITRs), e.g., 145 base ITRs.

In some embodiments, recombinant AAV (rAAV) comprises cis-acting 145-bp ITRs flanking vector transgene cassettes, e.g., providing up to 4.5 kb for packaging of foreign DNA. Subsequent to infection, rAAV can, in some instances, express a fusion protein of the invention and persist without integration into the host genome by existing episomally in circular head-to-tail concatemers. rAAV can be used, for example, in vitro and in vivo. In some embodiments, AAV-mediated gene delivery requires that the length of the coding sequence of the gene is equal or greater in size than the wild-type AAV genome.

AAV delivery of genes that exceed this size and/or the use of large physiological regulatory elements can be accomplished, for example, by dividing the protein(s) to be delivered into two or more fragments. In some embodiments, the N-terminal fragment is fused to an intein-N sequence. In some embodiments, the C- terminal fragment is fused to an intein-C sequence. In embodiments, the fragments are packaged into two or more AAV vectors. In some embodiments, dual AAV vectors are generated by splitting a large transgene expression cassette in two separate halves (5' and 3' ends, or head and tail), e.g., wherein each half of the cassette is packaged in a single AAV vector (of <5 kb). The re-assembly of the full-length transgene expression cassette can, in some embodiments, then be achieved upon co-infection of the same cell by both dual AAV vectors. In some embodiments, co-infection is followed by one or more of: (1) homologous recombination (HR) between 5' and 3' genomes (dual AAV overlapping vectors); (2) ITR-mediated tail- to-head concatemerization of 5' and 3' genomes (dual AAV trans-splicing vectors); and/or (3) a combination of these two mechanisms (dual AAV hybrid vectors). In some embodiments, the use of dual AAV vectors in vivo results in the expression of full-length proteins. In some embodiments, the use of the dual AAV vector platform represents an efficient and viable gene transfer strategy for transgenes of greater than about 4.0. 4.1, 4.2, 4.3, 4.4, 4.5. 4.6, 4.7, 4.8, 4.9, or 5.0 kb in size. In some embodiments, AAV vectors can also be used to transduce cells with target nucleic acids, e.g., in the in vitro production of nucleic acids and peptides. In some embodiments, AAV vectors can be used for in vivo and ex vivo gene therapy procedures (see, e.g., West et al., Virology 160:38-47 (1987); U.S. Patent No. 4,797,368; WO 93/24641; Kotin, Human Gene Therapy 5:793-801 (1994); Muzyczka, J. Clin. Invest.94: 1351 (1994); each of which is incorporated herein by reference in their entirety). Hie construction of recombinant AAV vectors is described in a number of publications, including U.S. Patent No.5,173,414; Tratschin et al., Mol. Cell. Biol.5:3251- 3260 (1985); Tratschin. et al.. Mol. Cell. Biol.4:2072-2081 (1984); Hermonat & Muzyczka, PNAS 81:6466-6470 (1984); and Samulski et al., J. Virol.63: 03822-3828 (1989) (incorporated by reference herein in their entirety).

In some embodiments, a gene modifying polypeptide described herein (e.g., with or without one or more guide nucleic acids) can be delivered using AAV, lentivirus, adenovirus or other plasmid or viral vector types, in particular, using formulations and doses from, for example, U.S. Patent No. 8,454,972 (formulations, doses for adenovirus), U.S. Patent No.8,404,658 (formulations, doses for AAV) and U.S. Patent No.5, 846, 946 (formulations, doses for DNA plasmids) and from clinical trials and publications regarding the clinical trials involving lentivirus, AAV and adenovirus. For example, for AAV, the route of administration, formulation and dose can be as described in U.S. Patent No.8, 454, 972 and as in clinical trials involving AAV. For adenovirus, the route of administration, formulation and dose can be as described in U.S. Patent No.8.404, 658 and as in clinical trials involving adenovirus. For plasmid delivery, the route of administration, formulation and dose can be as described in U.S. Patent No.5, 846.946 and as in clinical studies involving plasmids. Doses can be based on or extrapolated to an average 70 kg individual (e.g. a male adult human), and can be adjusted for patients, subjects, mammals of different weight and species. Frequency of administration is within the ambit of the medical or veterinary practitioner (e g., physician, veterinarian), depending on usual factors including the age, sex, general health, other conditions of the patient or subject and the particular condition or symptoms being addressed. In some embodiments, the viral vectors can be injected into the tissue of interest. For cell-type specific gene modifying, the expression of tire gene modifying polypeptide and optional guide nucleic acid can, in some embodiments, be driven by a cell-type specific promoter.

In some embodiments, AAV allows for low toxicity, for example, due to the purification method not requiring ultracentrifugation of cell particles that can activate the immune response. In some embodiments, AAV allows low probability of causing insertional mutagenesis, for example, because it does not substantially integrate into the host genome.

In some embodiments, AAV has a packaging limit of about 4.4, 4.5, 4.6, 4.7, or 4.75 kb. In some embodiments, a gene modify ing polypeptide-encoding sequence, promoter, and transcription terminator can fit into a single viral vector. SpCas9 (4. 1 kb) may. in some instances, be difficult to package into AAV. Therefore, in some embodiments, a gene modifying polypeptide coding sequence is used that is shorter in length than other gene modifying polypeptide coding sequences or base editors. In some embodiments, the gene modifying polypeptide encoding sequences are less than about 4.5 kb, 4.4 kb, 4.3 kb, 4.2 kb, 4.1 kb, 4 kb, 3.9 kb, 3.8 kb, 3.7 kb, 3.6 kb, 3.5 kb, 3.4 kb, 3.3 kb, 3.2 kb, 3.1 kb, 3 kb, 2.9 kb, 2.8 kb, 2.7 kb, 2.6 kb, 2.5 kb, 2 kb, or 1.5 kb.

An AAV can be AAV1. AAV2. AAV5 or any combination thereof. In some embodiments, the type of AAV is selected with respect to the cells to be targeted; e.g., AAV serotypes 1, 2, 5 or a hybrid capsid AAV1, AAV2, AAV5 or any combination thereof can be selected for targeting brain or neuronal cells; or AAV4 can be selected for targeting cardiac tissue. In some embodiments, AAV8 is selected for delivery to the liver. Exemplary AAV serotypes as to these cells are described, for example, in Grimm, D. et al, J. Virol.82: 5887-5911 (2008) (incorporated herein by reference in its entirety). In some embodiments, AAV refers all serotypes, subtypes, and naturally-occurring AAV as well as recombinant AAV. AAV may be used to refer to the virus itself or a derivative thereof. In some embodiments, AAV includes AAV1, AAV2, AAV3, AAV3B, AAV4, AAV5, AAV6, AAV6.2, AAV7, AAVrh.64Rl, AAVhu.37, AAVrh.8, AAVrh.32.33, AAV8, AAV9, AAV-DJ, AAV2/8, AAVrhlO, AAVLK03, AV10, AAV11, AAV 12, rhlO, and hybrids thereof, avian AAV, bovine AAV, canine AAV, equine AAV, primate AAV, non-primate AAV, and ovine AAV. The genomic sequences of various serotypes of AAV, as well as the sequences of the native terminal repeats (TRs), Rep proteins, and capsid subunits are known in the art. Such sequences may be found in the literature or in public databases such as GenBank. Additional exemplary AAV serotypes are listed in Table 18. Table 18. Exemplary AAV serotypes. In some embodiments, a pharmaceutical composition (e.g., comprising an AAV as described herein) has less than 10% empty capsids, less than 8% empty capsids, less than 7% empty capsids, less than 5% empty capsids, less than 3% empty capsids, or less than 1 % empty capsids. In some embodiments, tire pharmaceutical composition has less than about 5% empty capsids. In some embodiments, the number of empty capsids is below the limit of detection. In some embodiments, it is advantageous for the pharmaceutical composition to have low amounts of empty capsids, e.g.. because empty capsids may generate an adverse response (e.g., immune response, inflammatory response, liver response, and/or cardiac response), e.g., with little or no substantial therapeutic benefit.

In some embodiments, the residual host cell protein (rHCP) in the pharmaceutical composition is less than or equal to 100 ng/ml rHCP per 1 x 10 ¹³ vg/ml, e.g., less than or equal to 40 ng/ml rHCP per 1 x 10 ¹³ vg/ml or 1-50 ng/ml rHCP per 1 x 10 ¹³ vg/ml. In some embodiments, the pharmaceutical composition comprises less than 10 ng rHCP per 1.0 x 10 ¹³ vg, or less than 5 ng rHCP per 1.0 x 10 ^lj vg. less than 4 ng rHCP per 1.0 x 10 ¹³ vg, or less than 3 ng rHCP per 1.0 x 10 ¹³ vg, or any concentration in between. In some embodiments, the residual host cell DNA (hcDNA) in the pharmaceutical composition is less than or equal to 5 x 10 ⁶ pg/ml hcDNA per 1 x 10 ¹³ vg/ml, less than or equal to 1.2 x 10 ⁶ pg/ml hcDNA per 1 x 10 ¹³ vg/ml, or 1 x 10 ⁵ pg/ml hcDNA per 1 x 10 ¹³ vg/ml. In some embodiments, the residual host cell DNA in said pharmaceutical composition is less than 5.0 x 10 ⁵ pg per 1 x 10 ¹³ vg, less than 2.0 x 10 ⁵ pg per 1.0 x 10 ¹³ vg, less than 1.1 x 10 ⁵ pg per 1.0 x 10 ¹³ vg, less than 1.0 x 10 ⁵ pg hcDNA per 1.0 x 10 ¹³ vg, less than 0.9 x 10 ⁵ pg hcDNA per 1.0 x 10 ¹³ vg, less than 0.8 x 10 ⁵ pg hcDNA per 1.0 x 10 ¹³ vg, or any concentration in between.

In some embodiments, the residual plasmid DNA in the pharmaceutical composition is less than or equal to 1.7 x 10 ⁵ pg/ml per 1.0 x 10 ¹³ vg/ml, or 1 x 10 ⁵ pg/ml per 1 x 1.0 x 10 ¹³ vg/ml, or 1.7 x 10 ⁶ pg/ml per 1.0 x 10 ¹³ vg/ml. In some embodiments, the residual DNA plasmid in the pharmaceutical composition is less than 10.0 x 10 ⁵ pg by 1.0 x 10 ¹³ vg. less than 8.0 x 10 ⁵ pg by 1.0 x 10 ¹³ vg or less than 6.8 x 10 ⁵ pg by 1.0 x 10 ¹³ vg. In embodiments, the pharmaceutical composition comprises less than 0.5 ng per 1.0 x 10 ¹³ vg, less than 0.3 ng per 1.0 x 10 ¹³ vg, less than 0.22 ng per 1.0 x 10 ¹³ vg or less than 0.2 ng per 1.0 x 10 ¹³ vg or any intermediate concentration of bovine serum albumin (BSA). In embodiments, the benzonase in the phannaceutical composition is less than 0.2 ng by 1.0 x 10 ¹³ vg, less than 0.1 ng by 1.0 x 10 ¹³ vg. less than 0.09 ng by 1.0 x 10 ¹³ vg, less than 0.08 ng by 1.0 x 10 ¹³ vg or any intermediate concentration. In embodiments, Poloxamer 188 in the pharmaceutical composition is about 10 to 150 ppm, about 15 to 100 ppm or about 20 to 80 ppm. In embodiments, the cesium in the pharmaceutical composition is less than 50 pg / g (ppm), less than 30 pg / g (ppm) or less than 20 pg / g (ppm) or any intermediate concentration. In embodiments, the pharmaceutical composition comprises total impurities, e.g., as determined by SDS-PAGE, of less than 10%, less than 8%, less than 7%, less than 6%, less than 5%, less than 4%, less than 3%, less than 2%, or any percentage in between. In embodiments, the total purity, e.g., as determined by SDS-PAGE, is greater than 90%, greater than 92%, greater than 93%, greater than 94%, greater than 95%, greater than 96%, greater than 97%. greater than 98%, or any percentage in between. In embodiments, no single unnamed related impurity, e.g., as measured by SDS-PAGE, is greater than 5%, greater than 4%, greater than 3% or greater than 2%, or any percentage in between. In embodiments, the pharmaceutical composition comprises a percentage of fdled capsids relative to total capsids (e.g., peak 1 + peak 2 as measured by analytical ultracentrifugation) of greater than 85%, greater than 86%, greater than 87%, greater than 88%, greater than 89%, greater than 90%, greater than 91%, greater than 91.9%, greater than 92%, greater than 93%, or any percentage in between. In embodiments of the pharmaceutical composition, the percentage of filled capsids measured in peak 1 by analytical ultracentrifugation is 20- 80%, 25-75%, 30-75%, 35-75%, or 37.4-70.3%. In embodiments of the pharmaceutical composition, the percentage of filled capsids measured in peak 2 by analytical ultracentrifugation is 20-80%, 20-70%, 22- 65%, 24-62%, or 24.9-60.1%.

In one embodiment, the pharmaceutical composition comprises a genomic titer of 1.0 to 5.0 x 10 ¹³ vg / mb, 1.2 to 3.0 x 10 ¹³ vg / mL or 1.7 to 2.3 x 10 ¹³ vg / ml. In one embodiment, the pharmaceutical composition exhibits a biological load of less than 5 CFU / mL, less than 4 CFU / mL, less than 3 CFU / mL, less than 2 CFU / mL or less than 1 CFU / mL or any intermediate contraction. In embodiments, the amount of endotoxin according to USP, for example, USP <85> (incorporated by reference in its entirety) is less than 1.0 EU / mL, less than 0.8 EU / mL or less than 0.75 EU / mL. In embodiments, the osmolarity of a pharmaceutical composition according to USP, for example, USP <785> (incorporated by reference in its entirety) is 350 to 450 mOsm / kg, 370 to 440 mOsm / kg or 390 to 430 mOsm / kg. In embodiments, the pharmaceutical composition contains less than 1200 particles that are greater than 25 pm per container, less than 1000 particles that are greater than 25 pm per container, less than 500 particles that are greater than 25 pm per container or any intermediate value. In embodiments, the pharmaceutical composition contains less than 10,000 particles that are greater than 10 pm per container, less than 8000 particles that are greater than 10 pm per container or less than 600 particles that are greater than 10 pm per container.

In one embodiment, the pharmaceutical composition has a genomic titer of 0.5 to 5.0 x 10 ¹³ vg / mL, 1 .0 to 4.0 x 10 ¹³ vg / mL. 1 .5 to 3.0 x 10 ¹³ vg / ml or 1 .7 to 2.3 x 10 ¹³ vg / ml. In one embodiment, the pharmaceutical composition described herein comprises one or more of the following: less than about 0.09 ng benzonase per 1.0 x 10 ¹³ vg, less than about 30 pg / g (ppm ) of cesium, about 20 to 80 ppm Poloxamer 188, less than about 0.22 ng BSA per 1.0 x 10 ¹³ vg, less than about 6.8 x 10 ⁵ pg of residual DNA plasmid per 1.0 x 10 ¹³ vg, less than about 1 . 1 x 10 ⁵ pg of residual hcDNA per 1.0 x 10 ¹³ vg, less than about 4 ng of rHCP per 1.0 x 10 ¹³ vg, pH 7.7 to 8.3, about 390 to 430 mOsm / kg, less than about 600 particles that are > 25 pm in size per container, less than about 6000 particles that are > 10 pm in size per container, about 1.7 x 10 ¹³ - 2.3 x 10 ¹³ vg / mL genomic titer, infectious titer of about 3.9 x 10 ⁸ to 8.4 x 10 ¹⁰ IU per 1.0 x 10 ¹³ vg, total protein of about 100-300 pg per 1.0 x 10 ¹³ vg. mean survival of >24 days in A7SMA mice with about 7.5 x 10 ^r ' vg / kg dose of viral vector, about 70 to 130% relative potency based on an in vitro cell based assay and / or less than about 5% empty capsid. In various embodiments, the pharmaceutical compositions described herein comprise any of the viral particles discussed here, retain a potency of between ± 20%, between ± 15%, between ± 10% or within ± 5% of a reference standard. In some embodiments, potency is measured using a suitable in vitro cell assay or in vivo animal model.

Additional methods of preparation, characterization, and dosing AAV particles are taught in WO2019094253, which is incorporated herein by reference in its entirety.

Additional rAAV constructs that can be employed consonant with the invention include those described in Wang et al 2019, available at: //doi.org/10.1038/s41573-019-0012-9, including Table 1 thereof, which is incorporated by reference in its entirety.

Lipid Nanoparticles

The methods and systems provided herein may employ any suitable carrier or delivery modality, including, in certain embodiments, lipid nanoparticles (LNPs). Lipid nanoparticles, in some embodiments, comprise one or more ionic lipids, such as non-cationic lipids (e.g., neutral or anionic, or zwitterionic lipids); one or more conjugated lipids (such as PEG-conjugated lipids or lipids conjugated to polymers described in Table 5 of WO2019217941; incorporated herein by reference in its entirety); one or more sterols (e.g., cholesterol); and, optionally, one or more targeting molecules (e.g., conjugated receptors, receptor ligands, antibodies); or combinations of the foregoing.

Lipids that can be used in nanoparticle formations (e.g., lipid nanoparticles) include, for example those described in Table 4 of WO2019217941, which is incorporated by reference — e.g., a lipid- containing nanoparticle can comprise one or more of the lipids in Table 4 of WO2019217941. Lipid nanoparticles can include additional elements, such as polymers, such as the polymers described in Table 5 of WO2019217941, incorporated by reference.

In some embodiments, conjugated lipids, when present, can include one or more of PEG- diacylglycerol (DAG) (such as l-(monomethoxy-polyethyleneglycol)-2,3- dimyristoylglycerol (PEG- DMG)), PEG-dialkyloxypropyl (DAA), PEG-phospholipid, PEG- ceramide (Cer), a pegylated phosphatidylethanoloamine (PEG-PE), PEG succinate diacylglycerol (PEGS-DAG) (such as 4-0-(2',3'- di(tetradecanoyloxy)propyl-l-0-(w- methoxy(polyethoxy)ethyl) butanedioate (PEG-S-DMG)), PEG dialkoxypropylcarbam, N- (carbonyl-methoxypoly ethylene glycol 2000)- 1 ,2-distearoyl-sn-glycero-3- phosphoethanolamine sodium salt, and those described in Table 2 of W02019051289 (incorporated by reference), and combinations of tire foregoing.

