The Design and Application of DNA-Editing Enzymes as Base Editors

Literature Cited

1. 1.

   Conticello S, Langlois M, Neuberger M. 2007. Insights into DNA deaminases. Nat. Struct. Mol. Biol. 14:7–9
   [Google Scholar]
2. 2.

   Conticello S, Thomas C, Petersen-Mahrt S, Neuberger M. 2005. Evolution of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases. Mol. Biol. Evol. 22:367–77
   [Google Scholar]
3. 3.

   Di Noia JM, Neuberger MS. 2007. Molecular mechanisms of antibody somatic hypermutation. Annu. Rev. Biochem. 76:1–22
   [Google Scholar]
4. 4.

   Swanton C, McGranahan N, Starrett G, Harris R. 2015. APOBEC enzymes: mutagenic fuel for cancer evolution and heterogeneity APOBEC and cancer heterogeneity. Cancer Discov 5:704–12
   [Google Scholar]
5. 5.

   Pecori R, Di Giorgio S, LJ Paulo, Papavasiliou FN. 2022. Functions and consequences of AID/APOBEC-mediated DNA and RNA deamination. Nat. Rev. Genet. 23:8505–18
   [Google Scholar]
6. 6.

   Jumper J, Evans R, Pritzel A, Green T, Figurnov M et al. 2021. Highly accurate protein structure prediction with AlphaFold. Nature 596:583–89
   [Google Scholar]
7. 7.

   Kouno T, Silvas T, Hilbert B, Shandilya S, Bohn M et al. 2017. Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity. Nat. Commun. 8:15024
   [Google Scholar]
8. 8.

   Yang L, Briggs A, Chew W, Mali P, Guell M et al. 2016. Engineering and optimising deaminase fusions for genome editing. Nat. Commun. 7:13330
   [Google Scholar]
9. 9.

   Komor A, Kim Y, Packer M, Zuris J, Liu D. 2016. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533:420–24
   [Google Scholar]
10. 10.

    Koblan L, Doman J, Wilson C, Levy J, Tay T et al. 2018. Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. Nat. Biotechnol. 36:843–46
    [Google Scholar]
11. 11.

    Komor A, Zhao K, Packer M, Gaudelli N, Waterbury A et al. 2017. Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity. Sci. Adv. 3:eaao4774
    [Google Scholar]
12. 12.

    Zafra M, Schatoff E, Katti A, Foronda M, Breinig M et al. 2018. Optimized base editors enable efficient editing in cells, organoids and mice. Nat. Biotechnol. 36:888–93
    [Google Scholar]
13. 13.

    Kim Y, Komor A, Levy J, Packer M, Zhao K, Liu D. 2017. Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions. Nat. Biotechnol. 35:371–76
    [Google Scholar]
14. 14.

    Li X, Wang Y, Liu Y, Yang B, Wang X et al. 2018. Base editing with a Cpf1–cytidine deaminase fusion. Nat. Biotechnol. 36:324–27
    [Google Scholar]
15. 15.

    Kleinstiver B, Sousa A, Walton R, Tak Y, Hsu J et al. 2019. Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat. Biotechnol. 37:276–82
    [Google Scholar]
16. 16.

    Nishimasu H, Shi X, Ishiguro S, Gao L, Hirano S et al. 2018. Engineered CRISPR-Cas9 nuclease with expanded targeting space. Science 361:1259–62
    [Google Scholar]
17. 17.

    Miller S, Wang T, Randolph P, Arbab M, Shen M et al. 2020. Continuous evolution of SpCas9 variants compatible with non-G PAMs. Nat. Biotechnol. 38:471–81
    [Google Scholar]
18. 18.

    Hu J, Miller S, Geurts M, Tang W, Chen L et al. 2018. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature 556:57–63
    [Google Scholar]
19. 19.

    Walton R, Christie K, Whittaker M, Kleinstiver B. 2020. Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science 368:290–96
    [Google Scholar]
20. 20.

    Lee J, Jeong E, Lee J, Jung M, Shin E et al. 2018. Directed evolution of CRISPR-Cas9 to increase its specificity. Nat. Commun. 9:3048
    [Google Scholar]
21. 21.

    Gehrke J, Cervantes O, Clement M, Wu Y, Zeng J et al. 2018. An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nat. Biotechnol. 36:977–82
    [Google Scholar]
22. 22.

    Wu Y, Xu W, Wang F, Zhao S, Feng F et al. 2019. Increasing cytosine base editing scope and efficiency with engineered Cas9-PmCDA1 fusions and the modified sgRNA in rice. Front. Genet. 10:379
    [Google Scholar]
23. 23.

    Tan J, Zhang F, Karcher D, Bock R. 2020. Expanding the genome-targeting scope and the site selectivity of high-precision base editors. Nat. Commun. 11:629
    [Google Scholar]
24. 24.

