1932

Abstract

CRISPR-based genome editing holds promise for genome engineering and other applications in diverse organisms. Defining and improving the genome-wide and transcriptome-wide specificities of these editing tools are essential for realizing their full potential in basic research and biomedical therapeutics. This review provides an overview of CRISPR-based DNA- and RNA-editing technologies, methods to quantify their specificities, and key solutions to reduce off-target effects for research and improve therapeutic applications.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-genet-071719-030438
2021-11-23
2024-05-06
Loading full text...

Full text loading...

/deliver/fulltext/genet/55/1/annurev-genet-071719-030438.html?itemId=/content/journals/10.1146/annurev-genet-071719-030438&mimeType=html&fmt=ahah

Literature Cited

  1. 1. 
    Bae S, Park J, Kim J-S 2014. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30:147375
    [Google Scholar]
  2. 2. 
    Abbott TR, Dhamdhere G, Liu Y, Lin X, Goudy L et al. 2020. Development of CRISPR as an antiviral strategy to combat SARS-CoV-2 and influenza. Cell 181:4865–76.e12
    [Google Scholar]
  3. 3. 
    Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J et al. 2017. RNA targeting with CRISPR–Cas13. Nature 550:7675280–84
    [Google Scholar]
  4. 4. 
    Abudayyeh OO, Gootenberg JS, Franklin B, Koob J, Kellner MJ et al. 2019. A cytosine deaminase for programmable single-base RNA editing. Science 365:6451382–86
    [Google Scholar]
  5. 5. 
    Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM et al. 2016. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353:6299aaf5573
    [Google Scholar]
  6. 6. 
    Akhtar W, de Jong J, Pindyurin AV, Pagie L, Meuleman W et al. 2013. Chromatin position effects assayed by thousands of reporters integrated in parallel. Cell 154:4914–27
    [Google Scholar]
  7. 7. 
    Aman R, Ali Z, Butt H, Mahas A, Aljedaani F et al. 2018. RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol 19:11
    [Google Scholar]
  8. 8. 
    Anders C, Niewoehner O, Duerst A, Jinek M 2014. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513:7519569–73
    [Google Scholar]
  9. 9. 
    Anderson KR, Haeussler M, Watanabe C, Janakiraman V, Lund J et al. 2018. CRISPR off-target analysis in genetically engineered rats and mice. Nat. Methods 15:7512–14
    [Google Scholar]
  10. 10. 
    Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW et al. 2019. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576:7785149–57
    [Google Scholar]
  11. 11. 
    Arbab M, Shen MW, Mok B, Wilson C, Matuszek Ż et al. 2020. Determinants of base editing outcomes from target library analysis and machine learning. Cell 182:2463–80.e30
    [Google Scholar]
  12. 12. 
    Bolukbasi MF, Gupta A, Oikemus S, Derr AG, Garber M et al. 2015. DNA-binding-domain fusions enhance the targeting range and precision of Cas9. Nat. Methods 12:121150–56
    [Google Scholar]
  13. 13. 
    Bolukbasi MF, Liu P, Luk K, Kwok SF, Gupta A et al. 2018. Orthogonal Cas9–Cas9 chimeras provide a versatile platform for genome editing. Nat. Commun. 9:14856
    [Google Scholar]
  14. 14. 
    Brookhouser N, Nguyen T, Tekel SJ, Standage-Beier K, Wang X, Brafman DA 2020. A Cas9-mediated adenosine transient reporter enables enrichment of ABE-targeted cells. BMC Biol 18:1193
    [Google Scholar]
  15. 15. 
    Buchman AB, Brogan DJ, Sun R, Yang T, Hsu PD, Akbari OS 2020. Programmable RNA targeting using CasRx in flies. CRISPR J 3:3164–76
    [Google Scholar]
  16. 16. 
    Cameron P, Fuller CK, Donohoue PD, Jones BN, Thompson MS et al. 2017. Mapping the genomic landscape of CRISPR-Cas9 cleavage. Nat. Methods 14:6600–6
    [Google Scholar]
  17. 17. 
    Cano-Rodriguez D, Gjaltema RAF, Jilderda LJ, Jellema P, Dokter-Fokkens J et al. 2016. Writing of H3K4Me3 overcomes epigenetic silencing in a sustained but context-dependent manner. Nat. Commun. 7:112284