In some embodiments, sterols that can be incorporated into lipid nanoparticles include one or more of cholesterol or cholesterol derivatives, such as those in W02009/127060 or US2010/0130588, which are incorporated by reference. Additional exemplary sterols include phytosterols, including those described in Eygeris et al (2020), dx.doi.org/10.1021/acs.nanolett.0c01386, incorporated herein by reference.

In some embodiments, the lipid particle comprises an ionizable lipid, a non-cationic lipid, a conjugated lipid that inhibits aggregation of particles, and a sterol. The amounts of these components can be varied independently and to achieve desired properties. For example, in some embodiments, the lipid nanoparticle comprises an ionizable lipid is in an amount from about 20 mol % to about 90 mol % of the total lipids (in other embodiments it may be 20-70% (mol), 30-60% (mol) or 40-50% (mol); about 50 mol % to about 90 mol % of the total lipid present in the lipid nanoparticle), a non-cationic lipid in an amount from about 5 mol % to about 30 mol % of the total lipids, a conjugated lipid in an amount from about 0.5 mol % to about 20 mol % of the total lipids, and a sterol in an amount from about 20 mol % to about 50 mol % of the total lipids. The ratio of total lipid to nucleic acid (e.g., encoding the gene modifying polypeptide or template nucleic acid) can be varied as desired. For example, the total lipid to nucleic acid (mass or weight) ratio can be from about 10: 1 to about 30: 1.

In some embodiments, an ionizable lipid may be a cationic lipid, an ionizable cationic lipid, e.g., a cationic lipid that can exist in a positively charged or neutral form depending on pH, or an amine- containing lipid that can be readily protonated. In some embodiments, the cationic lipid is a lipid capable of being positively charged, e.g., under physiological conditions. Exemplary cationic lipids include one or more amine group(s) which bear the positive charge. In some embodiments, the lipid particle comprises a cationic lipid in formulation with one or more of neutral lipids, ionizable amine-containing lipids, biodegradable alkyn lipids, steroids, phospholipids including polyunsaturated lipids, structural lipids (e.g., sterols), PEG, cholesterol and polymer conjugated lipids. In some embodiments, the cationic lipid may be an ionizable cationic lipid. An exemplary cationic lipid as disclosed herein may have an effective pKa over 6.0. In embodiments, a lipid nanoparticle may comprise a second cationic lipid having a different effective pKa (e.g., greater than the first effective pKa), than the first cationic lipid. A lipid nanoparticle may comprise between 40 and 60 mol percent of a cationic lipid, a neutral lipid, a steroid, a polymer conjugated lipid, and a therapeutic agent, e.g., a nucleic acid (e.g., RNA) described herein (e.g., a template nucleic acid or a nucleic acid encoding a gene modifying polypeptide), encapsulated within or associated with the lipid nanoparticle. In some embodiments, the nucleic acid is co-formulated with the cationic lipid. The nucleic acid may be adsorbed to the surface of an LNP, e.g., an LNP comprising a cationic lipid. In some embodiments, the nucleic acid may be encapsulated in an LNP, e.g., an LNP comprising a cationic lipid. In some embodiments, the lipid nanoparticle may comprise a targeting moiety, e.g., coated with a targeting agent. In embodiments, the LNP formulation is biodegradable. In some embodiments, a lipid nanoparticle comprising one or more lipid described herein, e.g., Formula (i), (ii), (ii), (vii) and/or (ix) encapsulates at least 1%, at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98% or 100% of an RNA molecule, e.g., template RNA and/or a mRNA encoding the gene modifying polypeptide.

In some embodiments, tire lipid to nucleic acid ratio (mass/mass ratio: w/w ratio) can be in the range of from about 1 : 1 to about 25: 1. from about 10: 1 to about 14: 1, from about 3 : 1 to about 15: 1, from about 4: 1 to about 10: 1, from about 5: 1 to about 9: 1, or about 6: 1 to about 9: 1. The amounts of lipids and nucleic acid can be adjusted to provide a desired N/P ratio, for example, N/P ratio of 3, 4, 5, 6, 7, 8, 9, 10 or higher. Generally, the lipid nanoparticle formulation’s overall lipid content can range from about 5 mg/ml to about 30 mg/mL.

Exemplary ionizable lipids that can be used in lipid nanoparticle fonnulations include, without limitation, those listed in Table 1 ofWO2019051289, incorporated herein by reference. Additional exemplary' lipids include, without limitation, one or more of the following formulae: X of US2016/0311759; I of US20150376115 or in US2016/0376224; I, II or III of US20160151284; I, IA, II, or IIA of US20170210967; I-c of US20150140070; A of US2013/0178541; I of US2013/0303587 or US2013/0123338; I of US2015/0141678; II. Ill, IV, or V of US2015/0239926; I of US2017/0119904; I or II of WO2017/117528; A of US2012/0149894; A of US2015/0057373; A of WO2013/116126; A of US2013/0090372: A of US2013/0274523; A of US2013/0274504; A of US2013/0053572; A of W02013/016058; A of W02012/162210: 1 of US2008/042973: 1, II, III, or IV of US2012/01287670; I or II of US2014/0200257; I, II, or III of US2015/0203446; I or III of US2015/0005363; I, IA, IB, IC, ID, II, IIA, IIB, IIC, IID, or III-XXIV of US2014/0308304; of US2013/0338210; I, II, III, or IV of W02009/132131; A of US2012/01011478; I or XXXV of US2012/0027796; XIV or XVII of US2012/0058144: of US2013/0323269; I ofUS2011/0117125; I, IL or III of US2011/0256175; I, II, III, IV, V. VI. VII, VIII. IX. X, XI, XII of US2012/0202871; 1, IL 111. IV. V, VI, VII, VIII, X. XII, XIII, XIV. XV, or XVI of US201 1/0076335; I or II of US2006/008378; I of US2013/0123338; I or X-A-Y-Z of US2015/0064242; XVI, XVII, or XVIII of US2013/0022649; I, II, or III of US2013/0116307; I, II, or III of US2013/0116307; I or II of US2010/0062967; I-X of US2013/0189351; I of US2014/0039032; V of US2018/0028664; I of US2016/0317458; I of US2013/0195920; 5, 6, or 10 of US10,221,127; III-3 of WO2018/081480; 1-5 or 1-8 of W02020/081938; 18 or 25 of US9,867,888; A of US2019/0136231; II of WO2020/219876; 1 of US2012/0027803; OF-02 of US2019/0240349; 23 of US10,086,013; cKK- E12/A6 of Miao et al (2020); C12-200 of W02010/053572; 7C1 of Dahlman et al (2017); 304-013 or 503-013 of Whitehead et al; TS-P4C2 of US9,708,628; I ofW02020/106946; I of W02020/106946.

In some embodiments, tire ionizable lipid is MC3 (6Z,9Z,28Z,3 lZ)-heptatriaconta- 6,9,28,3 1- tetraen-19-yl-4-(dimethylamino) butanoate (DLin-MC3-DMA or MC3), e.g., as described in Example 9 of WO2019051289A9 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is the lipid ATX-002, e.g., as described in Example 10 ofWO2019051289A9 (incorporated by reference herein in its entirety)- In some embodiments, the ionizable lipid is (13Z,16Z)- A,A-dimethyl-3- nonyldocosa-13, 16-dien-l-amine (Compound 32), e.g., as described in Example 11 of WO2019051289A9 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is Compound 6 or Compound 22, e.g., as described in Example 12 ofWO2019051289A9 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is heptadecan- 9-yl 8-((2-hydroxyethyl)(6-oxo-6-(undecyloxy)hexyl)amino)octanoat e (SM-102); e.g., as described in Example 1 of US9,867,888(incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is 9Z,12Z)-3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3- (diethylamino)propoxy)carbonyl)oxy)methyl)propyl octadeca-9,12-dienoate (LP01) e.g., as synthesized in Example 13 of W02015/095340(incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is Di((Z)-non-2-en-l-yl) 9-((4- dimethylamino)butanoyl)oxy)heptadecanedioate (L319), e.g. as synthesized in Example 7, 8, or 9 of US2012/0027803 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is l,r-((2-(4-(2-((2-(Bis(2-hydroxydodecyl)amino)ethyl)(2 -hydroxydodecyl) amino)ethyl)piperazin- l-yl)ethyl)azanediyl)bis(dodecan-2-ol) (C12-200), e.g., as synthesized in Examples 14 and 16 of W02010/053572 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is; Imidazole cholesterol ester (ICE) lipid (3S, 10R, 13R, 17R)-10, 13-dimethyl-17- ((R)-6- methylheptan-2-yl)-2, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17-tetradecahydro-lH- cyclopenta[a]phenanthren-3-yl 3-(lH-imidazol-4-yl)propanoate, e.g., Structure (I) from W02020/106946 (incorporated by reference herein in its entirety).

Some non-limiting examples of lipid compounds that may be used (e.g., in combination with other lipid components) to fonn lipid nanoparticles for the delivery of compositions described herein, e.g., nucleic acid (e.g., RNA) described herein (e.g., a template nucleic acid or a nucleic acid encoding a gene modifying polypeptide) includes,

In some embodiments an LNP comprising Formula (i) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells. In some embodiments an LNP comprising Formula (ii) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

In some embodiments an LNP comprising Formula (iii) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells. In some embodiments an LNP comprising Formula (v) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

In some embodiments an LNP comprising Formula (vi) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

In some embodiments an LNP comprising Formula (viii) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

In some embodiments an LNP comprising Formula (ix) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

wherein

X ¹ is 0, NR ¹ , or a direct bond, X ² is C2-5 alkylene, X ³ is C(=0) or a direct bond, R ¹ is H or Me, R ³ is Ci-3 alkyl, R ² is Ci-3 alkyl, or R ² taken together with the nitrogen atom to which it is attached and 1-3 carbon atoms of X ² form a 4-. 5-, or 6-membered ring, or X ¹ is NR ¹ , R ¹ and R ² taken together with the nitrogen atoms to which they are attached form a 5- or 6-membered ring, or R ² taken together with R' and the nitrogen atom to which they are attached form a 5-, 6-, or 7-membered ring, Y ¹ is C2-12 alkylene, Y ² is selected from (in either orientation), (in either orientation), (in either orientation), n is 0 to 3, R ⁴ is Ci- 15 alkyl, Z ¹ is Ci-6 alkylene or a direct bond,

(in either orientation) or absent, provided that if Z ¹ is a direct bond, Z ² is absent;

R ⁵ is C5-9 alkyl or C6-10 alkoxy, R ⁶ is C5-9 alkyl or C6-10 alkoxy, W is methylene or a direct bond, and R ⁷ is H or Me, or a salt thereof, provided that if R ³ and R ² are C2 alkyls, X ¹ is 0, X ² is linear C3 alkylene, X ³ is C(=0), Y ¹ is linear Ce alkylene, (Y ² )n-R ⁴ is

, R ⁴ is linear C5 alkyl, Z ¹ is C2 alkylene, Z ² is absent, W is methylene, and R ⁷ is H, then R ⁵ and R ⁶ are not

Cx alkoxy. In some embodiments an LNP comprising Formula (xii) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

In some embodiments an LNP comprising Formula (xi) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

In some embodiments an LNP comprises a compound of Formula (xiii) and a compound of Formula (xiv).

In some embodiments an LNP comprising Formula (xv) is used to deliver a gene modifying composition described herein to the liver and/or hepatocyte cells.

In some embodiments an LNP comprising a formulation of Formula (xvi) is used to deliver a gene modifying composition described herein to the lung endothelial cells. (xviii)

(a)

In some embodiments, a lipid compound used to form lipid nanoparticles for the delivery of compositions described herein, e.g., nucleic acid (e.g., RNA) described herein (e.g., a template nucleic acid or a nucleic acid encoding a gene modifying polypeptide) is made by one of the following reactions:

Exemplary non-cationic lipids include, but are not limited to, distearoyl-sn-glycero- phosphoethanolamine, distearoylphosphatidylcholine (DSPC), dioleoylphosphatidylcholine (DOPC), dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylglycerol (DOPG), dipalmitoylphosphatidylglycerol (DPPG), dioleoyl-phosphatidylethanolamine (DOPE), 1,2-dioleoyl-sn- glycero-3 -phosphoethanolamine (DOPE), palmitoyloleoylphosphatidylcholine (POPC), palmitoyloleoylphosphatidylethanolamine (POPE), dioleoyl-phosphatidylethanolamine 4-(N- maleimidomethyl)-cyclohexane- 1 - carboxylate (DOPE-mal), dipalmitoyl phosphatidyl ethanolamine (DPPE), dimyristoylphosphoethanolamine (DMPE), distearoyl-phosphatidyl-ethanolamine (DSPE), monomethyl-phosphatidylethanolamine (such as 16-0-monomethyl PE), dimethylphosphatidylethanolamine (such as 16-O-dimethyl PE), 18-1 -trans PE, l-stearoyl-2-oleoyl- phosphatidy ethanolamine (SOPE), hydrogenated soy phosphatidylcholine (HSPC), egg phosphatidylcholine (EPC), dioleoylphosphatidylserine (DOPS), sphingomyelin (SM), dimyristoyl phosphatidylcholine (DMPC), dimyristoyl phosphatidylglycerol (DMPG), distearoylphosphatidylglycerol (DSPG), dierucoylphosphatidylcholine (DEPC), palmitoyloleyolphosphatidylglycerol (POPG), dielaidoyl-phosphatidylethanolamine (DEPE), lecithin, phosphatidylethanolamine, lysolecithin, lysophosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, sphingomyelin, egg sphingomyelin (ESM), cephalin, cardiolipin, phosphatidicacid, cerebrosides, dicetylphosphate, lysophosphatidylcholine, dilinoleoylphosphatidylcholine, or mixtures thereof. It is understood that other diacylphosphatidylcholine and diacylphosphatidylethanolamine phospholipids can also be used. The acyl groups in these lipids are preferably acyl groups derived from fatty acids having C 10-C24 carbon chains, e.g., lauroyl, myristoyl, paimitoyl, stearoyl, or oleoyl. Additional exemplary lipids, in certain embodiments, include, without limitation, those described in Kim et al. (2020) dx.doi.org/10.1021/acs.nanolett.0c01386, incorporated herein by reference. Such lipids include, in some embodiments, plant lipids found to improve liver transfection with mRNA (e g., DGTS). In some embodiments, the non-cationic lipid may have the following structure,

Other examples of non-cationic lipids suitable for use in the lipid nanopartieles include, without limitation, nonphosphorous lipids such as. e.g., stearylamine, dodeeylamine, hexadecylamine, acetyl palmitate, glycerol ricinoleate, hexadecyl stereate, isopropyl myristate, amphoteric acrylic polymers, triethanolamine-lauryl sulfate, alkyl-aryl sulfate polyethyloxylated fatty acid amides, dioctadecyl dimethyl ammonium bromide, ceramide, sphingomyelin, and the like. Other non-cationic lipids are described in WO2017/099823 or US patent publication US2018/0028664, tire contents of which is incorporated herein by reference in their entirety.

In some embodiments, the non-cationic lipid is oleic acid or a compound of Fonnula I, II. or IV of US2018/0028664, incorporated herein by reference in its entirety. The non-cationic lipid can comprise, for example, 0-30% (mol) of the total lipid present in the lipid nanoparticle. In some embodiments, the non-cationic lipid content is 5-20% (mol) or 10-15% (mol) ofthe total lipid present in the lipid nanoparticle. In embodiments, the molar ratio of ionizable lipid to the neutral lipid ranges from about 2: 1 to about 8: 1 (e.g., about 2: 1, 3: 1, 4: 1, 5: 1, 6: 1, 7: 1, or 8: 1).

In some embodiments, tire lipid nanoparticles do not comprise any phospholipids.

In some aspects, the lipid nanoparticle can further comprise a component, such as a sterol, to provide membrane integrity. One exemplary' sterol that can be used in the lipid nanoparticle is cholesterol and derivatives thereof. Non-limiting examples of cholesterol derivatives include polar analogues such as 5a-choiestanol, 53-coprostanol, choiesteryl-(2 -hydroxy)-ethyl ether, choiesteryl-(4'- hydroxy)-butyl ether, and 6-ketocholestanol; non-polar analogues such as 5a-cholestane, cholestenone, 5a-cholestanone, 5p- cholestanone, and cholesteryl decanoate; and mixtures thereof. In some embodiments, the cholesterol derivative is a polar analogue, e.g., choiesteryl-(4'-hydroxy)-butyl ether. Exemplary cholesterol derivatives are described in PCT publication W02009/ 127060 and US patent publication US2010/0130588, each of which is incorporated herein by reference in its entirety.

In some embodiments, the component providing membrane integrity, such as a sterol, can comprise 0-50% (mol) (e.g., 0-10%, 10-20%, 20-30%, 30-40%, or 40-50%) of the total lipid present in the lipid nanoparticle. In some embodiments, such a component is 20-50% (mol) 30-40% (mol) of tire total lipid content of the lipid nanoparticle.

In some embodiments, the lipid nanoparticle can comprise a polyethylene glycol (PEG) or a conjugated lipid molecule. Generally, these are used to inhibit aggregation of lipid nanoparticles and/or provide steric stabilization. Exemplary' conjugated lipids include, but are not limited to, PEG-lipid conjugates, polyoxazoline (POZ)-lipid conjugates, polyamide-lipid conjugates (such as ATTA-lipid conjugates), cationic-polymer lipid (CPL) conjugates, and mixtures thereof. In some embodiments, the conjugated lipid molecule is a PEG-lipid conjugate, for example, a (methoxy polyethylene glycol)- conjugated lipid.