    Zhong Z, Sretenovic S, Ren Q, Yang L, Bao Y et al. 2019. Improving plant genome editing with high-fidelity xCas9 and non-canonical PAM-targeting Cas9-NG. Mol. Plant 12:1027–36
    [Google Scholar]
25. 25.

    Endo M, Mikami M, Endo A, Kaya H, Itoh T et al. 2019. Genome editing in plants by engineered CRISPR–Cas9 recognizing NG PAM. Nat. Plants 5:14–17
    [Google Scholar]
26. 26.

    Doman J, Raguram A, Newby G, Liu D. 2020. Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors. Nat. Biotechnol. 38:620–28
    [Google Scholar]
27. 27.

    Ren B, Liu L, Li S, Kuang Y, Wang J et al. 2019. Cas9-NG greatly expands the targeting scope of the genome-editing toolkit by recognizing NG and other atypical PAMs in rice. Mol. Plant 12:1015–26
    [Google Scholar]
28. 28.

    Liu Z, Shan H, Chen S, Chen M, Zhang Q et al. 2019. Improved base editor for efficient editing in GC contexts in rabbits with an optimized AID-Cas9 fusion. FASEB J 33:9210–19
    [Google Scholar]
29. 29.

    Huang T, Zhao K, Miller S, Gaudelli N, Oakes B et al. 2019. Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors. Nat. Biotechnol. 37:626–31
    [Google Scholar]
30. 30.

    Rees H, Komor A, Yeh W, Caetano-Lopes J, Warman M et al. 2017. Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery. Nat. Commun. 8:15790
    [Google Scholar]
31. 31.

    Liang P, Sun H, Sun Y, Zhang X, Xie X et al. 2017. Effective gene editing by high-fidelity base editor 2 in mouse zygotes. Protein Cell 8:601–11
    [Google Scholar]
32. 32.

    Xu W, Song W, Yang Y, Wu Y, Lv X, Yuan S et al. 2019. Multiplex nucleotide editing by high-fidelity Cas9 variants with improved efficiency in rice. BMC Plant Biol 19:511
    [Google Scholar]
33. 33.

    Yuan J, Ma Y, Huang T, Chen Y, Peng Y et al. 2019. Genetic modulation of RNA splicing with a CRISPR-guided cytidine deaminase. Mol. Cell 72:380–94
    [Google Scholar]
34. 34.

    Tóth E, Varga E, Kulcsár P, Kocsis-Jutka V, Krausz S et al. 2020. Improved LbCas12a variants with altered PAM specificities further broaden the genome targeting range of Cas12a nucleases. Nucleic Acids Res 48:3722–33
    [Google Scholar]
35. 35.

    Huang T, Newby G, Liu D. 2021. Precision genome editing using cytosine and adenine base editors in mammalian cells. Nat. Protoc. 16:1089–128
    [Google Scholar]
36. 36.

    Rees H, Liu D. 2018. Base editing: precision chemistry on the genome and transcriptome of living cells. Nat. Rev. Genet. 19:770–88
    [Google Scholar]
37. 37.

    Porto E, Komor A, Slaymaker I, Yeo G. 2020. Base editing: advances and therapeutic opportunities. Nat. Rev. Drug Discov. 19:839–59
    [Google Scholar]
38. 38.

    Wolfe A, Li S, Goedderz C, Chen X 2020. The structure of APOBEC1 and insights into its RNA and DNA substrate selectivity. NAR Cancer 2:zcaa027
    [Google Scholar]
39. 39.

    Saraconi G, Severi F, Sala C, Mattiuz G, Conticello SG. 2014. The RNA editing enzyme APOBEC1 induces somatic mutations and a compatible mutational signature is present in esophageal adenocarcinomas. Genome Biol 15:417
    [Google Scholar]
40. 40.

    Harris R, Petersen-Mahrt S, Neuberger M. 2002. RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators. Mol. Cell 10:1247–53
    [Google Scholar]
41. 41.

    Grünewald J, Zhou R, Garcia S, Iyer S, Lareau C et al. 2019. Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors. Nature 569:433–37
    [Google Scholar]
42. 42.

    Zhou C, Sun Y, Yan R, Liu Y, Zuo E et al. 2019. Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis. Nature 571:275–78
    [Google Scholar]
43. 43.

    Salter J, Bennett R, Smith H. 2016. The APOBEC protein family: united by structure, divergent in function. Trends Biochem. Sci. 41:578–94
    [Google Scholar]
44. 44.

    Rosenberg B, Hamilton C, Mwangi M, Dewell S, Papavasiliou FN. 2011. Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA editing targets in transcript 3′ UTRs. Nat. Struct. Mol. Biol. 18:230–36
    [Google Scholar]
45. 45.

    Conticello SG. 2008. The AID/APOBEC family of nucleic acid mutators. Genome Biol 9:229
    [Google Scholar]
46. 46.