    [Google Scholar]
  18. 18. 
    Casas-Mollano JA, Zinselmeier MH, Erickson SE, Smanski MJ. 2020. CRISPR-Cas activators for engineering gene expression in higher eukaryotes. CRISPR J 3:5350–64
    [Google Scholar]
  19. 19. 
    Casini A, Olivieri M, Petris G, Montagna C, Reginato G et al. 2018. A highly specific SpCas9 variant is identified by in vivo screening in yeast. Nat. Biotechnol. 36:3265–71
    [Google Scholar]
  20. 20. 
    Chavez A, Tuttle M, Pruitt BW, Ewen-Campen B, Chari R et al. 2016. Comparative analysis of Cas9 activators across multiple species. Nat. Methods 13:7563–67
    [Google Scholar]
  21. 21. 
    Chen JS, Dagdas YS, Kleinstiver BP, Welch MM, Sousa AA et al. 2017. Enhanced proofreading governs CRISPR–Cas9 targeting accuracy. Nature 550:7676407–10
    [Google Scholar]
  22. 22. 
    Chen K-M, Harjes E, Gross PJ, Fahmy A, Lu Y et al. 2008. Structure of the DNA deaminase domain of the HIV-1 restriction factor APOBEC3G. Nature 452:7183116–19
    [Google Scholar]
  23. 23. 
    Cho SW, Kim S, Kim Y, Kweon J, Kim HS et al. 2014. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res 24:1132–41
    [Google Scholar]
  24. 24. 
    Cong L, Ran FA, Cox D, Lin S, Barretto R et al. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339:6121819–23
    [Google Scholar]
  25. 25. 
    Cox DBT, Gootenberg JS, Abudayyeh OO, Franklin B, Kellner MJ et al. 2017. RNA editing with CRISPR-Cas13. Science 358:63661019–27
    [Google Scholar]
  26. 26. 
    Crosetto N, Mitra A, Silva MJ, Bienko M, Dojer N et al. 2013. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat. Methods 10:4361–65
    [Google Scholar]
  27. 27. 
    Davis KM, Pattanayak V, Thompson DB, Zuris JA, Liu DR. 2015. Small molecule–triggered Cas9 protein with improved genome-editing specificity. Nat. Chem. Biol. 11:5316–18
    [Google Scholar]
  28. 28. 
    Doman JL, Raguram A, Newby GA, Liu DR. 2020. Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors. Nat. Biotechnol. 38:620–28
    [Google Scholar]
  29. 29. 
    East-Seletsky A, O'Connell MR, Burstein D, Knott GJ, Doudna JA 2017. RNA targeting by functionally orthogonal type VI-A CRISPR-Cas enzymes. Mol. Cell 66:3373–83.e3
    [Google Scholar]
  30. 30. 
    East-Seletsky A, O'Connell MR, Knight SC, Burstein D, Cate JHD et al. 2016. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature 538:7624270–73
    [Google Scholar]
  31. 31. 
    Eoh J, Gu L. 2019. Biomaterials as vectors for the delivery of CRISPR-Cas9. Biomater. Sci. 7:41240–61
    [Google Scholar]
  32. 32. 
    Friedland AE, Tzur YB, Esvelt KM, Colaiácovo MP, Church GM, Calarco JA. 2013. Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat. Methods 10:8741–43
    [Google Scholar]
  33. 33. 
    Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D et al. 2013. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat. Biotechnol. 31:9822–26
    [Google Scholar]
  34. 34. 
    Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK. 2014. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat. Biotechnol. 32:3279–84
    [Google Scholar]
  35. 35. 
    Gabriel R, Lombardo A, Arens A, Miller JC, Genovese P et al. 2011. An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat. Biotechnol. 29:9816–23
    [Google Scholar]
  36. 36. 
    Galonska C, Charlton J, Mattei AL, Donaghey J, Clement K et al. 2018. Genome-wide tracking of dCas9-methyltransferase footprints. Nat. Commun. 9:1597
    [Google Scholar]
  37. 37. 
    Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH et al. 2017. Programmable base editing of A·T to G·C in genomic DNA without DNA cleavage. Nature 551:7681464–71
    [Google Scholar]
  38. 38. 
    Gehrke JM, Cervantes O, Clement MK, Wu Y, Zeng J et al. 2018. An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nat. Biotechnol. 36:10977–82