Exemplary PEG-lipid conjugates include, but are not limited to, PEG-diacylglycerol (DAG) (such as l-(monomethoxy-polyethyleneglycol)-2,3-dimyristoylglycerol (PEG-DMG)), PEG-dialkyloxypropyl (DAA), PEG-phospholipid, PEG-ceramide (Cer), a pegylated phosphatidylethanoloamine (PEG-PE), 1,2- dimyristoyl-sn-glycerol. methoxypoly ethylene glycol (DMG-PEG-2K). PEG succinate diacylglycerol (PEGS-DAG) (such as 4-0-(2',3'-di(tetradecanoyloxy)propyl-l-0-(w-methoxy(polyeth oxy)ethyl) butanedioate (PEG-S-DMG)), PEG dialkoxypropylcarbam, N-(carbonyl-methoxypolyethylene glycol 2000)-1,2-distearoyl-sn-glycero-3-phosphoethanolamine sodium salt, or a mixture thereof. Additional exemplary PEG-lipid conjugates are described, for example, in US5,885,613, US6,287,591, US2003/0077829, US2003/0077829, US2005/0175682, US2008/0020058, US2011/0117125,

US2010/0130588, US2016/0376224, US2017/0119904, and US/099823, the contents of all of which are incorporated herein by reference in their entirety. In some embodiments, a PEG-lipid is a compound of Formula III, III-a-I, III-a-2, III-b-1, III-b-2, or V of US2018/0028664, the content of which is incorporated herein by reference in its entirety. In some embodiments, a PEG-lipid is of Formula II of US20150376115 or US2016/0376224, the content of both of which is incorporated herein by reference in its entirety. In some embodiments, the PEG-DAA conjugate can be, for example, PEG- dilauryloxypropyl, PEG- dimyristyloxypropyl, PEG-dipalmitj loxypropyl, or PEG-distearyloxypropyl. The PEG-lipid can be one or more of PEG-DMG, PEG-dilaurylglycerol, PEG-dipalmitoylglycerol, PEG- disterylglycerol, PEG-dilaurylglycamide, PEG-dimyristylglycamide, PEG- dipalmitoylglycamide, PEG- disterylglycamide. PEG-chole sterol (l-[8'-(Cholest-5-en-3 [beta]- oxy)carboxamido-3',6'-dioxaoctanyl] carbamoyl-[omega]-methyl-poly(ethylene glycol), PEG- DMB (3.4-Ditetradecoxylbenzyl- [omega]- methyl-poly(ethylene glycol) ether), and 1,2- dimyristoyl-sn-glycero-3-phosphoethanolamine-N- [methoxy(polyethylene glycol)-2000]. In some embodiments, the PEG-lipid comprises PEG-DMG, 1,2- dimyristoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(poly ethylene glycol)-2000] . In some embodiments, tire PEG-lipid comprises a structure selected from: (xxv).

In some embodiments, lipids conjugated with a molecule other than a PEG can also be used in place of PEG-lipid. For example, polyoxazoline (POZ)-lipid conjugates, polyamide-lipid conjugates (such as ATTA-lipid conjugates), and cationic-polymer lipid (GPL) conjugates can be used in place of or in addition to the PEG-lipid.

Exemplary conjugated lipids, i.e., PEG-lipids, (POZ)-lipid conjugates, ATTA-lipid conjugates and cationic polymer-lipids are described in the PCT and LIS patent applications listed in Table 2 of W02019051289A9 and in W02020106946A1, the contents of all of which are incorporated herein by reference in their entirety.

In some embodiments an LNP comprises a compound of Formula (xix). a compound of Formula (xxi) and a compound of Formula (xxv). In some embodiments an LNP comprising a formulation of Formula (xix), Formula (xxi) and Formula (xxv)is used to deliver a gene modifying composition described herein to the lung or pulmonary’ cells.

In some embodiments, a lipid nanoparticlc may comprise one or more cationic lipids selected from Formula (i), Formula (ii), Formula (iii), Formula (vii), and Fonnula (ix). In some embodiments, the LNP may further comprise one or more neutral lipid, e.g., DSPC, DPPC, DMPC, DOPC, POPC, DOPE, SM, a steroid, e.g., cholesterol, and/or one or more polymer conjugated lipid, e.g., a pegylated lipid, e.g., PEG-DAG, PEG-PE, PEG-S-DAG, PEG-cer or a PEG dialky oxypropyl carbamate.

In some embodiments, the PEG or the conjugated lipid can comprise 0-20% (mol) of the total lipid present in the lipid nanoparticle. In some embodiments, PEG or the conjugated lipid content is 0.5- 10% or 2-5% (mol) of the total lipid present in the lipid nanoparticle. Molar ratios of the ionizable lipid, non-cationic-lipid. sterol, and PEG/conjugated lipid can be varied as needed. For example, the lipid particle can comprise 30-70% ionizable lipid by mole or by total weight of the composition, 0-60% cholesterol by mole or by total weight of the composition, 0-30% non-cationic-lipid by mole or by total weight of the composition and 1-10% conjugated lipid by mole or by total weight of the composition. Preferably, the composition comprises 30-40% ionizable lipid by mole or by total weight of tire composition, 40-50% cholesterol by mole or by total weight of the composition, and 10- 20% non- cationic-lipid by mole or by total weight of the composition. In some other embodiments, the composition is 50-75% ionizable lipid by mole or by total weight of the composition, 20-40% cholesterol by mole or by total weight of the composition, and 5 to 10% non-cationic-lipid, by mole or by total weight of the composition and 1-10% conjugated lipid by mole or by total weight of the composition. The composition may contain 60-70% ionizable lipid by mole or by total weight of the composition, 25-35% cholesterol bymole or by total weight of the composition, and 5-10% non-cationic-lipid by mole or by total weight of the composition. The composition may also contain up to 90% ionizable lipid by mole or by total weight of the composition and 2 to 15% non-cationic lipid by mole or by total weight of the composition. The formulation may also be a lipid nanoparticle formulation, for example comprising 8-30% ionizable lipid by mole or by total weight of the composition, 5-30% non- cationic lipid by mole or by total weight of the composition, and 0-20% cholesterol by mole or by total weight of the composition; 4-25% ionizable lipid by mole or by total weight of the composition, 4-25% non-cationic lipid by mole or by total weight of the composition, 2 to 25% cholesterol by mole or by total weight of the composition, 10 to 35% conjugate lipid by mole or by total weight of the composition, and 5% cholesterol by mole or by total weight of the composition; or 2-30% ionizable lipid by mole or by total weight of the composition, 2-30% non-cationic lipid by mole or by total weight of tire composition, 1 to 15% cholesterol by mole or by total weight of the composition, 2 to 35% conjugate lipid by mole or by total weight of the composition, and 1-20% cholesterol by mole or by total weight of the composition: or even up to 90% ionizable lipid by mole or by total weight of the composition and 2-10% non-cationic lipids by mole or by total weight of the composition, or even 100% cationic lipid by mole or by total weight of the composition. In some embodiments, the lipid particle formulation comprises ionizable lipid, phospholipid, cholesterol and a PEG-ylated lipid in a molar ratio of 50: 10:38.5: 1.5. In some other embodiments, the lipid particle formulation comprises ionizable lipid, cholesterol and a PEG-ylated lipid in a molar ratio of 60:38.5: 1.5.

In some embodiments, the lipid particle comprises ionizable lipid, non-cationic lipid (e.g. phospholipid), a sterol (e g., cholesterol) and a PEG-ylated lipid, where the molar ratio of lipids ranges from 20 to 70 mole percent for the ionizable lipid, with a target of 40-60, the mole percent of non-cationic lipid ranges from 0 to 30, with a target of 0 to 15, the mole percent of sterol ranges from 20 to 70, with a target of 30 to 50, and the mole percent of PEG-ylated lipid ranges from 1 to 6, with a target of 2 to 5.

In some embodiments, the lipid particle comprises ionizable lipid / non-cationic- lipid / sterol / conjugated lipid at a molar ratio of 50: 10:38.5: 1.5.

In an aspect, the disclosure provides a lipid nanoparticle formulation comprising phospholipids, lecithin, phosphatidylcholine and phosphatidylethanolamine.

In some embodiments, one or more additional compounds can also be included. Those compounds can be administered separately or the additional compounds can be included in the lipid nanoparticles of the invention. In other words, the lipid nanoparticles can contain other compounds in addition to the nucleic acid or at least a second nucleic acid, different than the first. Without limitations, other additional compounds can be selected from the group consisting of small or large organic or inorganic molecules, monosaccharides, disaccharides, trisaccharides, oligosaccharides, polysaccharides, peptides, proteins, peptide analogs and derivatives thereof, peptidomimetics, nucleic acids, nucleic acid analogs and derivatives, an extract made from biological materials, or any combinations thereof.

In some embodiments, a lipid nanoparticle (or a formulation comprising lipid nanoparticles) lacks reactive impurities (e.g., aldehydes or ketones), or comprises less than a preselected level of reactive impurities (e.g., aldehydes or ketones). While not wishing to be bound by theory, in some embodiments, a lipid reagent is used to make a lipid nanoparticle formulation, and the lipid reagent may comprise a contaminating reactive impurity (e.g., an aldehyde or ketone). A lipid regent may be selected for manufacturing based on having less than a preselected level of reactive impurities (e.g., aldehydes or ketones). Without wishing to be bound by theory, in some embodiments, aldehydes can cause modification and damage of RNA, e.g., cross-linking between bases and/or covalently conjugating lipid to RNA (e.g., forming lipid-RNA adducts). This may, in some instances, lead to failure of a reverse transcriptase reaction and/or incorporation of inappropriate bases, e.g., at the site(s) of lesion(s), e.g., a mutation in a newly synthesized target DNA.

In some embodiments, a lipid nanoparticle formulation is produced using a lipid reagent comprising less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% total reactive impurity' (e.g., aldehyde) content. In some embodiments, a lipid nanoparticle formulation is produced using a lipid reagent comprising less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species. In some embodiments, a lipid nanoparticle formulation is produced using a lipid reagent comprising: (i) less than 5%, 4%. 3%, 2%, 1%. 0.9%, 0.8%, 0.7%, 0.6%. 0.5%, 0.4%, 0.3%, 0.2%. or 0.1% total reactive impunty (e.g., aldehyde) content; and (ii) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0. 1% of any single reactive impurity (e.g., aldehyde) species. In some embodiments, the lipid nanoparticle formulation is produced using a plurality of lipid reagents, and each lipid reagent of the plurality independently meets one or more criterion described in this paragraph. In some embodiments, each lipid reagent of the plurality meets the same criterion, e.g., a criterion of this paragraph.

In some embodiments, the lipid nanoparticle formulation comprises less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% total reactive impurity (e.g., aldehyde) content. In some embodiments, the lipid nanoparticle formulation comprises less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species. In some embodiments, the lipid nanoparticle formulation comprises: (i) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1%total reactive impurity (e.g., aldehyde) content; and (ii) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species.

In some embodiments, one or more, or optionally all, of the lipid reagents used for a lipid nanoparticle as described herein or a fonnulation thereof comprise less than 5%, 4%, 3%, 2%. 1%, 0.9%, 0.8%, 0.7%. 0.6%, 0.5%, 0.4%, 0.3%. 0.2%, or 0.1% total reactive impurity (e.g., aldehyde) content. In some embodiments, one or more, or optionally all, of the lipid reagents used for a lipid nanoparticle as described herein or a formulation thereof comprise less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species. In some embodiments, one or more, or optionally all, of the lipid reagents used for a lipid nanoparticle as described herein or a fonnulation thereof comprise: (i) less than 5%, 4%, 3%, 2%. 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%. 0.4%, 0.3%, 0.2%, or 0.1% total reactive impurity (e.g., aldehyde) content and (ii) less than 5%, 4%, 3%, 2%, 1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of any single reactive impurity (e.g., aldehyde) species.

In some embodiments, total aldehyde content and/or quantity' of any single reactive impurity (e.g., aldehyde) species is detennined by liquid chromatography (LC), e.g., coupled with tandem mass spectrometry (MS/MS), e.g., according to the method described in Example 40 of PCT/US21/20948. In some embodiments, reactive impurity (e.g., aldehyde) content and/or quantity of reactive impurity (e.g., aldehyde) species is determined by detecting one or more chemical modifications of a nucleic acid molecule (e.g., an RNA molecule, e.g., as described herein) associated with the presence of reactive impurities (e.g., aldehydes), e.g., in the lipid reagents. In some embodiments, reactive impurity (e.g., aldehyde) content and/or quantity of reactive impurity (e.g., aldehyde) species is detennined by detecting one or more chemical modifications of a nucleotide or nucleoside (e.g., a ribonucleotide or ribonucleoside, e.g., comprised in or isolated from a template nucleic acid, e.g., as described herein) associated with the presence of reactive impurities (e.g., aldehydes), e.g., in the lipid reagents, e.g., according to the method described in Example 41 of PCT/US21/20948. In embodiments, chemical modifications of a nucleic acid molecule, nucleotide, or nucleoside are detected by determining the presence of one or more modified nucleotides or nucleosides, e.g.. using LC-MS/MS analysis, e.g., according to the method described in Example 41 of PCT/US21/20948.

In some embodiments, a nucleic acid (e.g., RNA) described herein (e.g., a template nucleic acid or a nucleic acid encoding a gene modifying polypeptide) does not comprise an aldehyde modification, or comprises less than a preselected amount of aldehyde modifications. In some embodiments, on average, a nucleic acid has less than 50, 20, 10, 5, 2, or 1 aldehyde modifications per 1000 nucleotides, e.g., wherein a single cross-linking of two nucleotides is a single aldehyde modification. In some embodiments, the aldehyde modification is an RNA adduct (e.g., a lipid-RNA adduct). In some embodiments, the aldehyde- modified nucleotide is cross-linking between bases . In some embodiments, a nucleic acid (e.g., RNA) described herein comprises less than 50, 20, 10, 5, 2, or 1 cross-links between nucleotide.

In some embodiments, LNPs are directed to specific tissues by tire addition of targeting domains. For example, biological ligands may be displayed on the surface of LNPs to enhance interaction with cells displaying cognate receptors, thus driving association with and cargo delivery to tissues wherein cells express the receptor. In some embodiments, the biological ligand may be a ligand that drives delivery to the liver, e.g., LNPs that display GalNAc result in delivery of nucleic acid cargo to hepatocytes that display asialoglycoprotein receptor (ASGPR). The work of Akinc et al. Mol Ther 18(7): 1357-1364 (2010) teaches the conjugation of a trivalent GalNAc ligand to a PEG-lipid (GalNAc - PEG-DSG) to yield LNPs dependent on ASGPR for observable LNP cargo effect (see, e.g.. Figure 6 therein). Other ligand-displaying LNP formulations, e.g., incorporating folate, transferrin, or antibodies, are discussed in WO2017223135, which is incorporated herein by reference in its entirety, in addition to the references used therein, namely Kolhatkar et al., Curr Drug Discov Technol. 2011 8: 197-206; Musacchio and Torchilin, Front Biosci. 2011 16: 1388-1412; Yu et al., Mol Membr Biol. 2010 27:286- 298; Patil et al., Crit Rev Ther Drug Carrier Syst. 2008 25: 1-61 ; Benoit et al.. Biomacromolecules. 2011 12:2708-2714; Zhao et al., Expert Opin Drug Deliv. 2008 5:309-319; Akinc et al.. Mol Ther. 2010 18: 1357-1364; Srinivasan et al., Methods Mol Biol. 2012 820: 105-116; Ben-Arie et al., Methods Mol Biol. 2012 757:497-507; Peer 2010 J Control Release. 20:63-68; Peer et al., Proc Natl Acad Sci U S A. 2007 104:4095-4100; Kim et al., Methods Mol Biol. 2011 721:339-353; Subramanya et al., Mol Ther. 2010 18:2028-2037; Song et al., Nat Biotechnol. 2005 23:709-717; Peer et al., Science. 2008 319:627- 630; and Peer and Lieberman, Gene Ther. 2011 18: 1127-1133.

In some embodiments, LNPs are selected for tissue-specific activity by the addition of a Selective ORgan Targeting (SORT) molecule to a formulation comprising traditional components, such as ionizable cationic lipids, amphipathic phospholipids, cholesterol and polyethylene glycol) (PEG) lipids.

The teachings of Cheng et al. Nat Nanotechnol 15(4): 313-320 (2020) demonstrate that the addition of a supplemental 'SORT' component precisely alters the in vivo RNA delivery profile and mediates tissuespecific (e.g., lungs, liver, spleen) gene delivery and editing as a function of the percentage and biophysical property of the SORT molecule.

In some embodiments, the LNPs comprise biodegradable, ionizable lipids. In some embodiments, the LNPs comprise (9Z,12Z)-3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3- (diethylamino)propoxy)carbonyl)oxy)methyl)propyl octadeca-9,12-dienoate, also called 3- ((4,4- bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy)car bonyl)oxy)metliyl)propyl (9Z,12Z)- octadeca-9,12-dienoate) or another ionizable lipid. See, e.g, lipids of WO2019/067992, WO/2017/173054, W02015/095340, and WO2014/136086, as well as references provided therein. In some embodiments, the term cationic and ionizable in the context of LNP lipids is interchangeable, e.g., wherein ionizable lipids are cationic depending on the pH.

In some embodiments, an LNP described herein comprises a lipid described in Table 19

In some embodiments, multiple components of a gene modifying system may be prepared as a single LNP formulation, e.g., an LNP formulation comprises mRNA encoding for the gene modifying polypeptide and an RNA template. Ratios of nucleic acid components may be varied in order to maximize the properties of a therapeutic. In some embodiments, the ratio of RNA template to mRNA encoding a gene modifying polypeptide is about 1 : 1 to 100: 1, e.g., about 1 : 1 to 20: 1, about 20: 1 to 40: 1, about 40: 1 to 60: 1, about 60: 1 to 80: 1, or about 80: 1 to 100: 1, by molar ratio. In other embodiments, a system of multiple nucleic acids may be prepared by separate formulations, e.g., one LNP formulation comprising a template RNA and a second LNP formulation comprising an mRNA encoding a gene modifying polypeptide. In some embodiments, the system may comprise more than two nucleic acid components formulated into LNPs. In some embodiments, the system may comprise a protein, e.g., a gene modifying polypeptide, and a template RNA formulated into at least one LNP formulation.