    Chen K, Harjes E, Gross P, Fahmy A, Lu Y et al. 2008. Structure of the DNA deaminase domain of the HIV-1 restriction factor APOBEC3G. Nature 452:116–19
    [Google Scholar]
47. 47.

    Thuronyi B, Koblan L, Levy J, Yeh W, Zheng C et al. 2019. Continuous evolution of base editors with expanded target compatibility and improved activity. Nat. Biotechnol. 37:1070–79
    [Google Scholar]
48. 48.

    Gumulya Y, Gillam EMJ. 2017. Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the ‘retro’ approach to protein engineering. Biochem. J. 474:1–19
    [Google Scholar]
49. 49.

    Park S, Beal P. 2019. Off-target editing by CRISPR-guided DNA base editors. Biochemistry 58:3727–34
    [Google Scholar]
50. 50.

    Zuo E, Sun Y, Yuan T, He B, Zhou C et al. 2019. A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects. Nat. Methods 17:600–4
    [Google Scholar]
51. 51.

    Yu Y, Leete T, Born D, Young L, Barrera L et al. 2020. Cytosine base editors with minimized unguided DNA and RNA off-target events and high on-target activity. Nat. Commun. 11:2052
    [Google Scholar]
52. 52.

    Wang X, Li J, Wang Y, Yang B, Wei J et al. 2018. Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion. Nat. Biotechnol. 36:946–49
    [Google Scholar]
53. 53.

    Coelho MA, Li S, Pane LS, Firth M, Ciotta G et al. 2018. BE-FLARE: a fluorescent reporter of base editing activity reveals editing characteristics of APOBEC3A and APOBEC3B. BMC Biol 16:150
    [Google Scholar]
54. 54.

    St. Martin A, Salamango D, Serebrenik A, Shaban N, Brown WL et al. 2018. A fluorescent reporter for quantification and enrichment of DNA editing by APOBEC–Cas9 or cleavage by Cas9 in living cells. Nucleic Acids Res 46:e84
    [Google Scholar]
55. 55.

    St. Martin A, Salamango DJ, Serebrenik AA, Shaban NM, Brown WL, Harris RS 2019. A panel of eGFP reporters for single base editing by APOBEC-Cas9 editosome complexes. Sci. Rep. 9:497
    [Google Scholar]
56. 56.

    Lee S, Ding N, Sun Y, Yuan T, Li J et al. 2020. Single C-to-T substitution using engineered APOBEC3G-nCas9 base editors with minimum genome-and transcriptome-wide off-target effects. Sci. Adv. 6:eaba1773
    [Google Scholar]
57. 57.

    Ma Y, Zhang J, Yin W, Zhang Z, Song Y, Chang X 2016. Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells. Nat. Methods 13:1029–35
    [Google Scholar]
58. 58.

    Ito F, Fu Y, Kao S, Yang H, Chen X. 2017. Family-wide comparative analysis of cytidine and methylcytidine deamination by eleven human APOBEC proteins. J. Mol. Biol. 429:1787–99
    [Google Scholar]
59. 59.

    Hou S, Lee JM, Myint W, Matsuo H, Yilmaz NS, Schiffer CA. 2021. Structural basis of substrate specificity in human cytidine deaminase family APOBEC3s. J. Biol. Chem. 297:100909
    [Google Scholar]
60. 60.

    Maiti A, Hou S, Schiffer C, Matsuo H. 2021. Interactions of APOBEC3s with DNA and RNA. Curr. Opin. Struct. Biol. 67:195–204
    [Google Scholar]
61. 61.

    Liu Z, Chen S, Shan H, Jia Y, Chen M, Song Y et al. 2020. Precise base editing with CC context-specificity using engineered human APOBEC3G-nCas9 fusions. BMC Biol 18:111
    [Google Scholar]
62. 62.

    Nishida K, Arazoe T, Yachie N, Banno S, Kakimoto M et al. 2016. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science 353:aaf8729
    [Google Scholar]
63. 63.

    Hess G, Frésard L, Han K, Lee C, Li A et al. 2016. Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells. Nat. Methods 13:1036–42
    [Google Scholar]
64. 64.

    Wang M, Yang Z, Rada C, Neuberger MS. 2009. AID upmutants isolated using a high-throughput screen highlight the immunity/cancer balance limiting DNA deaminase activity. Nat. Struct. Mol. Biol. 16:769–76
    [Google Scholar]
65. 65.

    Qiao Q, Wang L, Meng F, Hwang J, Alt F, Wu H. 2017. AID recognizes structured DNA for class switch recombination. Mol. Cell 67:361–73
    [Google Scholar]
66. 66.

    Schaub M, Keller W. 2002. RNA editing by adenosine deaminases generates RNA and protein diversity. Biochimie 84:791–803
    [Google Scholar]
67. 67.

    Gaudelli N, Komor A, Rees H, Packer M, Badran A et al. 2017. Programmable base editing of A·T to G·C in genomic DNA without DNA cleavage. Nature 551:464–71
    [Google Scholar]
68. 68.

    Kim J, Malashkevich V, Roday S, Lisbin M, Schramm VL, Almo SC. 2006. Structural and kinetic characterization of Escherichia coli TadA, the wobble-specific tRNA deaminase. Biochemistry 45:6407–16
    [Google Scholar]
69. 69.

    Losey H, Ruthenburg A, Verdine G. 2006. Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA. Nat. Struct. Mol. Biol. 13:153–59
    [Google Scholar]
70. 70.

    Lapinaite A, Knott G, Palumbo C, Lin-Shiao E, Richter M et al. 2020. DNA capture by a CRISPR-Cas9–guided adenine base editor. Science 369:566–71
    [Google Scholar]
71. 71.

    Alseth I, Dalhus B, Bjørås M. 2014. Inosine in DNA and RNA. Curr. Opin. Genet. Dev. 26:116–23
    [Google Scholar]
72. 72.

    Grünewald J, Zhou R, Iyer S, Lareau C, Garcia S, Aryee M, Joung J. 2019. CRISPR DNA base editors with reduced RNA off-target and self-editing activities. Nat. Biotechnol. 37:1041–48
    [Google Scholar]
73. 73.

    Rallapalli K, Komor A, Paesani F. 2020. Computer simulations explain mutation-induced effects on the DNA editing by adenine base editors. Sci. Adv. 6:eaaz2309
    [Google Scholar]
74. 74.

    Richter M, Zhao K, Eton E, Lapinaite A, Newby G et al. 2020. Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity. Nat. Biotechnol. 38:883–91
    [Google Scholar]
75. 75.

    Gaudelli N, Lam D, Rees H, Solá-Esteves N, Barrera L et al. 2020. Directed evolution of adenine base editors with increased activity and therapeutic application. Nat. Biotechnol. 38:892–900
    [Google Scholar]
76. 76.

    Rallapalli K, Ranzau B, Ganapathy K, Paesani F, Komor A. 2022. Combined theoretical, bioinformatic, and biochemical analyses of RNA editing by adenine base editors. CRISPR J 5:294–310
    [Google Scholar]
77. 77.

    Kim H, Jeong Y, Hur J, Kim J, Bae S. 2019. Adenine base editors catalyze cytosine conversions in human cells. Nat. Biotechnol. 37:1145–48
    [Google Scholar]
78. 78.

    Chen L, Zhang S, Xue N, Hong M, Zhang X et al. 2022. Engineering a precise adenine base editor with minimal bystander editing. Nat. Chem. Biol. 19:101–10
    [Google Scholar]
79. 79.

    Neugebauer ME, Hsu A, Arbab M, Krasnow NA, McElroy AN et al. 2022. Evolution of an adenine base editor into a small, efficient cytosine base editor with low off-target activity. Nat. Biotechnol. https://doi.org/10.1038/s41587-022-01533-6
    [Google Scholar]
80. 80.

    Chen L, Zhu B, Ru G, Meng H, Yan Y et al. 2022. Re-engineering the adenine deaminase TadA-8e for efficient and specific CRISPR-based cytosine base editing. Nat. Biotechnol. https://doi.org/10.1038/s41587-022-01532-7
    [Crossref] [Google Scholar]
81. 81.

    Gaudelli N, Yu Y, Slaymaker I, Gehrke JM, Lee S et al. 2022. Nucleobase editors having reduced off-target deamination and methods of using same to modify a nucleobase target sequence US Patent Appl17/427,422
82. 82.

    Rees H, Wilson C, Doman J, Liu D. 2019. Analysis and minimization of cellular RNA editing by DNA adenine base editors. Sci. Adv. 5:eaax5717
    [Google Scholar]
83. 83.

    Grünewald J, Zhou R, Lareau C, Garcia S, Iyer S et al. 2020. A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing. Nat. Biotechnol. 38:861–64
    [Google Scholar]
84. 84.

    Sakata R, Ishiguro S, Mori H, Tanaka M, Tatsuno K et al. 2020. Base editors for simultaneous introduction of C-to-T and A-to-G mutations. Nat. Biotechnol. 38:865–69
    [Google Scholar]
85. 85.

    Li C, Zhang R, Meng X, Chen S, Zong Y et al. 2020. Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors. Nat. Biotechnol. 38:875–82
    [Google Scholar]
86. 86.

    Zhang X, Zhu B, Chen L, Xie L, Yu W et al. 2020. Dual base editor catalyzes both cytosine and adenine base conversions in human cells. Nat. Biotechnol. 38:856–60
    [Google Scholar]
87. 87.

    Xie J, Huang X, Wang X, Gou S, Liang Y et al. 2020. ACBE, a new base editor for simultaneous C-to-T and A-to-G substitutions in mammalian systems. BMC Biol 18:131
    [Google Scholar]
88. 88.