In some embodiments, the average LNP diameter of tire LNP formulation may be between 10s of nm and 100s of nm, e.g., measured by dynamic light scattering (DLS). In some embodiments, the average LNP diameter of the LNP formulation may be from about 40 nm to about 150 nm, such as about 40 nm, 45 nm, 50 nm. 55 nm, 60 nm, 65 nm, 70 nm, 75 nm. 80 nm, 85 nm, 90 nm, 95 nm, 100 nm, 105 nm, 110 nm, 115 nm. 120 nm, 125 nm. 130 nm, 135 nm. 140 nm, 145 nm, or 150 nm. In some embodiments, the average LNP diameter of the LNP formulation may be from about 50 nm to about 100 nm, from about 50 nm to about 90 nm, from about 50 nm to about 80 nm, from about 50 nm to about 70 nm, from about 50 nm to about 60 nm, from about 60 nm to about 100 nm, from about 60 nm to about 90 nm, from about 60 nm to about 80 nm, from about 60 nm to about 70 nm, from about 70 nm to about 100 nm, from about 70 nm to about 90 nm, from about 70 nm to about 80 nm. from about 80 nm to about 100 nm, from about 80 nm to about 90 nm, or from about 90 nm to about 100 nm. In some embodiments, the average LNP diameter of the LNP formulation may be from about 70 nm to about 100 nm. In a particular embodiment, the average LNP diameter of the LNP formulation may be about 80 nm. In some embodiments, the average LNP diameter of the LNP formulation may be about 100 nm. In some embodiments, the average LNP diameter of the LNP formulation ranges from about 1 mm to about 500 mm, from about 5 mm to about 200 mm, from about 10 mm to about 100 mm, from about 20 mm to about 80 mm, from about 25 mm to about 60 mm, from about 30 mm to about 55 mm, from about 35 mm to about 50 mm, or from about 38 mm to about 42 mm.

An LNP may, in some instances, be relatively homogenous. A polydispersity index may be used to indicate the homogeneity of an LNP, e.g., tire particle size distribution of the lipid nanoparticles. A small (e.g., less than 0.3) polydispersity index generally indicates a narrow particle size distribution. An LNP may have a polydispersity index from about 0 to about 0.25, such as 0.01, 0.02, 0.03, 0.04. 0.05, 0.06, 0.07. 0.08. 0.09, 0.10, 0.11, 0.12, 0.13. 0.14. 0.15, 0.16, 0.17, 0.18, 0.19. 0.20. 0.21, 0.22, 0.23, 0.24, or 0.25. In some embodiments, the poly dispersity index of an LNP may be from about 0.10 to about 0.20.

The zeta potential of an LNP may be used to indicate the electrokinetic potential of the composition. In some embodiments, tire zeta potential may describe tire surface charge of an LNP. Lipid nanoparticles with relatively low charges, positive or negative, are generally desirable, as more highly charged species may interact undesirably with cells, tissues, and other elements in the body. In some embodiments, the zeta potential of an LNP may be from about -10 mV to about +20 mV, from about -10 mV to about +15 mV, from about -10 mV to about +10 mV, from about -10 mV to about +5 mV, from about -10 mV to about 0 mV, from about -10 mV to about -5 mV, from about -5 mV to about +20 mV, from about -5 mV to about +15 mV, from about -5 mV to about +10 mV, from about -5 mV to about +5 mV, from about -5 mV to about 0 mV, from about 0 mV to about +20 mV, from about 0 mV to about +15 mV. from about 0 mV to about +10 mV, from about 0 mV to about +5 mV, from about +5 mV to about +20 mV, from about +5 mV to about +15 mV, or from about +5 mV to about +10 mV.

The efficiency of encapsulation of a protein and/or nucleic acid, e.g ., gene modifying polypeptide or mRNA encoding the polypeptide, describes the amount of protein and/or nucleic acid that is encapsulated or otherwise associated with an LNP after preparation, relative to the initial amount provided. The encapsulation efficiency is desirably high (e.g., close to 100%). Hie encapsulation efficiency may be measured, for example, by comparing the amount of protein or nucleic acid in a solution containing the lipid nanoparticle before and after breaking up the lipid nanoparticle with one or more organic solvents or detergents. An anion exchange resin may be used to measure the amount of free protein or nucleic acid (e.g., RNA) in a solution. Fluorescence may be used to measure the amount of free protein and/or nucleic acid (e.g.. RNA) in a solution. For the lipid nanoparticles described herein, the encapsulation efficiency of a protein and/or nucleic acid may be at least 50%, for example 50%. 55%. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%. In some embodiments, the encapsulation efficiency may be at least 80%. In some embodiments, the encapsulation efficiency may be at least 90%. In some embodiments, the encapsulation efficiency may be at least 95%.

An LNP may optionally comprise one or more coatings. In some embodiments, an LNP may be formulated in a capsule, film, or table having a coating. A capsule, film, or tablet including a composition described herein may have any useful size, tensile strength, hardness or density.

Additional exemplary lipids, formulations, methods, and characterization of LNPs are taught by W02020061457, which is incorporated herein by reference in its entirety.

In some embodiments, in vitro or ex vivo cell lipofections are performed using Lipofectamine MessengerMax (Thermo Fisher) or TransIT-mRNA Transfection Reagent (Minis Bio). In certain embodiments, LNPs are formulated using the GenVoy ILM ionizable lipid mix (Precision NanoSystems). In certain embodiments, LNPs are formulated using 2,2-dilinoleyl-4-dimethylaminoethyl- [l,3]-dioxolane (DLin-KC2-DMA) or dilinoleylmethyl-4-dimethylaminobutyrate (DLin-MC3-DMA or MC3), tire formulation and in vivo use of which are taught in Jayaraman et al. Angew Chem Int Ed Engl 51(34):8529-8533 (2012), incorporated herein by reference in its entirety.

LNP fonnulations optimized for the delivery of CRISPR-Cas systems, e.g., Cas9-gRNA RNP, gRNA, Cas9 mRNA, are described in WO2019067992 and W02019067910, both incorporated by reference.

Additional specific LNP formulations useful for delivery of nucleic acids are described in US8158601 and US8168775, both incorporated by reference, which include formulations used in patisiran, sold under the name ONPATTRO.

Exemplary dosing of gene modifying LNP may include about 0.1, 0.25. 0.3, 0.5, 1, 2, 3, 4, 5, 6, 8, 10, or 100 mg/kg (RNA). Exemplary dosing of AAV comprising a nucleic acid encoding one or more components of the system may include an MOI of about 10 ¹¹ , 10 ¹² , 10 ¹³ , and 10 ¹⁴ vg/kg. Kits, Articles of Manufacture, and Pharmaceutical Compositions

In an aspect the disclosure provides a kit comprising a gene modifying polypeptide or a gene modifying system, e.g., as described herein. In some embodiments, the kit comprises a gene modifying polypeptide (or a nucleic acid encoding the polypeptide) and a template RNA (or DNA encoding the template RNA). In some embodiments, the kit further comprises a reagent for introducing the system into a cell, e.g., transfection reagent, LNP, and the like. In some embodiments, the kit is suitable for any of the methods described herein. In some embodiments, the kit comprises one or more elements, compositions (e.g., phannaceutical compositions), gene modifying polypeptides, and/or gene modifying systems, or a functional fragment or component thereof, e.g., disposed in an article of manufacture. In some embodiments, the kit comprises instructions for use thereof.

In an aspect, the disclosure provides an article of manufacture, e.g., in which a kit as described herein, or a component thereof, is disposed.

In an aspect, the disclosure provides a phannaceutical composition comprising a gene modifying polypeptide or a gene modifying system, e.g., as described herein. In some embodiments, the phannaceutical composition further comprises a pharmaceutically acceptable carrier or excipient. In some embodiments, the pharmaceutical composition comprises a template RNA and/or an RNA encoding the polypeptide. In embodiments, the pharmaceutical composition has one or more (e.g., 1 , 2, 3, or 4) of the following characteristics:

(a) less than 1% (e.g., less than 0.5%, 0.4%, 0.3%, 0.2%, or 0.1%) DNA template relative to the template RNA and/or the RNA encoding the polypeptide, e.g., on a molar basis;

(b) less than 1% (e.g., less than 0.5%, 0.4%. 0.3%, 0.2%, or 0. 1%) uncapped RNA relative to the template RNA and/or the RNA encoding the polypeptide, e.g., on a molar basis;

(c) less than 1% (e.g., less than 0.5%, 0.4%, 0.3%, 0.2%, or 0.1%) partial length RNAs relative to the template RNA and/or the RNA encoding the polypeptide, e.g., on a molar basis;

(d) substantially lacks unreacted cap dinucleotides.

Chemistry, Manufacturing, and Controls (CMC)

Purification of protein therapeutics is described, for example, in Franks, Protein Biotechnology: Isolation, Characterization, and Stabilization. Humana Press (2013); and in Cutler, Protein Purification Protocols (Methods in Molecular Biology) , Humana Press (2010).

In some embodiments, a gene modifying system, polypeptide, and/or template nucleic acid (e.g., template RNA) conforms to certain quality standards. In some embodiments, a gene modifying system, polypeptide, and/or template nucleic acid (e.g., template RNA) produced by a method described herein conforms to certain quality standards. Accordingly, the disclosure is directed, in some aspects, to methods of manufacturing a gene modifying system, polypeptide, and/or template nucleic acid (e.g., template RNA) that conforms to certain quality standards, e.g., in which said qualify standards are assayed. The disclosure is also directed, in some aspects, to methods of assaying said quality standards in a gene modifying system, polypeptide, and/or template nucleic acid (e.g., template RNA). In some embodiments, quality standards include, but are not limited to, one or more (e.g., 1, 2, 3, 4, 5, 6. 7, 8, 9, 10, 11, or 12) of the following:

(i) the length of the template RNA, e.g., whether the template RNA has a length that is above a reference length or within a reference length range, e.g., whether at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% of the template RNA present is greater than 100, 125, 150, 175, or 200 nucleotides long;

(ii) the presence, absence, and/or length of a polyA tail on the template RNA, e.g., whether at least 80%. 85%. 90%. 95%, 96%, 97%, 98%, or 99% of the template RNA present contains a polyA tail (e.g., a polyA tail that is at least 5, 10, 20, 30, 50, 70, 100 nucleotides in length);

(iii) the presence, absence, and/or type of a 5 ' cap on the template RNA, e.g., whether at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% of the template RNA present contains a 5' cap, e.g., whether that cap is a 7-methylguanosine cap, e.g., a 0-Me-m7G cap;

(iv) the presence, absence, and/or type of one or more modified nucleotides (e.g., selected from pseudouridine, dihydrouridine, inosine, 7-methylguanosine, 1-N-methylpseudouridine (1-Me-T), 5- methoxyuridine (5-MO-U), 5 -methylcytidine (5mC), or a locked nucleotide) in the template RNA, e g., whether at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% of the template RNA present contains one or more modified nucleotides;

(v) the stability of the template RNA (e.g., over time and/or under a pre-selected condition), e.g., whether at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% of the template RNA remains intact (e.g., greater than 100, 125, 150, 175, or 200 nucleotides long) after a stability test;

(vi) the potency of the template RNA in a system for modifying DNA, e.g., whether at least 1% of target sites are modified after a system comprising the template RNA is assayed for potency;

(vii) tire length of the polypeptide, first polypeptide, or second polypeptide, e.g., whether the polypeptide, first polypeptide, or second polypeptide has a length that is above a reference length or within a reference length range, e.g., whether at least 80%, 85%, 90%, 95%. 96%. 97%. 98%, or 99% of the polypeptide, first polypeptide, or second polypeptide present is greater than 600, 650, 700. 750, 800, 850, 900, 950, 1000, 1050, 1 100, 1 150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1600, 1700, 1800, 1900, or 2000 amino acids long (and optionally, no larger than 2500, 2000, 1500, 1400, 1300, 1200,

1100, 1000, 900, 800, 700, or 600 amino acids long); (viii) the presence, absence, and/or type of post-translational modification on the polypeptide, first polypeptide, or second polypeptide, e.g., whether at least 80, 85, 90, 95, 96, 97, 98, or 99% of the polypeptide, first polypeptide, or second polypeptide contains phosphorylation, methylation, acetylation, myristoylation, palmitoylation, isoprenylation, glipyatyon, or lipoylation, or any combination thereof;

(ix) the presence, absence, and/or type of one or more artificial, synthetic, or non-canonical amino acids (e.g., selected from ornithine, (3-alanine, GABA. 5-Aminolevulinic acid. PABA. a D-amino acid (e.g., D-alanine or D-glutamate), aminoisobutyric acid, dehydroalanine, cystathionine, lanthionine, Djenkolic acid, Diaminopimelic acid, Homoalanine, Norvaline, Norleucine, Homonorleucine, homoserine, O-methyl-homoserine and O-ethyl-homoserine, ethionine, selenocysteine, selenohomocysteine, selenomethionine, selenoethionine, tellurocysteine, or telluromethionine) in the polypeptide, first polypeptide, or second polypeptide, e.g.. whether at least 80%, 85%, 90%. 95%. 96%, 97%, 98%, or 99% of the polypeptide, first polypeptide, or second polypeptide present contains one or more artificial, synthetic, or non-canonical amino acids;

(x) the stability of the polypeptide, first polypeptide, or second polypeptide (e.g., over time and/or under a pre-selected condition), e.g., whether at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% of the polypeptide, first polypeptide, or second polypeptide remains intact (e.g., greater than 600, 650, 700, 750. 800, 850. 900, 950. 1000, 1050, 1100, 1150, 1200, 1250, 1300. 1350, 1400, 1450, 1500, 1600, 1700, 1800, 1900, or 2000 amino acids long (and optionally, no larger than 2500, 2000, 1500, 1400, 1300, 1200, 1100, 1000, 900, 800, 700, or 600 amino acids long)) after a stability test;

(xi) the potency of the polypeptide, first polypeptide, or second polypeptide in a system for modifying DNA, e.g., whether at least 1% of target sites are modified after a system comprising tire polypeptide, first polypeptide, or second polypeptide is assayed for potency; or

(xii) the presence, absence, and/or level of one or more of a pyrogen, virus, fungus, bacterial pathogen, or host cell protein, e.g., whether the system is free or substantially free of pyrogen, virus, fungus, bacterial pathogen, or host cell protein contamination.

In some embodiments, a system or pharmaceutical composition described herein is endotoxin free.

In some embodiments, the presence, absence, and/or level of one or more of a pyrogen, virus, fungus, bacterial pathogen, and/or host cell protein is determined. In embodiments, whether the system is free or substantially free of pyrogen, virus, fungus, bacterial pathogen, and/or host cell protein contamination is determined.

In some embodiments, a pharmaceutical composition or system as described herein has one or more (e.g., 1, 2, 3, or 4) of the following characteristics: (a) less than 1% (e.g., less than 0.5%, 0.4%, 0.3%, 0.2%, or 0.1%) DNA template relative to the template RNA and/or the RNA encoding the polypeptide, e.g., on a molar basis;

(b) less than 1% (e.g., less than 0.5%, 0.4%, 0.3%, 0.2%, or 0. 1%) uncapped RNA relative to the template RNA and/or the RNA encoding the polypeptide, e.g., on a molar basis;

(c) less than 1% (e.g., less than 0.5%, 0.4%, 0.3%, 0.2%, or 0.1%) partial length RNAs relative to the template RNA and/or the RNA encoding the polypeptide, e.g.. on a molar basis:

(d) substantially lacks unreacted cap dinucleotides.

EXAMPLES

Example 1: Trans-recruitment of an RNA template for RNA-based gene modification

This example describes the use of an exemplary three (3)-component RNA gene modifying system for the targeted editing of a sequence in the human genome (FIG. 1). More specifically, in this exemplary' system, a (1) gene modifying polypeptide binds (2) a guide RNA molecule and (3) a transtemplate RNA (ttRNA) molecule, together forming a gene modifying complex, which binds and nicks the target locus and performs templated incorporation of the desired edit in one strand of the genomic DNA. Host repair pathways cause the incorporation of the edit in the second strand, and ligation of the DNA nick. This example further describes the introduction of the 3-component system to mammalian cells for in vitro gene modifying as a means of evaluating the efficacy of various gene modifying system configurations and ttRNA recruitment interactions on editing activity in human cells.

1) Gene modifying polypeptide:

The gene modifying polypeptide of this exemplary’ system includes:

1. a Cas-nuclease with one endonuclease domain inactivated (e.g. Spy N863A Cas9),

2. a reverse transcriptase (RT), and

3. optionally an RNA binding domain (RED; as in Table 31). The RBD may comprise one or more RBP repeats, e.g., 1-5 repeats in tandem with or without intervening peptide linker sequences.

These 2-3 domains are brought together either by covalent linkage using (1) peptide linkers, as in Table 10 (FIG. 2A), or (2) intein pairs, as in Table 33, or (3) by the dimerization of two fusion domains (FDs) that (a) is induced by chemical binding or specific wavelengths of light Table 34, or (b) occurs intrinsically in a ligand-free interaction Tables 35 and 36 (FIG. 2B). The FDs may be repeated, in some instances, 1-30 times in tandem with or without intervening peptide linker sequences.

The 2-3 domains can be assembled in any of the following configurations, where the linkers indicated below can optionally be replaced with intein- or FD-pairs:

• Cas9 - linker - RT - linker - (RBP repeat) _n

• RT - linker - Cas9 - linker - (RBP repeat) _n

• (RBP repeat) _n - linker - Cas9 - linker - RT

• (RBP repeat) _n - linker - RT - linker - Cas9

• Cas9 - linker - (RBP repeat) _n - linker - RT

• RT - linker - (RBP rcpcat) _n - linker - Cas9

2) Exemplary Guide RNA:

The guide RNA (gRNA) molecule (5‘-

GCCGAAGCACTGCACGCCGTGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTA GTCCGTT ATCAACTTGAAAAAGTGGCACCGAGTCGGTGC -3’; SEQ ID NO: 16,701) binds Cas9 and contains a spacer sequence complementary to tire exemplary target genomic locus, resulting in localization of tire gene modifying complex to the exemplary target genomic locus.

3) Trans-template RNA (ttRNA):

An exemplary ttRNA molecule contains a PBS-template region, 3’ to 5’, as below (and as diagrammed in FIG. 3A-3B):

1. a 1-17 nt primer binding site (PBS; as in Table 37) that basepairs with the nicked DNA strand allowing primer extension of the nicked DNA, follow ed immediately by

2. a 0-20 nt region of homology with the target locus (homology 1; as in Table 38. “homology 1”)

3. the desired modification to the genome - insertion, deletion, or substitution (edit; as in Table 38, “edit”) 4. a 0-500 nt region of homology with the target locus (homology 2; as in Table 39, '‘homology 2”).

The exemplary ttRNA may optionally also include:

5. an RBD recruitment site (RRS; as in Table 40). The RRS may be repeated 1-5 times, e.g., 1-4 times, in tandem with or without intervening RNA linker sequences.

The exemplary ttRNA may optionally also include:

6. one or two end-protecting RNA secondary structure (end block; as in Table 41) that protects the ttRNA molecule from exonuclease -mediated degradation.

These components of the ttRNA may be assembled in any of the below configurations, where the RRSs may be joined to the PBS-template by an RNA linker sequence of up to 20 nts (the longest sequence being 5’-ACTAACATACAACTAACATA-3’):

• (RRS)n - linker - PBS-template

• (RRS)n - linker - PBS-template - end block

• PBS-template - linker - (RRS)n

• end-block - PBS-template - linker - (RRS) _n

• end block - (RRS) _U - linker - PBS-template

• end block - (RRS) _n - linker - PBS-template - end block

• PBS-template - linker - (RRS) _n - end block

• end-block - PBS-template - linker - (RRS) _n - end block

• end-block - PBS-template - end block

Evaluation of 3 -component trans-gene modifying system configurations:

To determine the genome-editing capacity of the various configurations of the trans-gene modifying complex, mammalian HEK293T or U2OS cell lines are generated earn ing a genomic landing pad that expresses one of the following: i. 150 or 250 bp GFP insertion reporter line: a non-fluorescent partially-deleted-GFP cell line, in which GFP -expression is restored via a 150 or 250 bp insertion of the deleted coding sequence; or ii. mKate2 or mCherry insertion reporter line: a GFP-expressing cell line, which loses GFP- expression and gains mKate2 or mCherry expression via the interruption of the GFP coding sequence with a >700 (e.g., >700 or >750) bp insertion that introduces the mKate2 or mCherry coding sequence.

The gene modify ing polypeptide is introduced into these cells by transfection of DNA plasmid or mRNA, or by packaging of DNA plasmid into Lentivirus. The cells are additionally co- transfected/electroporated with a ttRNA-expressing DNA plasmid or ncRNA, and a gRNA- expressing DNA plasmid or ncRNA that are together designed to: i. 150 or 250 bp GFP insertion reporter line: restore the GFP coding sequence; or ii. mKate2 or mCherry insertion reporter line: interrupt the GFP coding sequence with an mKate2 or mCherry coding sequence.

To assess the genome-editing capacity of the trans-gene modifying system configurations, cells are analyzed by flow cytometry 4-10 days post-transfection/electroporation of ttRNA and gRNA. The fidelity of the edits are also assessed by collecting genomic DNA 3-10 days post-transfection/ electroporation of the ttRNA and gRNA. The frequency of the intended versus unintended mutations at target loci are analyzed by amplicon sequencing.

Example 2: Trans-recruitment of an RNA template for RNA-based gene modifying via engagement of the second DNA strand by a Cas9-complex

This example describes the use of a RNA-based gene modifying system having up to five components for the targeted editing of a sequence in the human genome (FIGS 4A-4B). More specifically, a (1) gene modifying polypeptide binds (2) a guide RNA molecule and (3) a trans-template RNA (ttRNA) molecule, together forming a gene modifying complex, which binds and nicks the target locus and performs templated incorporation of tire desired edit in one strand of the genomic DNA. An additional (4) Cas9 (e.g., a dCas9 or nCas9 domain (FIG. 4A) or such a domain as part of a second different gene modifying polypeptide (FIG. 4B) molecule is recruited to the nicked DNA strand by the trans-template RNA (e.g., by an 5’ end block containing a gRNA spacer), or by (5) its species-matched guide RNA, to form a second complex. The second complex may extend the bubble and facilitate large insertions, and may also be used to introduce a nick on the second strand to initiate second strand synthesis, and/or signal to the cell’s endogenous repair system (e.g., mismatch repair system) that the edited strand should be copied and maintained. This example further describes the introduction of the 5 component system to mammalian cells for in vitro gene modifying as a means of evaluating the efficacy of various gene modifying system configurations and ttRNA recruitment interactions on editing activity in human cells.

1) Gene modifying polypeptide:

The gene modifying polypeptide includes:

1. a Cas-nuclease with one endonuclease domain inactivated (e.g. Spy N863A Cas9),

2. a reverse transcriptase (RT), and

3. optionally an RNA binding domain (RBD; as in Table 31). The RBD may comprise one or more RBP repeats, e.g., 1-5 repeats in tandem with or without intervening peptide linker sequences.

These 2-3 domains are brought together either by covalent linkage using (1) peptide linkers, as in Table 10, or (2) intein pairs, as in Table 33, or by tire dimerization of two fusion domains (FDs) that (a) is induced by chemical binding or or specific wavelengths of light Table 34. or (b) occurs intrinsically in a ligand-free interaction Tables 35 and 36. The FDs may, in some instances, be repeated 1-30 times in tandem with or without intervening peptide linker sequences.

The 2-3 domains can be assembled in any of the following configurations, where the linkers indicated below can, in some instances, be replaced with intein- or FD-pairs.:

• Cas9 - linker - RT - linker - (RBP repeat) _n

• RT - linker - Cas9 - linker - (RBP repeat) _n

• (RBP repeat) _n - linker - Cas9 - linker - RT

• (RBP repeat) _n - linker - RT - linker - Cas9

• Cas9 - linker - (RBP repeat) _n - linker - RT

• RT - linker - (RBP repeat) _n - linker - Cas9

2) Exemplary Guide RNA: The guide RNA (gRNA) molecule (5’-

GCCGAAGCACTGCACGCCGTGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTA GTCCGTT

ATCAACTTGAAAAAGTGGCACCGAGTCGGTGC -3’; SEQ ID NO: 16,701) binds Cas9 and contains a spacer sequence complementary to the exemplary target genomic locus, resulting in localization of the gene modifying complex to the exemplary' target genomic locus.

3) Trans-template RNA (ttRNA):

An exemplary ttRNA molecule contains a PBS-template region, 3’ to 5’, as below:

1. an 1-17 nt primer binding site (PBS; as in Tabic 37) that basepairs with the nicked DNA strand allowing primer extension of the nicked DNA, followed immediately by

2. a 0-20 nt region of homology with the target locus (homology 1; as in Table 38. ‘“homology 1”)

3. the desired modification to the genome - insertion, deletion, or substitution (edit; as in Table 38, “edit”)

4. a 0-500 nt region of homology with the target locus (homology 2; as in Table 39, “homology 2”).

The exemplary ttRNA may optionally also include:

5. an RBD recruitment site (RRS; as in Table 40). The RRS may be repeated 1-5 times (e.g., 1- 4 times) in tandem with or without intervening RNA linker sequences.

The exemplary ttRNA may optionally also include:

6. one or two end-protecting RNA secondary structure (end block; as in Table 41) that protects the ttRNA molecule from exonuclease-mediated degradation.

These components of the ttRNA may be assembled in any of the below configurations, where the RRSs may be joined to the PBS-template by an RNA linker sequence of up to 20 nts (the longest sequence being 5’-ACTAACATACAACTAACATA-3’; SEQ ID NO: 16,702):

• (RRS)n - linker - PBS-template

• (RRS)n - linker - PBS-template - end block

• PBS-template - linker - (RRS) _n • end-block - PBS-template - linker - (RRS) _n

• end block - (RRS) _n - linker - PBS-template

• end block - (RRS) _U - linker - PBS-template - end block

• PBS-template - linker - (RRS) _n - end block

• end-block - PBS-template - linker - (RRS) _n - end block

• end-block - PBS-template - end block

4) Additional (second) Cas9 or different gene modifying polypeptide:

An additional nickase (e.g., Spy N863A Cas9, or an orthogonal Cas9) or catalytically inactive (“dead”) Cas9 as in Table 43, which binds the nicked DNA strand by pairing with a gRNA scaffold and/or gRNA spacer contained in the ttRNA (FIG. 4B), or which binds a separate gRNA (FIG. 4A; see also 5. below). A nickase Cas9 paired with a full spacer is used to introduce a nick on the second, unnicked strand. Alternatively, a dead Cas9 or a nickase paired with a gRNA-2 having a spacer with less than 17 nt complementarity to the target opens up the DNA bubble for long RT reactions, without nicking the second strand. An additional nickase or catalytically inactive Cas9 may be a separate domain (e.g., FIG. 4A) or a part of an additional (second) gene modifying polypeptide different from (1) (FIG. 4B).

5) Optional second Cas9/different -paired guide RNA:

The second guide RNA (gRNA-2) molecule with a spacer sequence complementary to the nicked strand, as in Table 44, may be added to recruit the 2 ^nd Cas9 to the nicked DNA strand for DNA bubble extension or second strand nicking. A gRNA-2 spacer may be folly complementary to the target strand to stimulate the nickase activity of the 2 ^nd Cas9, or it may contain 17 or fewer nucleotides of complementarity to inhibit nicking by the 2 ^nd Cas9.

To determine the genome-editing capacity of the various configurations of the trans-gene modifying system complex, mammalian HEK293T or U2OS cell lines are generated carrying a genomic landing pad that expresses one of the following: i. 150 or 250 bp GFP insertion reporter line: a non-fluorescent partially-deleted-GFP cell line, in which GFP -expression is restored via a 150 or 250 bp insertion of the deleted coding sequence; or ii. mKate2 or mCherry insertion reporter line: a GFP -expressing cell line, which loses GFP- expression and gains mKate2 or mCherry expression via tire interruption of the GFP coding sequence with a >700 (e.g.. >750) bp insertion that introduces the mKate2 or mCherry coding sequence.

The gene modifying polypeptide is introduced in these cells by transfection of DNA plasmid or mRNA, or by packaging of DNA plasmid into Lentivirus. The cells are additionally co- transfected/electroporated with 1) a ttRNA-expressing DNA plasmid or ncRNA, 2) a gRNA- expressing DNA plasmid or ncRNA that are together designed to: i. 150 or 250 bp GFP insertion reporter line: restore a GFP coding sequence; or ii. mKate2 or mCherry insertion reporter line: interrupt the GFP coding sequence with an mKate2 or mCherry coding sequence. along with 3) a DNA plasmid or mRNA expressing a 2nd Cas9, and optionally 4) a gRNA-2 -expressing DNA plasmid or ncRNA.

To assess the genome-editing capacity of the trans-gene modifying system configurations, cells are analyzed by flow cytometry 4-10 days post-transfection/electroporation of ttRNA and gRNA. The fidelity of the edits are also assessed by collecting genomic DNA 3-10 days post-transfection/ electroporation of the ttRNA and gRNA. The frequency of the intended versus unintended mutations at target loci are analyzed by amplicon sequencing.

Example 3: Generation of Exemplary Drivers

This example describes the generation of exemplary drivers for use in the three, four, or five component RNA-based gene modifying systems described in Examples 1 and 2.

1) Gene modifying polypeptide:

A series of 216 exemplary gene modifying polypeptides were generated containing:

1. a Cas-nuclease with one endonuclease domain inactivated (in this example, Spy N863A Cas9), 2. either of two reverse transcriptases (RTs) (the RTs of the gene modifying polypeptide encoded by: PLV10993 or PLV10990/RNAIVT338), and

3. an RNA binding domain (RBD) containing 1, 2, or 4 RBP repeats (in this example, 1, 2, or 4 MCPv2 domains as provided in Table 31), with each RBP repeat connected to the other RBP repeats by one of 4 linker peptides from Table 10.

These 3 domains were connected using peptide linkers, e.g., as found in Table 10.

The sequence of the RT of the gene modifying polypeptide encoded by PLV10990/RNAIVT338 and the sequence of the RT of the gene modifying polypeptide encoded by PLV 10993 are provided below.

PLV10990/RNAIVT338 RT:

TAPLEEEYRLFLEAPIQNVTLLEQWKREIPKVWAEINPPGLASTQAPIHVQLLSTAL PVRVRQYPIT LEAKRSLRETIRKFRAAGILRPVHSPWNTPLLPVRKSGTSEYRMVQDLREVNKRVETIHP TVPNP YTLLSLLPPDRIWYSVLDLKDAFFCIPLAPESQLIFAFEWADAEEGESGQLTWTRLPQGF KNSPTL FNEALNRDLQGFRLDHPSVSLLQYVDDLLIAADTQAACLSATRDLLMTLAELGYRVSGKK AQLC QEEVTYLGFKIHKGSRSLSNSRTQAILQIPVPKTKRQVREFLGKIGYCRLFIPGFAELAQ PLYAATR PGNDPLVWGEKEEEAFQSLKLALTQPPALALPSLDKPFQLFVEETSGAAKGVLTQALGPW KRPV AYLSKRLDPVAAGWPRCLRAIAAAALLTREASKLTFGQDIEITSSHNLESLLRSPPDKWL TNARIT QYQVLLLDPPRVRFKQTAALNPATLLPETDDTLPIHHCLDTLDSLTSTRPDLTDQPLAQA EATLFT

DGSSYIRDGKRYAGAAVVTLDSVIWAEPLPIGTSAQKAELIALTKALEWSKDKSVNI YTDSRYAF ATLHVHGMIYRERGWLTAGGKAIKNAPEILALLTAVWLPKRVAVMHCKGHQKDDAPTSTG NR RADEVAREVAIRPLSTQATIS (SEQ ID NO: 16,706)

PLV 10993 RT:

TLNIEDEHRLHETSKEPDVSLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATST PVSIKQYP MSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDI HPTVP NPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQ GFKN SPTLFNEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRA SAKKA Q1CQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKTPRQLREFLGKAGFCRLFIPGFAE MAAP LYPLTKPGTLFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQ KLGP WRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQP PDR WLSNARMTHYQALLLDTDRVQFGPVVALNPATLLPLPEEGLQHNCLDILAEAHGTRPDLT DQPL PDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAE GKK LNVYTDSRYAFATAHIHGEIYRRRGWLTSEGI<EII<NI<DEILALLI< ;ALFLPI<RLSIIHCPGHQI<GHS AEARGNRMADQAARKAAITETPDTSTLL (SEQ ID NO: 16,707)

The series of 216 exemplary gene modifying polypeptides encompassed a subset of the configurations set forth in Examples 1 and 2:

• Configuration 1 : Cas9 - linker (RBP repeat) _n - linker - RT

• Configuration 2: RT - linker - (RBP repeat) _n - linker - Cas9

• Configuration 3: Cas9 - linker - RT - linker - (RBP repeat) _n

The sequences of the exemplary gene modifying polypeptides are given below:

Table SI. Exemplary gene modifying sequences for Configuration 1 (i.e., Cas9 - linker (RBP repeat)n - linker - RT)

Table S2. Exemplary gene modifying sequences for Configuration 2 (i.e., RT linker - (RBP repeat)n - linker - Cas9)

Table S3. Exemplary gene modifying sequences for Configuration 3 (i.e., Cas9 - linker - RT- linker - (RBT repeat)n)

2) Guide RNA:

The guide RNA (gRNA) molecule (5’-

GCCGAAGCACTGCACGCCGTGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTA GTCCGTT ATCAACTTGAAAAAGTGGCACCGAGTCGGTGC -3’; SEQ ID NO: 16,708) binds Cas9 and contains a spacer sequence complementary to the target locus, resulting in localization of the gene modifying complex to tire target genomic locus.

Example 4: Generation of Trans Templates for the Incorporation of Long Insertions

This example describes the generation of exemplary trans templates for use in the three, four, or five component RNA-based gene modifying systems described in Examples 1 and 2, and in Examples 1 -5 of PCT Application PCT/US2022/076064, which Examples are herein incorporated by reference, for the insertion of long 150 base pair edits into the 150 bp GFP restoration reporter cell lines.

A series of 121 ttRNAs were constructed with each of the following regions:

1 . a primer binding site (PBS) that is 13 nucleotides in length that base pairs with the nicked DNA strand allowing primer extension of the nicked DNA, followed immediately by

2. a homology 1 region with homology to the target GFP locus

3. the exemplary desired modification: a 150 nucleotide insertion sequence which restores the coding sequence of the EGFP reporter gene, as well as a PAM-nullifying mutation to prevent multiple turnover cutting at the target site.

4. a 12 - 102 nucleotide homology 2 region with homology to the target GFP locus.

5. an RBD recruitment site (RRS) containing 1, or 4 MS2 sequences (lx, 2x, or 4x MS2) with intervening RNA linker sequences, or an ePEG control (a pseudoknot).

6. either no 5’ end -protecting RNA secondary structure or one of the following 5 ’end-protecting RNA secondary structures: a. ePEG b. a Cas9 scaffold lacking a spacer sequence c. a Cas9 scaffold with a 15 nucleotide spacer sequence, which should result in binding but not nicking of the target strand, also referred to herein as shorter spacer sequence d. a Cas9 scaffold with a 20 nucleotide spacer sequence, which should result in nicking of tire target strand, also referred to herein as longer spacer sequence 7. either an 8 or 16 nucleotide linker between the RRS and PBS

These components were assembled in the below configuration (if no 5’ end protecting structure was selected, then no such structure was included in that template RNA):

(RRS)n - linker - PBS-template - 5’ end block

The sequences of the exemplary ttRNAs generated are given in the below table.