    Cravens A, Jamil O, Kong D, Sockolosky J, Smolke C. 2021. Polymerase-guided base editing enables in vivo mutagenesis and rapid protein engineering. Nat. Commun. 12:1579
    [Google Scholar]
89. 89.

    Gammage P, Moraes C, Minczuk M. 2018. Mitochondrial genome engineering: the revolution may not be CRISPR-ized. Trends Genet 34:101–10
    [Google Scholar]
90. 90.

    Mok B, Moraes M, Zeng J, Bosch D, Kotrys A et al. 2020. A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing. Nature 583:631–37
    [Google Scholar]
91. 91.

    Kim YG, Smith J, Durgesha M, Chandrasegaran S. 1998. Chimeric restriction enzyme: Gal4 fusion to FokI cleavage domain. Biol. Chem. 379:489–95
    [Google Scholar]
92. 92.

    Kim YG, Chandrasegaran S. 1994. Chimeric restriction endonuclease. PNAS 91:883–87
    [Google Scholar]
93. 93.

    Kim YG, Cha J, Chandrasegaran S. 1996. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. PNAS 93:1156–60
    [Google Scholar]
94. 94.

    Li L, Wu L, Chandrasegaran S. 1992. Functional domains in Fok I restriction endonuclease. PNAS 89:4275–79
    [Google Scholar]
95. 95.

    Pavletich N, Pabo C. 1991. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 Å. Science 252:809–17
    [Google Scholar]
96. 96.

    Isalan M, Klug A, Choo Y. 1998. Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers. Biochemistry 37:12026–33
    [Google Scholar]
97. 97.

    Wolfe S, Greisman H, Ramm E, Pabo C. 1999. Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J. Mol. Biol. 285:1917–34
    [Google Scholar]
98. 98.

    Pabo CO, Peisach E, Grant RA. 2001. Design and selection of novel Cys₂His₂ zinc finger proteins. Annu. Rev. Biochem. 70:313–40
    [Google Scholar]
99. 99.

    Sera T, Uranga C. 2002. Rational design of artificial zinc-finger proteins using a nondegenerate recognition code table. Biochemistry 41:7074–81
    [Google Scholar]
100. 100.

     Christian M, Cermak T, Doyle E, Schmidt C, Zhang F et al. 2010. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186:757–61
     [Google Scholar]
101. 101.

     Moscou MJ, Bogdanove AJ. 2009. A simple cipher governs DNA recognition by TAL effectors. Science 326:1501
     [Google Scholar]
102. 102.

     Boch J, Scholze H, Schornack S, Landgraf A, Hahn S et al. 2009. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326:1509–12
     [Google Scholar]
103. 103.

     Iyer L, Zhang D, Rogozin I, Aravind L. 2011. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Nucleic Acids Res 39:9473–97
     [Google Scholar]
104. 104.

     Moraes M, Hsu F, Huang D, Bosch D, Zeng J et al. 2021. An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations. eLife 10:e62967
     [Google Scholar]
105. 105.

     Berríos K, Evitt N, DeWeerd R, Ren D, Luo M et al. 2021. Controllable genome editing with split-engineered base editors. Nat. Chem. Biol. 17:1262–70
     [Google Scholar]
106. 106.

     Long J, Liu N, Tang W, Xie L, Qin F et al. 2021. A split cytosine deaminase architecture enables robust inducible base editing. FASEB J 35:e22045
     [Google Scholar]
107. 107.

     Levy J, Yeh W, Pendse N, Davis J, Hennessey E et al. 2020. Cytosine and adenine base editing of the brain, liver, retina, heart and skeletal muscle of mice via adeno-associated viruses. Nat. Biomed. Eng. 4:97–110
     [Google Scholar]
108. 108.

     Ryu S, Koo T, Kim K, Lim K, Baek G et al. 2018. Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy. Nat. Biotechnol. 36:536–39
     [Google Scholar]
109. 109.

     Katrekar D, Xiang Y, Palmer N, Saha A, Meluzzi D, Mali P 2022. Comprehensive interrogation of the ADAR2 deaminase domain for engineering enhanced RNA editing activity and specificity. eLife 11:e75555
     [Google Scholar]
110. 110.

     Mok BY, Kotrys AV, Raguram A, Huang TP, Mootha VK, Liu DR. 2022. CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA. Nat. Biotechnol. 40:91378–87
     [Google Scholar]
111. 111.

     Cho S-I, Lee S, Mok YG, Lim K, Lee J et al. 2022. Targeted A-to-G base editing in human mitochondrial DNA with programmable deaminases. Cell 185:1764–76
     [Google Scholar]
112. 112.

     Lim K, Cho S-I, Kim J-S. 2022. Nuclear and mitochondrial DNA editing in human cells with zinc finger deaminases. Nat. Commun. 13:366
     [Google Scholar]
113. 113.

     Kang B, Bae S, Lee S, Lee J, Kim A et al. 2021. Chloroplast and mitochondrial DNA editing in plants. Nat. Plants 7:899–905
     [Google Scholar]
114. 114.