Table El 1.1 - Exemplary ttRNA Sequences

Example 5: Evaluation of Long Insertion Activity of Exemplary Gene Modifying Polypeptides Using Trans Template RNAs with a 3-component system

This example describes the evaluation of exemplary three (3)-component gene modifying systems in the targeted insertion of a 150 nt sequence in the human genome. The gene modifying systems, each comprised of (1) a gene modifying polypeptide generated in Example 3 (and demonstrated to have transrecruitment and rewrite activity in Examples 7 and 9 of PCT Application PCT/US2022/076064. which Examples are herein incorporated by reference). (2) a trans template RNA (ttRNA) generated in Example 4, and (3) exemplary gRNA PLV4165. A pool of the following gene modifying polypeptides was used: PL12113, PL12109, and

PL12096, the amino acid sequences of which are provided in Example 3.

The ttRNA used are given in Table E12 below, the nucleic acid sequences of which are provided in Example 4.

Table E12 - Exemplary ttRNA Sequences Used in This Example (Sequences Provided in Example 4)

“Pseudoknof ’ in the “5 ’ end block contents” field indicates that ttRNAs comprised a 5 ’ end block that, while assuming a secondary /tertiary structure thought to protect the 5 ’ end of the ttRNA from degradation, is not capable of binding to a Cas domain, e.g., tire Cas domain of the gene modifying polypeptide. Similarly, “Pseudoknot” in the “RRS or substitute sequence” field indicates that ttRNAs comprised (proximal to the 3 ’ end and in place of an RRS) a secondary/tertiary structure drought to protect the 3’ end of the ttRNA from degradation, and that is not capable of binding to an RBD, e.g., the RBD of the gene modifying polypeptide. Cas9 scaffold ttRNAs (“Scaffold”) comprise a 5’ end block containing a gRNA scaffold sequence compatible with the Cas9 domain of the gene modifying polypeptide, but the 5' end block lacks a gRNA spacer sequence. Cas9 scaffold + spacer ttRNAs comprise a 5 ’ end block and a gRNA scaffold sequence compatible witii tire Cas9 domain of the gene modifying polypeptide and a shorter (“Scaffold + Shorter Spacer”) or longer (“Scaffold + Longer Spacer”) gRNA spacer sequence . It is thought that a shorter gRNA spacer is sufficient for binding of a Cas9 domain but insufficient for nicking of the target DNA, whereas a longer gRNA spacer is sufficient for both binding and nicking. ttRNAs contained a 12 nucleotide homology 2 region or a 46 nucleotide homology 2 region.

The sequence of tire gRNA that comprises the 3 ^rd component of the gene modify ing system is as below

PLV4165:

GCCGAAGCACTGCACGCCGTGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTA GTCCGTTATCAAC TTGAAAAAGTGGCACCGAGTCGGTGC ( SEQ ID NO: 16,714)

To assess the capacity of the trans-gene modifying system to write long insertions into the genome, 150 nt restoration reporter cell lines (U2OS) were analyzed by flow cytometry 4 days post- nucleofection of the gene modifying systems.

The 3-component gene modifying system was nucleofected into the U2OS 150 bp truncated GFP reporter-expressing cell line. All 3 components of the gene modifying system were delivered by nucleofection of plasmids expressing each of the 3 components. Specifically, 600 ng of gene modifying polypeptide plasmid DNA is combined with 150 ng ttRNA- and 150 ng gRNA-expressing plasmids. The modifying polypeptide, ttRNA and gRNA in plasmid DNA format were added to 20pL SE buffer containing 250,000 U2OS 150 bp truncated GFP reporter-expressing cells, and the cells were nucleofected using program DN-100. After nucleofection, cells were grown at 37°C, 5% CCE for at least 4 days prior to fluorescence readout by flow cytometry. GFP expression is indicative of cells in which the 150 nucleotide insertion was accurately written into the genome.

FIG. 5 shows a graph of % GFP positive cells after treating the GFP reporter-expressing cell line with a gene modifying system comprising a ttRNA having the characteristics indicated on the X-axis or with a control gene modifying system. The results showed that very low levels (background) of GFP positive cells were observed when cells were treated with control gene modifying systems lacking one or more components. The results further showed that no GFP positive cell level above background was observed when cells were treated with gene modifying systems comprising ttRNAs having a pseudoknotcontaining 5’ end block or a Cas9 scaffold-containing 5' end block, regardless of the presence or absence of an RRS or the number of RRS repeats in the template RNA. These results suggest that ttRNAs comprising 5 ’ end blocks lacking a means to associate a gene modifying polypeptide and/or ttRNA to a genomic target, or lacking a means to stably associate with a gene modifying polypeptide, are unable to facilitate rewriting of 150 nucleotide long insertions into the genome, regardless of the presence or strength of the interaction between RED and RRS. In contrast, approximately 1 .5% GFP positive cells (indicative of successful insertion) were observed when cells were treated with gene modifying systems comprising ttRNAs having 5’ end blocks comprising a Cas9 gRNA scaffold and 15 nucleotide gRNA spacer wherein the ttRNA comprised an RRS. This result suggests that the ability of the 5’ end block to associate the gene modifying polypeptide (e.g., via the Cas9 domain) and/or the ttRNA to the genomic target, or to stably associate with the gene modifying polypeptide, enables the ttRNA to facilitate insertion of a 150 nucleotide sequence into the genome when the ttRNA is capable of associating with the RED via an RRS. The results further show that approximately 1.6-2.8% GFP positive cells were observed when cells were treated with gene modifying systems comprising ttRNAs having 5 ’ end blocks comprising a Cas9 gRNA scaffold and 20 nucleotide gRNA spacer wherein the ttRNA comprised an RRS. This result suggests that the ability’ of the 5’ end block to associate the gene modifying polypeptide and/or ttRNA to the genomic target (or to stably associate with the gene modifying polypeptide) and induce nicking of the target DNA enables the ttRNA to facilitate insertion of a 150 nucleotide sequence into the genome when the ttRNA is capable of associating with the RED via an RRS. The result further suggests that the ability’ of tire 5' end block to induce nicking of the target DNA via its association with a gene modifying polypeptide increases the rewriting rate for 150 nucleotide insertions. The % GFP positive cells was somewhat lower when a ttRNA contained a 5' end block comprising a Cas9 gRNA scaffold and 20 nucleotide gRNA spacer and lacked an RRS.

The results together support the interpretation that a ttRNA anchored to a target genomic DNA site (e.g., the complex of the target genomic DNA site, a first gene modifying polypeptide, and a gRNA) by two different associations (e.g., here an RBD:RRS interaction with the first gene modifying polypeptide, and a 5’ end block gRNA scaffold/spacer interaction with the target genomic DNA (e.g., mediated by a second gene modifying polypeptide)) enables a gene modifying system to site -specifically insert a 150 nucleotide long sequence into genomic DNA. The results further support the interpretation that a 5' end block that facilitates nicking (e.g., by comprising a gRNA spacer of suitable length and sequence identity) improves the efficiency of insertion of the 150 nucleotide long sequence.

Additionally, the results showed that a 12 nucleotide long homology 2 region was not sufficient for a ttRNA to facilitate insertion of the 150 nucleotide long sequence, regardless of the features of the 5’ end block sequence and RRS. The results showed that a 46 nucleotide long homology 2 region was sufficient, when present with an RRS (either lx MS2 or 4x MS2) and a 5’ end block sequence containing a gRNA scaffold and a gRNA spacer (either 15 or 20 nucleotides in length), to facilitate insertion of the 150 nucleotide long sequence. These results suggest that a longer homology 2 region is needed to successfully insert longer (e.g., 150 nucleotide long) nucleotide sequences, and that the benefit of the longer homology 2 region can be combined with that of a 20 nucleotide 5’ end block gRNA spacer to increase the editing efficiency of the gene modifying system.

Example 6: Evaluating the Roles of ttRNA Components and Different Gene Modifying Polypeptide Domain Configurations in Long Insertion Activity

This example describes the evaluation of exemplary three (3)-component gene modify ing systems in the targeted insertion of a 150 nt sequence in the human genome. Hie gene modifying systems each comprised (1) a gene modifying polypeptide generated in Example 3 (and demonstrated to have transrecruitment and rewrite activity in Examples 7 and 9 of PCT Application PCT/US2022/076064, which Examples are herein incorporated by reference), (2) a trans template RNA (ttRNA) comprising either of two different homology region lengths and with or without RRSs, and (3) exemplary gRNA PLV4165.

Four different individual gene modifying polypeptides were used in this Example; amino acid sequences of which are provided in Example 3.

The ttRNA used are given in Table E13 below. ttRNAs contained:

• An RRS containing either 1 or 4 MS2 repeats, or a secondary structure-containing nucleic acid sequence that does not bind to an RBD (Pseudoknot). • A 5’ end block sequence containing a gRNA scaffold sequence compatible with the Cas9 domain of the gene modifying polypeptides and a gRNA spacer containing either 15 nucleotides or 20 nucleotides.

Table E13 - Exemplary ttRNA Sequences Used in This Example (Sequences Provided in Example 4)

“Pseudoknot” in the “5’ end block contents” field indicates that ttRNAs comprised a 5’ end block that, while assuming a secondary /tertiary structure thought to protect the 5 ’ end of the ttRNA from degradation, is not capable of binding to a Cas domain, e.g., tire Cas domain of the gene modifying polypeptide. Similarly, “Pseudoknot” in the “RRS or substitute sequence” field indicates that ttRNAs comprised (proximal to the 3 ’ end and in place of an RRS) a secondary/tertiary structure drought to protect the 3’ end of the ttRNA from degradation, and that is not capable of binding to an RBD, e.g., the RED domain of the gene modifying polypeptide. Cas9 scaffold ttRNAs (“Scaffold”) comprise a 5’ end block containing a gRNA scaffold sequence compatible with the Cas9 domain of the gene modifying polypeptide, but the 5' end block lacks a gRNA spacer sequence. Cas9 scaffold + spacer ttRNAs comprise a 5 ’ end block and a gRNA scaffold sequence compatible with the Cas9 domain of the gene modifying polypeptide and a shorter (“Scaffold + Shorter Spacer”) or longer (“Scaffold + Longer Spacer”) gRNA spacer sequence. It is thought that a shorter gRNA spacer is sufficient for RNA-directed binding of a Cas9 domain to the genomic target but insufficient for nicking of the target DNA, whereas a longer gRNA spacer is sufficient for both binding and nicking. The sequence of the gRNA that comprises the 3 ^rd component of the gene modifying system is as below

PLV4165:

GCCGAAGCACTGCACGCCGTGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTA GTCCGTTATCAAC TTGAAAAAGTGGCACCGAGTCGGTGC ( SEQ 1D NO: 16,714)

To assess the capacity of the trans-gene modifying system to write long insertions into the genome, 150 nt restoration reporter cell lines (U2OS) were analyzed by flow cytometry and amplicon sequencing 4-days post-transfection/electroporation of the gene modifying systems.

The 3 -component gene modifying system was nucleofected into the U2OS 150 bp insertion GFP reporter-expressing cell line. All 3 components of the gene modifying system were delivered by nucleofection in DNA format. Specifically, 300 ng of gene modifying polypeptide plasmid DNA is combined with 300 ng of ttRNA- and 150 ng of gRNA-cxprcssing plasmids. The modifying polypeptide, ttRNA and gRNA in plasmid DNA format were added to 20pL SE buffer containing 270,000 U2OS 150 bp insertion GFP reporter-expressing cells, and the cells were nucleofected using program DN-100. After nucleofection, cells were grown at 37°C, 5% CO ₂ for at least 4 days prior to harvest and (1) fluorescence readout of GFP restoration by flow cytometry or (2) sequencing readout of accurate sequence insertion by amplicon sequencing. GFP expression or sequencing reads containing the desired 150 nucleotides at the target site w ithin the GFP locus is indicative of the insertion having been accurately w ritten into the genome. FIG. 6A-6D show graphs of % GFP positive cells after treating the 150 bp insertion GFP reporter-expressing cell line with a gene modifying system comprising a ttRNA having the characteristics indicated on tire X-axis and above the graph (PL 15349, PL 15377, and PL 15405 for longer spacer; PL15348, PL15376, or PL15404 for shorter spacer) or with H2O only or a no-ttRNA and no-gRNA control gene modifying system (left 3 bars of each graph; the ttRNAs in the no-ttRNA and no-gRNA conditions were PL15349 and PL15348). The results showed that three different configurations of gene modifying polypeptide were capable of facilitating insertion of the 150 nucleotide fragment into the genome of the cell: Cas9-RBD-RT, Cas9-RT-RBD, and RT-RBD-Cas9. Of these, RT-RBD-Cas9 configuration gene modifying polypeptides achieved the highest % GFP positive cells, suggesting that this configuration has the highest editing activity for 150 nucleotide insertions.

The results also show that, in the presence of a 5 ’ end block sequence containing a gRNA scaffold and gRNA spacer of either 15 (short spacer; binding capable) or 20 (long spacer; binding and nicking capable) nucleotides in length, either lx MS2 or 4x MS2 RRS was sufficient to facilitate insertion of the 150 nucleotide fragment. However, an RRS containing 4 repeats of the MS2 sequence yielded a higher editing rate than an RRS containing a single MS2 sequence, suggesting that a longer RRS (e.g., a stronger or longer-lived RRS:RBD interaction) improves 150 nucleotide editing in the presence of an anchoring 5' end block sequence. The results also show that substituting a sequence having secondary structure (pseudoknot) but incapable of binding to an RBD in place of the RRS produced a ttRNA that facilitated 150 nucleotide fragment insertion. This suggests that in the presence of an anchoring 5’ end block sequence (comprising a gRNA scaffold and gRNA spacer), the RRS-RBD interaction is not necessary for 150 nucleotide fragment insertion but when present may improve editing efficiency. The results further demonstrate that ttRNAs comprising a 5’ end block that facilitates Cas domain nicking of the target site (e g., by comprising a gRNA scaffold and a gRNA spacer of sufficient length, e.g., 20 nucleotides) may facilitate higher rates of 150 nucleotide insertion than ttRNAs comprising 5’ end block sequences that do not facilitate nicking (e.g., by comprising a gRNA scaffold and a gRNA spacer of a shorter length insufficient for Cas domain nicking).

FIGs. 7A-7D show graphs of % perfect editing at the GFP locus as seen by next-generation sequencing data from amplicon sequencing. Perfectly edited reads were defined as any reads that perfectly matched the expected edited sequence, as well as reads that contained the correct insertion size and included one or more ”N" base calls (i.e. no clear base identification at certain sequence positions) due to limitations of the sequencing technology at these read lengths. The results largely corroborated the observation and interpretation of the flow cytometry results of FIGs. 6A-6D. Briefly, the results showed that three different configurations of gene modifying polypeptide were capable of facilitating insertion of the 150 nucleotide fragment into tire GFP locus: Cas9-RBD-RT, Cas9-RT-RBD, and RT-RBD-Cas9. Over 4% and up to 8% perfect editing was observed with the RT-RBD-Cas9 configuration of the gene modifying polypeptide. The amplicon sequencing results also confirmed that ttRNAs comprising a 5’ end block that may facilitate Cas domain nicking of the target site (e.g., by comprising a gRNA scaffold and a gRNA spacer of sufficient length, e.g., 20 nucleotides) promotes higher rates of 150 nucleotide insertion than ttRNAs comprising 5' end block sequences that do not facilitate nicking (e.g., by comprising a gRNA scaffold and a gRNA spacer of a shorter length insufficient for Cas domain nicking). Finally, the results from amplicon sequencing readout also support the interpretation that an RRS containing 4 repeats may have a higher editing rate than an RRS containing a single MS2 sequence, suggesting that a longer RRS (e.g., a stronger or longer-lived RRS:RBD interaction) assists in 150 nucleotide insertion in the presence of an anchoring 5’ end block sequence. Furthermore and in agreement with the flow cytometry results, the RRS-RBD interaction is secondary to the anchoring 5’ end block in its ability to insert a 150 nucleotide sequence in the genome.

To assess the capacity of additional trans-gene modifying systems (described in Example 9 and having different gene modifying polypeptide configurations) to write long insertions into the genome, 150 nt restoration reporter cell lines (U2OS) were analyzed by flow cytometry 4-days post-electroporation of the gene modifying systems.

Table Nl. Exemplary driver amino acid sequences. The 3 -component gene modifying system was nucleofected into the U2OS 150 bp insertion GFP reporter-expressing cell line. All 3 components of the gene modifying system were delivered by nucleofection in DNA format. Specifically, 300 ng of gene modifying polypeptide plasmid DNA is combined with 500 ng of ttRNA- and 150 ng of gRNA-expressing plasmids. The modifying polypeptide, ttRNA and gRNA in plasmid DNA format were added to 20pL SE buffer containing 250,000 U2OS 150 bp insertion GFP reporter-expressing cells, and the cells were nucleofected using program DN-100. After nucleofection, cells were grown at 37° C, 5% CO? for at least 4 days prior to harvest and fluorescence readout of GFP restoration by flow cytometry. GFP expression is indicative of the insertion having been accurately written into the genome.

FIG. 14 shows a graph of % GFP positive cells after treating the 150 bp insertion GFP reporterexpressing cell line with a gene modifying system comprising a ttRNA having 4 MS2 repeats (PE15377) or 1 MS2 repeat (PE15349). The gene modifying polypeptide is indicated in X-axis labels. X-axis labels also indicate the nature of control samples, e.g., the presence or absence of gRNA plasmid, H2O only, no-driver (no gene modifying polypeptide), or no-template (ttRNA) control gene modifying system, or an inactive gene modifying system in which the RT domain of the polypeptide is mutated (RT mutant). The results showed that the additional two configurations of gene modifying polypeptide (RT-Cas9-MCP, and MCP-RT-Cas9) were capable of facilitating insertion of the 150 nucleotide fragment into the genome of the cell. Of these, MCP-RT-Cas9 configuration gene modifying polypeptides achieved similar levels of % GFP positive cells relative to RT-RBD-Cas9, suggesting that this configuration also has the highest editing activity observed for 150 nucleotide insertions. Also tested was a N55K of the MCP region, which also showed strong editing activity in this assay.

Additional trans-gene modifying systems containing alternative RBP domains (as compared to the MCP-containing drivers) were generated as described herein and evaluated for their ability to write long insertions into the genome when paired with their cognate RRS sequences (as in Table ##, e.g. MCP variants with MS2 variants; PCP variants with PP7 variants; Com variants with com variants). 150 nt restoration reporter cell lines (U2OS) were analyzed by flow' cytometry and amplicon sequencing 4-days post-electroporation of the gene modifying systems containing the alternative RBP domains with cognate RRS sequences.

Table N2. Amino acid sequences for exemplary RBP/RRS pairing drivers

Table N3. Exemplary template RNA sequences

The 3 -component gene modifying system was nucleofected into the U2OS 150 bp insertion GFP reporter-expressing cell line. All 3 components of the gene modifying system were delivered by nucleofection in DNA format. Specifically, 300 ng of gene modifying polypeptide plasmid DNA is combined with 500 ng of ttRNA- and 150 ng of gRNA-expressing plasmids. The modifying polypeptide, ttRNA and gRNA in plasmid DNA format were added to 20pL SE buffer containing 250,000 U2OS 150 bp insertion GFP reporter-expressing cells, and the cells were nucleofected using program DN-100. After nucleofection, cells were grown at 37°C, 5% CO ₂ for at least 4 days prior to harvest and ( 1 ) fluorescence readout of GFP restoration by flow cytometry or (2) sequencing readout of accurate sequence insertion by amplicon sequencing. GFP expression or sequencing reads containing the desired 150 nucleotides at the target site w ithin the GFP locus is indicative of the insertion having been accurately written into the genome. FIG. 15A shows a graph of % GFP positive cells after treating tire 150 bp insertion GFP reporterexpressing cell line with a gene modifying system comprising a gRNA, and a gene modifying polypeptide and ttRNA encoding cognate RBP/RRS pairs (e.g. MCP variants with MS2 variants: PCP variants with PP7 variants; Com variants with com variants) as indicated in X-axis labels. Controls are also indicated by X-axis labels: H20 only, no-driver (gene modifying polypeptide), no gRNA or no-template (ttRNA) control gene modifying system, or an inactive gene modifying system in which the RT domain of the polypeptide is mutated (left 5 bars of the graph). The results showed that all 3 cognate RBP/RRS pairs (MCP/MS2, PCP/PP7, Com/com) in 3 tested polypeptide configurations, were capable of facilitating insertion of the 150 nucleotide fragment into the genome of the cell. Gene modifying polypeptides paired with non-cognate RRS-comprising ttRNAs had lower % GFP positive cells (data not shown). These results indicate that the gene modifying system is capable of inserting 150 bp into the genome with various RBP/RRS pairs, and the increased % GFP positive cells for cognate pairs for efficient insertion activity indicates that the specific interaction between cognate RBPs and RRSs enhance the efficiency of 150 nt insertion.

FIG. 15B shows a graph of % perfect editing at the GFP locus as seen by next-generation sequencing data from amplicon sequencing. Perfectly edited reads were defined as any reads that perfectly matched the expected edited sequence, as well as reads that contained the correct insertion size and included one or more “N” base calls (i.e. no clear base identification at certain sequence positions) due to limitations of the sequencing technology at these read lengths. The results largely corroborated the observation and interpretation of the flow cytometry results of FIG. 15A. Briefly, the results showed that the three tested RBP/RRS pairs (MCP/MS2, PCP/PP7, and Com/com) w ere capable of facilitating insertion of the 150 nucleotide fragment into the GFP locus in all tested configurations of the polypeptide (FIG. 15B). Over 12% and up to 26% perfect editing was observed for all tested configurations and RBP/RRS pairs. The amplicon sequencing results also confirmed that cognate pairing of RBPs and RRSs enhances the % perfect edit above non-cognate pairs (data not shown). Finally, the results from amplicon sequencing readout also show higher % perfect editing for PCP/PP7 or Com/com than for MCP/MS2 in some cases, indicating that these RBP/RRS pairs are as effective or more effective in these gene modifying systems.

An additional trans-gene modifying system was generated with a gene modifying polypeptide containing an alternative exemplary RT domain, Marathon, derived from a group II intron. The capacity of the additional trans-gene modifying systems to write long insertions into the 150 nt restoration reporter cell lines (U2OS) was assessed and compared to systems containing tire AVIRE RT-containing drivers examined above using flow cytometry and amplicon sequencing 4-days post-electroporation of tire gene modifying systems.

Table N4. Exemplary Marathon driver sequences

An exemplary Marathon RT domain sequence is provided below as SEQ ID NO: 17,101:

DTSNLMEQILSSDNLNRAYLQVVRNKGAEGVDGMKYTELKEHLAKNGETIKGQLRTR KYKPQPARRVEIP KPDGGVRNLGVPTVTDRFIQQAIAQVLTPIYEEQFHDHSYGFRPNRCAQQAILTALNIMN DGNDWIVDID LEKFFDTVNHDKLMTLIGRTIKDGDVISIVRKYLVSGIMIDDEYEDSIVGTPQGGNLSPL LANIMLNELD KEMEKRGLNFVRYADDCI IMVGSEMSANRVMRNISRFIEEKLGLKVNMTKSKVDRPSGLKYLGFGFYFDP RAHQFKAKPHAKSVAKFKKRMKELTCRSWGVSNSYKVEKLNQLIRGWINYFKIGSMKTLC KELDSRIRYR LRMCIWKQWKTPQNQEKNLVKLGIDRNTARRVAYTGKRIAYVCNKGAVNVAISNKRLASF GLISMLDYYI EKCVTC (SEQ ID NO: 17,101) The 3-component gene modifying system was nucleofected into the U2OS 150 bp insertion GFP reporter-expressing cell line. All 3 components of the gene modifying system were delivered by nucleofection in DNA format. Specifically, 100 ng of gene modifying polypeptide plasmid DNA is combined with 500 ng of ttRNA- and 150 ng of gRNA-expressing plasmids. The modifying polypeptide, ttRNA and gRNA in plasmid DNA fomiat were added to 20pL SE buffer containing 250,000 U2OS 150 bp insertion GFP reporter-expressing cells, and the cells were nucleofected using program DN-100. After nucleofection. cells were grown at 37°C, 5% CO ₂ for at least 4 days prior to harvest and fluorescence readout of GFP restoration by flow cytometry. GFP expression is indicative of the insertion having been accurately written into the genome. FIG. 16 shows a graph of % GFP positive cells after treating the 150 bp insertion GFP reporterexpressing cell line with a gene modifying system comprising agRNA, ttRNA and a gene modifying polypeptide comprising an exemplary Marathon RT in various polypeptide configurations as indicated in X-axis labels (Config 1, Config 2, and Config 3 are as described in Example 3), or with H2O only or no- gRNA negative control gene modifying systems. The results showed that gene modifying polypeptides comprising the Marathon RT were capable of inserting the 150 bp sequence to restore the GFP locus in any of the 3 tested polypeptide configurations when co-delivered with a full gene modifying system (i.e. not in the absence of the gRNA). Several additional point mutants of the Marathon RT domain were generated that have not yielded effective editing in this system (data not shown). The results show that trans gene modifying systems utilizing a variety of different RT domains are capable of facilitating inserting long (e.g., 150 nucleotide) sequences into target DNA.

Taken together, these data further support the interpretation that the system has a degree of modularity, and that alternate RBP/RRS pairs or RTs may be functional in this system for insertion of sequences into the genome.

Example 7: Evaluation of Long Insertion Activity of an Exemplary Gene Modifying Polypeptide Using A Range of Trans Template RNA Dosages with a 3-component system

This example describes the evaluation of exemplary three (3)-component gene modifying systems in the targeted insertion of a 150 nt sequence in the human genome. The gene modifying systems each comprised (1) a gene modifying polypeptide generated in Example 3 (and demonstrated to have transrecruitment and rewrite activity in Examples 7 and 9 of PCT Application PCT/US2022/076064, which Examples are herein incorporated by reference), (2) varying levels of a trans template RNA (ttRNA) comprising 4 RRSs , and (3) exemplary gRNA PLV4165.

Two gene modifying polypeptides were used in this Example; amino acid sequences of which are provided in Example 3.

• PL12109: RT-RBD-DBD; One MCP domain

• PL12113: RT-RBD-DBD; Two MCP domains

The ttRNAs used in this Example are PL15376 and PL15377 and nucleotide sequences are provided in Example 4. The ttRNAs contained:

• An RRS containing 4 MS2 repeats. • A 5’ end block sequence containing a gRNA scaffold sequence compatible with the Cas9 domain of the gene modifying polypeptides and a gRNA spacer containing either 15 nucleotides or 20 nucleotides.

• A 15 nucleotide long gRNA spacer can bind Cas9 and the target DNA but is not expected to nick the DNA. A longer 20 nucleotide gRNA spacer is sufficient for both binding and nicking. The sequence of the gRNA that comprises the 3 ^rd component of the gene modifying system is as below

PLV4165:

GCCGAAGCACTGCACGCCGTGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTA GTCC GTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGC (SEQ ID NO: 16.714)

To assess the capacity of the trans-gene modifying system to write long insertions into the genome, 150 nt restoration reporter cell lines (U2OS) were analyzed by flow cytometry and amplicon sequencing 4-days post-transfection/electroporation of the gene modifying systems.

The 3-component gene modifying system was nucleofected into the U2OS 150 bp insertion GFP reporter-expressing cell line. All 3 components of the gene modifying system were delivered by nucleofection in DNA format. Specifically, 300 ng of gene modifying polypeptide plasmid DNA was combined with 50, 150, 300, or 500 ng of ttRNA-expressing plasmid DNA () and 150 ng of gRNA- expressing plasmid DNA. The modifying polypeptide, ttRNA and gRNA in plasmid DNA format were added to 20 pF SE buffer containing 270,000 U2OS 150 bp insertion GFP reporter-expressing cells, and the cells were nucleofected using program DN-100. After nucleofection, cells were grown at 37 C, 5% CO ₂ for at least 4 days prior to harvest and (1) fluorescence readout of GFP restoration by flow cytometry or (2) sequencing readout of accurate sequence insertion by amplicon sequencing. GFP expression or sequencing reads containing the desired 150 nucleotides at the target site within the GFP locus is indicative of the insertion having been accurately written into the genome.

FIGs. 8A-8B show graphs of % GFP positive cells after treating the GFP reporter-expressing cell line with gene modifying systems comprising varying levels of exemplary ttRNA PL15376 or PL15377 comprising 4 MS2 sequences and a 5 ’ end block sequence containing a gRNA scaffold sequence and a gRNA spacer of either 15 (short) or 20 (long) nucleotides (ttRNA plasmid level indicated on the X-axis, boxes 4-7 from left) or with H2O only (box 1 from left) or a missing component control (boxes 2 and 3 from left, missing polypeptide and missing gRNA controls, ttRNAs used are indicated above the graphs). Dotted line marks the background level of signal observed from the “no polypeptide” control. The results showed that increasing amounts of the ttRNA can improve editing efficiency. The highest dose of the ttRNA-expressing plasmid (500 ng) with 5’ end block sequence containing a gRNA scaffold sequence and a 20 nucleotide spacer sequence capable of nicking yielded the highest editing at 11% GFP positive cells above background (using signal from the “no polypeptide” control as background), suggesting that editing efficiency of 150 nucleotide insertions can be further increased by increasing the level of ttRNA with which a cell is treated. Furthermore, the results indicate that increasing amounts of the ttRNA with 5’ end block sequence containing a gRNA scaffold sequence and a 15 nucleotide spacer sequence incapable of nicking but capable of binding DNA can yield up to 5% GFP positive cells above background. This result suggests that although a secondary nick is more efficient, titrating tire nonnicking template can yield higher 150 nucleotide insertions and substantial editing.

FIGs. 9A-9B shows a graph of % perfect editing at the GFP locus as seen by next-generation sequencing data from amplicon sequencing. The results followed a pattern similar to the flow cytometry results shown in FIGs. 8A-8B. Briefly, the results showed that increasing amounts of the ttRNA can improve editing efficiency. At tire highest dose of the ttRNA-expressing plasmid (500 ng) with 5’ end block sequence containing a gRNA scaffold sequence and a 20-nucleotide spacer sequence capable of nicking, as high as 37% mean perfect editing/rewrite was observed, suggesting that editing efficiency of 150 nucleotide insertions can be further increased by increasing the level of ttRNA with which a cell is treated. Furthermore, the results indicate that increasing amounts of the ttRNA with 5’ end block sequence containing a gRNA scaffold sequence and a 15 -nucleotide spacer sequence incapable of nicking but capable of binding DNA can yield up to 24% mean perfect editing/rewrite. As observed from the flow cytometry data, this result suggests that although a secondary nick is more efficient, titrating the nonnicking template can also yield 150 nucleotide insertions and substantial editing.

Of note, the 150 bp insertion GFP-reporter cell line contains 2 copies of the target locus. Without wishing to be bound by theory, when these cells are transfected with higher amounts of ttRNA-expressing plasmids (as in this example), it is possible that both copies of the reporter gene get edited by the genemodifying system. In this experiment we observe a higher editing % from amplicon sequencing (Fig. 9), which quantifies the number of edited genomes than from flow cytometry (Fig. 8), which quantifies the number of cells containing at least 1 copy of the desired edit. This suggests that both copies of the reporter are perfectly edited in the majority of GFP -expressing cells by the gene modifying system.

Example 8: Evaluation of Long Insertion Activity of Exemplary Gene Modifying Polypeptides Using Trans Template RNAs with a 5-component system

This example describes the evaluation of exemplary gene modifying systems having up to five components in the targeted insertion of a 150 nt sequence in the human genome. The gene modifying systems each comprise (1) a gene modifying polypeptide generated in Example 3 (and demonstrated to have trans-recruitment and rewrite activity in Examples 7 and 9 of PCT Application PCT/US2022/076064, which is herein incorporated by reference in its entirety), (2) a trans template RNA (ttRNA) generated in Example 4, (3) exemplary gRNA PLV4165, an additional (4) Cas9 or different gene modifying polypeptide molecule recruited to the nicked DNA strand by the trans-template RNA (e.g., by an 5' end block containing a gRNA spacer), or by (5) its species-matched gRNA.

More specifically, a gene modifying polypeptide binds the guide RNA molecule and a ttRNA molecule, together forming a gene modifying complex, which binds and nicks the target locus and performs template-directed incorporation of the desired edit in one strand of the genomic DNA. The additional Cas9 or different gene modifying polypeptide molecule is recruited to the nicked DNA strand by ttRNA (e.g., by a 5’ end block containing a gRNA spacer), or by its species-matched gRNA, forming the second complex. The second complex may extend the bubble of unwound/single -stranded DNA and facilitate large insertions, and may also be used to introduce a nick on the second strand to initiate second strand synthesis, and/or signal to the cell’s endogenous repair system that the edited strand should be copied and maintained.

To assess the genome-editing capacity of the gene modifying system, a 5-component gene modifying system is transfected/electroporated into the HEK293T/U2OS 150 bp insertion GFP reporterexpressing cell line. All components of the gene modifying system are delivered by nucleofection in DNA format. Specifically. 200-800 ng of gene modifying polypeptide plasmid DNA is combined with 50-200 ng ttRNA and 50-200 ng gRNA in plasmid format. An additional 50-200 ng of Cas9- or different gene modifying polypeptide -encoding plasmid DNA and/or 25-100 ng of a second gRNA-encoding plasmid are also transfected/nucleofected together with the gene modifying system. The 4-5 plasmids encoding the gene modifying system are added to 25pL SF/SE buffer containing 250,000 HEK293T/U2OS 150 bp insertion GFP reporter-expressing cells, and the cells are nucleofected using program DS-150/DN-100. After nucleofection, cells are grown at 37°C, 5% CO ₂ for at least 3 days prior to cell lysis and genomic DNA extraction, or fluorescence readout by flow cytometry. To analyze gene editing activity, primers flanking the GFP locus can be used to amplify across the locus. Amplicons are analyzed via short read sequencing using an Illumina MiSeq. Conversion of the GFP- 150 bp deletion gene sequence to a fully restored GFP coding sequence indicate successful editing. In some embodiments, the assay will indicate that at least 10%, 20%, 30%, 40%, 50%, 60%. or 70% of copies of the GFP- 150 bp deletion sequence in the sample are converted to the fully restored GFP sequence. Example 9: Generation of Additional Exemplary Drivers

This example describes the generation of exemplary drivers and trans templates for use in the three, four, or five component RNA-based gene modifying systems described in Examples herein.

An additional set of 10 exemplary gene modifying polypeptides was generated containing:

1. a Cas-nuclease with one endonuclease domain inactivated (in this example, Spy N863A Cas9),

2. a reverse transcriptase (RT) (in this example, the RT of the gene modifying polypeptide encoded by: PLV10990/RNAIVT338 as in Example 3), and

3. an RNA binding domain (RBD) containing 1, 2, or 4 RBP repeats (in this example, 1, 2, or 4 MCPv2 repeats as provided in Table 31), with each repeat connected to the other RBP repeats by one of 4 linker peptides from Table 10, or with an alternate dimer junction as described in Peabody & Lim (1996) NAR.

The alternate MCPv2 dimer junction described in #3, removes the 3 N-terminal amino acids (M, A. S) of the second MCPv2 repeat in the dimer, and replaces it with an alanine, e.g., as shown in the following sequences:

MASNFTQFVLVDNGGTGDVTVAPSNFANGIAEWISSNSRSQAYKVTCSVRQSSAQNR KY TIKVEVPKGAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY [linker] -

MASNFTQFVLVDNGGTGDVTVAPSNFANGIAEWISSNSRSQAYKVTCSVRQSSAQNR KY TIKVEVPKGAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY, the [linker] is replaces with an alanine, and the bolded/underlined sequence in the second copy of MCPv2 (above) is removed, to produce the below sequence:

MASNFTQFVLVDNGGTGDVTVAPSNFANGIAEWISSNSRSQAYKVTCSVRQSSAQNR KY TIKVEVPKGAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY - A

NFTQFVLVDNGGTGDVTVAPSNFANGIAEWISSNSRSQAYKVTCSVRQSSAQNRKYT IK VEVPKGAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY.