     Barrera-Paez JD, Moraes CT. 2022. Mitochondrial genome engineering coming-of-age. Trends Genet. 38:8869–80. Erratum. 2023. Trends Genet. 39:89
     [Google Scholar]
115. 115.

     Adashi E, Rubenstein D, Mossman J, Schon E, Cohen I. 2021. Mitochondrial disease: replace or edit?. Science 373:1200–1
     [Google Scholar]
116. 116.

     Lindahl T. 1979. DNA glycosylases, endonucleases for apurinic/apyrimidinic sites, and base excision-repair. Prog. Nucleic Acid Res. Mol. Biol. 22:135–92
     [Google Scholar]
117. 117.

     Krokan H, Bjoras M. 2013. Base excision repair. Cold Spring Harb. Perspect. Biol. 5:a012583
     [Google Scholar]
118. 118.

     Gu S, Bodai Z, Cowan Q, Komor A. 2021. Base editors: expanding the types of DNA damage products harnessed for genome editing. Gene Genome Ed 1:100005
     [Google Scholar]
119. 119.

     Nambiar T, Baudrier L, Billon P, Ciccia A. 2022. CRISPR-based genome editing through the lens of DNA repair. Mol. Cell 82:348–88
     [Google Scholar]
120. 120.

     Parikh S, Mol C, Slupphaug G, Bharati S, Krokan H, Tainer J. 1998. Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA. EMBO J 17:5214–26
     [Google Scholar]
121. 121.

     Ahn W, Aroli S, Kim J, Moon J, Lee G et al. 2019. Covalent binding of uracil DNA glycosylase UdgX to abasic DNA upon uracil excision. Nat. Chem. Biol. 15:607–14
     [Google Scholar]
122. 122.

     Lau A, Wyatt M, Glassner B, Samson L, Ellenberger T. 2000. Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG. PNAS 97:13573–78
     [Google Scholar]
123. 123.

     Zhang L, Lu X, Lu J, Liang H, Dai Q et al. 2012. Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA. Nat. Chem. Biol. 8:328–30
     [Google Scholar]
124. 124.

     Kurt I, Zhou R, Iyer S, Garcia S, Miller B et al. 2021. CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells. Nat. Biotechnol. 39:41–46
     [Google Scholar]
125. 125.

     Chen L, Park JE, Paa P, Rajakumar PD, Prekop H-T et al. 2021. Programmable C:G to G:C genome editing with CRISPR-Cas9-directed base excision repair proteins. Nat. Commun. 12:1384
     [Google Scholar]
126. 126.

     Zhao D, Li J, Li S, Xin X, Hu M et al. 2021. Glycosylase base editors enable C-to-A and C-to-G base changes. Nat. Biotechnol. 39:35–40
     [Google Scholar]
127. 127.

     Koblan L, Arbab M, Shen M, Hussmann J, Anzalone A et al. 2021. Efficient C·G-to-G·C base editors developed using CRISPRi screens, target-library analysis, and machine learning. Nat. Biotechnol. 39:1414–25
     [Google Scholar]
128. 128.

     Hsu P, Lander E, Zhang F. 2014. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157:1262–78
     [Google Scholar]
129. 129.

     Moore L, Le T, Fan G 2013. DNA methylation and its basic function. Neuropsychopharmacology 38:23–38
     [Google Scholar]
130. 130.

     Holtzman L, Gersbach CA. 2018. Editing the epigenome: reshaping the genomic landscape. Annu. Rev. Genom. Hum. Genet. 19:43–71
     [Google Scholar]
131. 131.

     Pósfai J, Bhagwat A, Pósfai G, Roberts R. 1989. Predictive motifs derived from cytosine methyltransferases. Nucleic Acids Res 17:2421–35
     [Google Scholar]
132. 132.

     Martin J, McMillan F. 2002. SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold. Curr. Opin. Struct. Biol. 12:783–93
     [Google Scholar]
133. 133.

     Zhang Z, Lu R, Wang P, Yu Y, Chen D et al. 2018. Structural basis for DNMT3A-mediated de novo DNA methylation. Nature 554:387–91
     [Google Scholar]
134. 134.

     Gao L, Emperle M, Guo Y, Grimm SA, Ren W et al. 2020. Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms. Nat. Commun. 11:3355
     [Google Scholar]
135. 135.

     Song J, Rechkoblit O, Bestor T, Patel D. 2011. Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation. Science 331:1036–40
     [Google Scholar]
136. 136.

     Bestor T, Verdine G. 1994. DNA methyltransferases. Curr. Opin. Cell Biol. 6:380–89
     [Google Scholar]
137. 137.

     Cheng X. 1995. Structure and function of DNA methyltransferases. Annu. Rev. Biophys. Biomol. Struct. 24:293–318
     [Google Scholar]
138. 138.