These 3 domains are connected using peptide linkers, e.g., as found in Table 10, (in this example by SEQ ID: (217)). The set of 10 exemplar} gene modifying polypeptides encompassed a subset of the configurations set forth in Examples 1 and 2:

• RT - linker - Cas9 - linker - (RBP repeat) _n

• (RBP repeat) _n - linker - RT - linker - Cas9 The sequences of tire exemplary gene modifying polypeptides are given in Table S5 and Table S6 below:

Table S5. Exemplary gene modifying sequences for Configuration 1 (i.e., RT - linker - Cas9 - linker - (RBP repeat),,)

Table S6. Exemplary gene modifying sequences for Configuration 2 (i.e., (RBP repeat) _n - linker - RT linker - Cas9)

Example 10: Evaluation of Sequence Replacement Activity of Exemplary Gene Modifying Polypeptides Using Trans Template RNAs with a 5-component system

This example describes tire evaluation of exemplary gene modifying systems having up to five components in the targeted insertion of a 150 nt sequence in the human genome and deletion of a variable number of endogenous nucleotides (referred to herein as replacement). The gene modifying systems each comprise (1) a gene modifying polypeptide generated in Example 3 (and demonstrated to have transrecruitment and rewrite activity in Examples 7 and 9 of PCT Application PCT/US2022/076064, which is herein incorporated by reference in its entirety), or in Example 9, (2) a trans template RNA (ttRNA) in which the post-edit homology region encompasses the spacer encoded by the 5’ end block of the ttRNA, as depicted in Fig. 10A, (in this example as in ttRNA sequences described in Table S7, PL25358-25379, and PL25351-25357), (3) exemplary gRNA PLV4165, an additional (4) Cas9 or different gene modifying polypeptide molecule recruited to the nicked DNA strand by the trans-template RNA (e g., by an 5’ end block containing a gRNA spacer), or by (5) its species-matched gRNA.

Table S7. Exemplary ttRNA sequences

More specifically, a gene modifying polypeptide binds the guide RNA molecule and a ttRNA molecule, together forming a gene modifying complex, which binds and nicks the target locus and performs template-directed incorporation of the desired edit in a first strand of the genomic DNA. By designing post-edit homology regions that are complementary to sequences distant from the insertion site (Fig. 10B), the intervening sequences are deleted (grey box in Fig. 10C), and in effect replaced by novel sequences encoded in the ttRNA. The additional Cas9 or different gene modifying polypeptide molecule is recruited to the nicked DNA strand by ttRNA (e.g., by a 5’ end block containing a gRNA spacer), or by its species-matched gRNA, forming tire second complex. The second complex may extend the bubble of unwound/single -stranded DNA and facilitate large insertions, and may also be used to introduce a nick on the second strand to initiate second strand synthesis, and/or signal to the cell's endogenous repair system that the edited strand should be copied and maintained. Without wishing to be bound by theory, the length of one or both components of the post-edit homology region (i.e. Fig. 10C, ‘’primer” and/or ’‘extension”) may be adjusted to alter the number of endogenous nucleotides deleted.

To assess the genome-editing capacity of the gene modifying system, the gene modifying system was electroporated into the U2OS reporter cell lines designed to generate GFP signal upon successful sequence replacement. Specifically, these cells contain a reporter cassette consisting of a GFP sequence with a 150 bp deletion in the coding sequence that knocks out fluorescence, and in which 50 bp, 150 bp, 250 bp, or 350 bp of non-GFP DNA (a disruption sequence) was introduced that does not produce a fluorescent protein. In order to produce a GFP signal, the gene modifying complex must replace the 50- 350 bp disruption sequence with the 150 bp of deleted GFP coding sequence that is encoded in the ttRNA. Cells expressing GFP therefore indicate that precise sequence replacement has occurred at the reporter locus.

All components of the gene modifying system were delivered by nucleofection in DNA format. Specifically, lOOng of gene modifying polypeptide plasmid DNA was combined with 500 ng ttRNA and 150 ng gRNA in plasmid format. The 3 plasmids encoding the gene modifying system were added to 25pL SE buffer containing 250,000 U2OS cells carrying the sequence replacement reporter cassette, and the cells were nucleofected using program DN-100. After nucleofection, cells were grown at 37°C, 5% CO ₂ for 4 days prior to analysis of GFP signal by flow cytometry. GFP expression is indicative of cells in which the 150 nucleotide insertion was accurately written into the genome, replacing the 50-350 bp disruption sequence. FIG. 13 shows a graph of % GFP positive cells after treating the sequence -replacement reporter cell lines with a gene modifying system comprising a ttRNA having the characteristics indicated on the X-axis or with a control gene modifying system. The results showed that no GFP positive cells were observed when cells were treated with control gene modify ing systems lacking one component, or with a control gene modifying system in which the gene modifying polypeptide has an inactivated RT domain.

In contrast, approximately 8%, 6%, 7%. and 3% GFP positive cells (indicative of successful sequence replacement) were observed when cells with 50 bp, 150 bp, 250 bp, and 350 bp GFP disruptions, respectively, were treated with gene modifying systems comprising all components of the gene modifying system, and ttRNAs having 5 ’ end blocks comprising a Cas9 gRNA scaffold and 20 nucleotide gRNA spacer wherein the ttRNA comprised a pseudoknot at its 3’ end. This result indicates that the gene modifying complexes precisely replace sequences in the genome with the desired insertion cassette encoded in the ttRNA. This suggests that the ability of the 5‘ end block to associate the gene modifying polypeptide (e.g., via the Cas9 domain) and/or the ttRNA to the genomic target and induce nicking of the target DNA is sufficient to facilitate precise sequence replacement in the genome.

The results further show that approximately 16%, 17%, 22%, and 13% GFP positive cells were observed when cells with 50 bp, 150 bp, 250 bp, and 350 bp GFP disruptions, respectively, were treated with gene modifying systems comprising ttRNAs having 5’ end blocks comprising a Cas9 gRNA scaffold and 20 nucleotide gRNA spacer wherein the ttRNA comprised an RRS. Uris result indicates that precise sequence replacement is increased for gene modifying systems comprising ttRNAs having an RRS by the ability of the ttRNA to stably associate with the RBP domain of the gene modifying polypeptide via an RRS.

These results suggest that the presence of RRS structures at the 3 ’ end of the ttRNA, which are predicted to enable stable association with the RBP domain of the gene modifying polypeptide, enhance precise replacement of the 50-350 bp of disruption sequence with the intended 150 bp GFP coding sequence. The result further suggests that the ability of tire ttRNA to stably associate with the RBP domain of the gene modifying polypeptide via the RRS sequence increases the rate of precise sequence replacement of the 50-350 bp of disruption sequence with the intended 150 bp insertion sequence encoded in the ttRNA.

The results together support the interpretation that a ttRNA anchored to a target genomic DNA site (e.g., tire complex of the target genomic DNA site, a first gene modifying polypeptide, and a gRNA) by two different associations (e.g., here an RBP:RRS interaction with the first gene modifying polypeptide, and a 5’ end block gRNA scaffold/spacer interaction with the target genomic DNA (e.g.. mediated by a second gene modifying polypeptide)) enables a gene modifying system to site -specifically replace up to 350 bp of genomic sequence with a 150 bp insertion sequence encoded in the ttRNA. The results further support the interpretation that the efficiency of such a sequence replacement is improved by tire interaction of the RBP with the RRS.

Example 11: Evaluating the Role of Homology Arm Position (e.g., Post-edit Homology Region) on Long Insertion Activity of Exemplary Gene Modifying Polypeptides Using Trans Template RNAs with a 5-component system

This example describes the evaluation of exemplary gene modifying systems having up to five components in the targeted insertion of a 150 nt sequence in the human genome. The gene modifying systems each comprise (1) a gene modifying polypeptide generated in Example 3 (and demonstrated to have trans-recruitment and rewrite activity in Examples 7 and 9 of PCT Application PCT/US2022/076064. which is herein incorporated by reference in its entirety), or in Example 9, (2) a trans template RNA (ttRNA) in which a region of homology (e.g., the post-edit homology region) encompasses the spacer encoded by the 5 ’ end block of the ttRNA, and/or is complementary to the sequence immediately 5’ of the second nick as depicted in Fig. 11, (in this example as in ttRNA sequences described in Table S7 and S8, PL24822 and PL25346-25350 and PL25351-25357), (3) exemplary gRNA PLV4165, an additional (4) Cas9 or different gene modify ing polypeptide molecule recruited to the nicked DNA strand by the trans-template RNA (e.g., by an 5’ end block containing a gRNA spacer), or by (5) its species-matched gRNA.

Table S8. Exemplary ttRNA sequences

More specifically, a gene modifying polypeptide binds the guide RNA molecule and a ttRNA molecule, together forming a gene modifying complex, which binds and nicks the target locus and performs template-directed incorporation of the desired edit in a first strand of the genomic DNA. Hie additional Cas9 or different gene modifying polypeptide molecule is recruited to the nicked DNA strand by ttRNA (e.g., by a 5’ end block containing a gRNA spacer), or by its species-matched gRNA, forming the second complex. The second complex may extend the bubble of unwound/single-stranded DNA and facilitate large insertions, and may also be used to introduce a nick on the second strand to initiate second strand synthesis, and/or signal to the cell’s endogenous repair system that the edited strand should be copied and maintained. The ttRNAs are designed to comprise a homology region, e.g., a post-edit homology region, that is positioned to encompass the sequence at the site of the 2 ^nd nick. Given the complementarity of the region of homology encoded in the ttRNA to the sequence 5’ of the 2 ^nd nick, the nicked DNA may then be used as a primer, and the newly synthesized cDNA may be used as a template for replication of the inserted sequence in the second strand of the genomic target.

It is contemplated that to assess the genome-editing capacity of the gene modify ing system, a gene modifying system having up to five components is electroporated into the HEK293T/U2OS 150 bp insertion GFP reporter-expressing cell line. All 4-5 components of the gene modifying system are delivered by nucleofection in DNA/RNA format. Specifically, 200-800 ng of gene modifying polypeptide plasmid DNA (or 1-4 ug mRNA) is combined with 50-200 ng ttRNA and 50-200 ng gRNA in plasmid format (or 2.5-10 uM ttRNA and 2.5-10 uM gRNA in RNA format). An additional 50-200 ng of Cas9- or different gene modify ing polypeptide-encoding plasmid DNA (or 1-4 ug mRNA) and/or 25-100 ng of a second gRNA-encoding plasmid (or 1-10 uM gRNA in RNA format) are also nucleofected together with the gene modifying system. The 4-5 plasmids or RNAs encoding the gene modifying system are added to 25pL SF/SE buffer containing 250,000 HEK293T/U2OS 150 bp insertion GFP reporter-expressing cells, and the cells are nucleofected using program DS-150/DN-100. After nucleofection, cells are grown at 37°C, 5% CO ₂ for at least 3 days prior to cell lysis and genomic DNA extraction. To analyze gene editing activity, primers flanking the GFP locus can be used to amplify across the locus. Amplicons arc analyzed via short read sequencing, e.g. using an Illumina MiSeq. Replacement of the genomic sequence with the template sequence encoded in the ttRNA or insertion of the template sequence encoded in the ttRNA will indicate successful editing.

In one example, to assess the genome -editing capacity of the gene modifying system, a 4- component gene modifying system was electroporated into the U2OS 150 bp insertion GFP reporterexpressing cell line. All 4 components of the gene modifying system were delivered by nucleofection in DNA format. Specifically, 100 ng of gene modifying polypeptide plasmid DNA was combined with 500 ng ttRNA and 150 ng gRNA in plasmid format. The 3 plasmids expressing the 4-component system were added to 20j.iL SE buffer containing 250,000 U2OS 150 bp insertion GFP reporter-expressing cells, and the cells were nucleofected using program DN-100. After nucleofection, cells were grown at 37°C, 5% CO ₂ for 4 days prior to cell lysis and genomic DNA extraction. To analyze gene editing activity, primers flanking the GFP locus were used to amplify across the locus. Amplicons were analyzed via short read sequencing, e.g. using an Illumina MiSeq. Replacement of the genomic sequence with the template sequence encoded in the ttRNA or insertion of tire template sequence encoded in the ttRNA indicated successful editing.

FIG. 17 shows a graph of % perfect editing at the GFP locus as seen by next-generation sequencing data from amplicon sequencing after treating the 150 bp insertion GFP reporter-expressing cell line with a gene modifying system comprising a gRNA plasmid, a gene modifying polypeptide, and a ttRNA having the primer length (as illustrated in FIGs. 10A-10C and 11A-11C) indicated in X-axis labels, or with H2O only or a no-driver (gene modifying polypeptide), no gRNA or no-template (ttRNA) control gene modifying system (left 4 bars of the graph). Perfectly edited reads were defined as any reads that perfectly matched the expected edited sequence, as well as reads that contained the correct insertion size and included one or more “N" base calls (i.e. no clear base identification at certain sequence positions) due to limitations of the sequencing technology at these read lengths. Hie results show that the length of the primer impact editing efficiency, where overall, shortening of the primer results in decreased integration efficiency, particularly at primer lengths below 20 nt. The impact of primer length is more significant in the absence of an extension of the homology region past the primer (FIG. 17, “extension = 0 nt"), whereas the presence of an extension of the homology region rescued editing efficiency for templates containing primers shorter than 20 nt (FIG. 17, compare “extension = 0 nt" to “extension = 15 nt"). These data support the interpretation that the length of the priming sequence is important for editing efficiency, and that for short primers, an extension sequence may be included to augment editing efficiency.

Example 12: Evaluation of Long Insertion Activity of Exemplary Gene Modifying Polypeptides Using Trans Template RNAs with a 6-component system

This example describes the evaluation of exemplary gene modifying systems having up to six components in the targeted insertion of a 150 nt sequence in the human genome. The gene modifying systems each comprise (1) a gene modifying polypeptide generated in Example 3 (and demonstrated to have trans-recruitment and rewrite activity in Examples 7 and 9 of PCT Application PCT/US2022/076064, which is herein incorporated by reference in its entirety), or in Example 9, (2) a trans template RNA (ttRNA) in which the spacer encoded by the 5’ end block of the ttRNA is shorter than 16 nt to enable template anchoring without concomitant nicking of the genomic target (as depicted in Fig. 12, in this example as in ttRNA sequences described in Table s9), (3) exemplary’ gRNA PLV4165, two additional (4-5) Cas9 or different gene modifying polypeptide molecules recruited to the nicked DNA strand by the trans-template RNA (e.g., by an 5’ end block containing a gRNA spacer), and by (6) an additional species-matched gRNA.

Table S9. Exemplary ttRNA sequences

More specifically, a gene modifying polypeptide binds the guide RNA molecule and a ttRNA molecule, together forming a gene modifying complex, which binds and nicks the target locus and performs template-directed incorporation of the desired edit in a first strand of the genomic DNA. Hie additional Cas9 or different gene modifying polypeptide molecule is recruited to the nicked DNA strand by ttRNA (e.g., by a 5’ end block containing a gRNA spacer), forming a second complex, and by the additional species-matched gRNA, forming a third complex. The second complex may extend the bubble of unwound/ single-stranded DNA and facilitate large insertions, while the third complex is used to introduce a nick on the second strand to initiate second strand synthesis, and/or signal to the cell’s endogenous repair system that the edited strand should be copied and maintained.

To assess the genome-editing capacity of the gene modifying system, a 6-component gene modifying system is electroporated into the HEK293T/U2OS 150 bp insertion GFP reporter-expressing cell line. All 6 components of the gene modifying system are delivered by nucleofection in DNA/RNA format. Specifically, 200-800 ng of gene modifying polypeptide plasmid DNA (or 1-4 ug mRNA) is combined with 50-200 ng ttRNA and 50-200 ng gRNA in plasmid format (or 2.5-10 uM ttRNA and 2.5- 10 uM gRNA in RNA format). An additional 50-200 ng of Cas9- or different gene modifying polypeptide-encoding plasmid DNA (or 1-4 ug mRNA) and/or 25-100 ng of a second gRNA-encoding plasmid (or 1-10 uM gRNA in RNA format) are also nucleofected together with the gene modifying system. The plasmids or RNAs encoding the gene modifying system are added to 25pL SF/SE buffer containing 250,000 HEK293T/U2OS 150 bp insertion GFP reporter-expressing cells, and the cells are nucleofected using program DS-150/DN-100. After nucleofection, cells are grown at 37°C, 5% CO? for at least 3 days prior to cell lysis and genomic DNA extraction. To analyze gene editing activity, primers flanking the GFP locus can be used to amplify across the locus. Amplicons are analyzed via short read sequencing, e.g. using an Illumina MiSeq. Replacement of tire genomic sequence with the template sequence encoded in the ttRNA or insertion of the template sequence encoded in the ttRNA will indicate successful editing.

It should be understood that for all numerical bounds describing some parameter in this application, such as ’‘about,” “at least,” “less than,” and “more than,” the description also necessarily encompasses any range bounded by the recited values. Accordingly, for example, the description “at least 1, 2, 3, 4, or 5” also describes, inter alia, tire ranges 1-2, 1-3, 1-4, 1-5, 2-3, 2-4, 2-5, 3-4, 3-5, and 4-5, et cetera.

For all patents, applications, or other reference cited herein, such as non-patent literature and reference sequence information, it should be understood that they are incorporated by reference in their entirety for all purposes as well as for the proposition that is recited. Where any conflict exists between a document incorporated by reference and tire present application, this application will control. All infomration associated with reference gene sequences disclosed in this application, such as GenelDs or accession numbers (typically referencing NCBI accession numbers), including, for example, genomic loci, genomic sequences, functional annotations, allelic variants, and reference mRNA (including, e.g., exon boundaries or response elements) and protein sequences (such as conserved domain structures), as well as chemical references (e.g., PubChem compound, PubChem substance, or PubChem Bioassay entries, including the annotations therein, such as structures and assays, et cetera), are hereby incorporated by reference in their entirety.

Headings used in this application are for convenience only and do not affect the interpretation of this application.