     Carvin C, Parr R, Kladde M. 2003. Site-selective in vivo targeting of cytosine-5 DNA methylation by zinc-finger proteins. Nucleic Acids Res 31:6493–501
     [Google Scholar]
139. 139.

     Mlambo T, Nitsch S, Hildenbeutel M, Romito M, Müller M et al. 2018. Designer epigenome modifiers enable robust and sustained gene silencing in clinically relevant human cells. Nucleic Acids Res 46:4456–68
     [Google Scholar]
140. 140.

     Li F, Papworth M, Minczuk M, Rohde C, Zhang Y et al. 2007. Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes. Nucleic Acids Res 35:100–12
     [Google Scholar]
141. 141.

     Rivenbark A, Stolzenburg S, Beltran A, Yuan X, Rots M et al. 2012. Epigenetic reprogramming of cancer cells via targeted DNA methylation. Epigenetics 7:350–60
     [Google Scholar]
142. 142.

     Kungulovski G, Jeltsch A. 2016. Epigenome editing: state of the art, concepts, and perspectives. Trends Genet 32:101–13
     [Google Scholar]
143. 143.

     Groote M, Verschure P, Rots M. 2012. Epigenetic editing: targeted rewriting of epigenetic marks to modulate expression of selected target genes. Nucleic Acids Res 40:10596–613
     [Google Scholar]
144. 144.

     Thakore P, Black J, Hilton I, Gersbach C 2016. Editing the epigenome: technologies for programmable transcription and epigenetic modulation. Nat. Methods 13:127–37
     [Google Scholar]
145. 145.

     Liu X, Wu H, Ji X, Stelzer Y, Wu X et al. 2016. Editing DNA methylation in the mammalian genome. Cell 167:233–47
     [Google Scholar]
146. 146.

     Vojta A, Dobrinić P, Tadić V, Bočkor L, Korać P et al. 2016. Repurposing the CRISPR-Cas9 system for targeted DNA methylation. Nucleic Acids Res 44:5615–28
     [Google Scholar]
147. 147.

     Amabile A, Migliara A, Capasso P, Biffi M, Cittaro D et al. 2016. Inheritable silencing of endogenous genes by hit-and-run targeted epigenetic editing. Cell 167:219–32
     [Google Scholar]
148. 148.

     McDonald J, Celik H, Rois L, Fishberger G, Fowler T et al. 2016. Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation. Biol. Open 5:866–74
     [Google Scholar]
149. 149.

     Galonska C, Charlton J, Mattei AL, Donaghey J, Clement K et al. 2018. Genome-wide tracking of dCas9-methyltransferase footprints. Nat. Commun. 9:597
     [Google Scholar]
150. 150.

     Stepper P, Kungulovski G, Jurkowska R, Chandra T, Krueger F et al. 2017. Efficient targeted DNA methylation with chimeric dCas9–Dnmt3a–Dnmt3L methyltransferase. Nucleic Acids Res 45:1703–13
     [Google Scholar]
151. 151.

     O'Geen H, Bates SL, Carter SS, Nisson KA, Halmai J et al. 2019. Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner. Epigenet. Chromatin 12:26
     [Google Scholar]
152. 152.

     Nuñez J, Chen J, Pommier G, Cogan J, Replogle J et al. 2021. Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell 184:2503–19
     [Google Scholar]
153. 153.

     Lin L, Liu Y, Xu F, Huang J, Daugaard T et al. 2018. Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases. Gigascience 7:giy011
     [Google Scholar]
154. 154.

     Pflueger C, Tan D, Swain T, Nguyen T, Pflueger J et al. 2018. A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs. Genome Res 28:1193–206
     [Google Scholar]
155. 155.

     Huang Y-H, Su J, Lei Y, Brunetti L, Gundry MC et al. 2017. DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A. Genome Biol 18:176
     [Google Scholar]
156. 156.

     Marx N, Grünwald-Gruber C, Bydlinski N, Dhiman H, Ngoc Nguyen L et al. 2018. CRISPR-based targeted epigenetic editing enables gene expression modulation of the silenced beta-galactoside alpha-2, 6-sialyltransferase 1 in CHO cells. Biotechnol. J. 13:1700217
     [Google Scholar]
157. 157.

     Lu A, Wang J, Sun W, Huang W, Cai Z et al. 2019. Reprogrammable CRISPR/dCas9-based recruitment of DNMT1 for site-specific DNA demethylation and gene regulation. Cell Discov 5:22
     [Google Scholar]
158. 158.

     Hofacker D, Broche J, Laistner L, Adam S, Bashtrykov P, Jeltsch A. 2020. Engineering of effector domains for targeted DNA methylation with reduced off-target effects. Int. J. Mol. Sci. 21:502
     [Google Scholar]
159. 159.

     Lei Y, Zhang X, Su J, Jeong M, Gundry MC et al. 2017. Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein. Nat. Commun. 8:16026
     [Google Scholar]
160. 160.

     Xiong T, Meister G, Workman R, Kato N, Spellberg M et al. 2017. Targeted DNA methylation in human cells using engineered dCas9-methyltransferases. Sci. Rep. 7:6732
     [Google Scholar]
161. 161.

     Kohli R, Zhang Y. 2013. TET enzymes, TDG and the dynamics of DNA demethylation. Nature 502:472–79
     [Google Scholar]
162. 162.

     Wu H, Zhang Y. 2014. Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell 156:45–68
     [Google Scholar]
163. 163.

     Ranzau B, Komor A. 2018. Genome, epigenome, and transcriptome editing via chemical modification of nucleobases in living cells. Biochemistry 58:330–35
     [Google Scholar]
164. 164.

     Hu L, Lu J, Cheng J, Rao Q, Li Z et al. 2015. Structural insight into substrate preference for TET-mediated oxidation. Nature 527:118–22
     [Google Scholar]
165. 165.

     Aik W, McDonough M, Thalhammer A, Chowdhury R, Schofield C. 2012. Role of the jelly-roll fold in substrate binding by 2-oxoglutarate oxygenases. Curr. Opin. Struct. Biol. 22:691–700
     [Google Scholar]
166. 166.

     Hashimoto H, Pais J, Zhang X, Saleh L, Fu Z et al. 2014. Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA. Nature 506:391–95
     [Google Scholar]
167. 167.

     Chen H, Kazemier H, Groote M, Ruiters M, Xu G, Rots M. 2014. Induced DNA demethylation by targeting Ten-Eleven Translocation 2 to the human ICAM-1 promoter. Nucleic Acids Res 42:1563–74
     [Google Scholar]
168. 168.

     Maeder M, Angstman J, Richardson M, Linder S, Cascio V et al. 2013. Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nat. Biotechnol. 31:1137–42
     [Google Scholar]
169. 169.

     Choudhury S, Cui Y, Lubecka K, Stefanska B, Irudayaraj J. 2016. CRISPR-dCas9 mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter. Oncotarget 7:46545
     [Google Scholar]
170. 170.

     Okada M, Kanamori M, Someya K, Nakatsukasa H, Yoshimura A. 2017. Stabilization of Foxp3 expression by CRISPR-dCas9-based epigenome editing in mouse primary T cells. Epigenet. Chromatin 10:24
     [Google Scholar]
171. 171.

     Liu X, Wu H, Krzisch M, Wu X, Graef J et al. 2018. Rescue of fragile X syndrome neurons by DNA methylation editing of the FMR1 gene. Cell 172:979–92
     [Google Scholar]
172. 172.

     Kang JG, Park JS, Ko J-H, Kim Y-S. 2019. Regulation of gene expression by altered promoter methylation using a CRISPR/Cas9-mediated epigenetic editing system. Sci. Rep. 9:11960
     [Google Scholar]
173. 173.

     Baumann V, Wiesbeck M, Breunig CT, Braun JM, Köferle A et al. 2019. Targeted removal of epigenetic barriers during transcriptional reprogramming. Nat. Commun. 10:2119
     [Google Scholar]
174. 174.

     Josipović G, Tadić V, Klasić M, Zanki V, Beuceheli I et al. 2019. Antagonistic and synergistic epigenetic modulation using orthologous CRISPR/dCas9-based modular system. Nucleic Acids Res 47:9637–57
     [Google Scholar]
175. 175.

     Xu X, Tan X, Tampe B, Wilhelmi T, Hulshoff MS et al. 2018. High-fidelity CRISPR/Cas9-based gene-specific hydroxymethylation rescues gene expression and attenuates renal fibrosis. Nat. Commun. 9:3509
     [Google Scholar]
176. 176.

     Hanzawa N, Hashimoto K, Yuan X, Kawahori K, Tsujimoto K et al. 2020. Targeted DNA demethylation of the Fgf21 promoter by CRISPR/dCas9-mediated epigenome editing. Sci. Rep. 10:5181
     [Google Scholar]
177. 177.

     Morita S, Noguchi H, Horii T, Nakabayashi K, Kimura M et al. 2016. Targeted DNA demethylation in vivo using dCas9–peptide repeat and scFv–TET1 catalytic domain fusions. Nat. Biotechnol. 34:1060–65
     [Google Scholar]
178. 178.

     Xu X, Tao Y, Gao X, Zhang L, Li X et al. 2016. A CRISPR-based approach for targeted DNA demethylation. Cell Discov 2:16009
     [Google Scholar]
179. 179.

     Taghbalout A, Du M, Jillette N, Rosikiewicz W, Rath A et al. 2019. Enhanced CRISPR-based DNA demethylation by Casilio-ME-mediated RNA-guided coupling of methylcytosine oxidation and DNA repair pathways. Nat. Commun. 10:4296
     [Google Scholar]
180. 180.

     Sood AJ, Viner C, Hoffman MM. 2019. DNAmod: the DNA modification database. J. Cheminform. 11:30
     [Google Scholar]