    [Google Scholar]
  39. 39. 
    Frock RL, Hu J, Meyers RM, Ho Y-J, Kii E, Alt FW 2015. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat Biotechnol. 33:2179–86
    [Google Scholar]
  40. 40. 
    Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA et al. 2013. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154:2442–51
    [Google Scholar]
  41. 41. 
    Gootenberg JS, Abudayyeh OO, Kellner MJ, Joung J, Collins JJ, Zhang F 2018. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 360:6387439–44
    [Google Scholar]
  42. 42. 
    Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ et al. 2017. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356:6336438–42
    [Google Scholar]
  43. 43. 
    Grünewald J, Zhou R, Garcia SP, Iyer S, Lareau CA et al. 2019. Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors. Nature 569:7756433–37
    [Google Scholar]
  44. 44. 
    Grünewald J, Zhou R, Iyer S, Lareau CA, Garcia SP et al. 2019. CRISPR DNA base editors with reduced RNA off-target and self-editing activities. Nat. Biotechnol. 37:91041–48
    [Google Scholar]
  45. 45. 
    Guilinger JP, Thompson DB, Liu DR. 2014. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat. Biotechnol. 32:6577–82
    [Google Scholar]
  46. 46. 
    Guo X, Wessels H-H, Méndez-Mancilla A, Haro D, Sanjana NE. 2020. Transcriptome-wide Cas13 guide RNA design for model organisms and viral RNA pathogens. bioRxiv 2020.08.20.259762. https://doi.org/10.1101/2020.08.20.259762
  47. 47. 
    He B, Peng W, Huang J, Zhang H, Zhou Y et al. 2020. Modulation of metabolic functions through Cas13d-mediated gene knockdown in liver. Protein Cell 11:7518–24
    [Google Scholar]
  48. 48. 
    Heigwer F, Kerr G, Boutros M. 2014. E-CRISP: fast CRISPR target site identification. Nat. Methods 11:2122–23
    [Google Scholar]
  49. 49. 
    Holden LG, Prochnow C, Chang YP, Bransteitter R, Chelico L et al. 2008. Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications. Nature 456:7218121–24
    [Google Scholar]
  50. 50. 
    Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S et al. 2013. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 31:9827–32
    [Google Scholar]
  51. 51. 
    Hu JH, Miller SM, Geurts MH, Tang W, Chen L et al. 2018. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature 556:769957–63
    [Google Scholar]
  52. 52. 
    Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ et al. 2013. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat. Biotechnol. 31:3227–29
    [Google Scholar]
  53. 53. 
    Iyer V, Boroviak K, Thomas M, Doe B, Riva L et al. 2018. No unexpected CRISPR-Cas9 off-target activity revealed by trio sequencing of gene-edited mice. PLOS Genet 14:7e1007503
    [Google Scholar]
  54. 54. 
    Jiang F, Taylor DW, Chen JS, Kornfeld JE, Zhou K et al. 2016. Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage. Science 351:6275867–71
    [Google Scholar]
  55. 55. 
    Jin S, Fei H, Zhu Z, Luo Y, Liu J et al. 2020. Rationally designed APOBEC3B cytosine base editors with improved specificity. Mol. Cell 79:5728–740.e6
    [Google Scholar]
  56. 56. 
    Jin S, Gao Q, Gao C 2021. An unbiased method for evaluating the genome-wide specificity of base editors in rice. Nat. Protoc. 16:1431–57
    [Google Scholar]
  57. 57. 
    Jin S, Zong Y, Gao Q, Zhu Z, Wang Y et al. 2019. Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice. Science 364:6437292–95
    [Google Scholar]
  58. 58. 
    Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:6096816–21
    [Google Scholar]
  59. 59. 
    Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E et al. 2014. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343:61761247997
    [Google Scholar]
  60. 60. 
    Kempton HR, Qi LS. 2019. When genome editing goes off-target. Science 364:6437234–36
    [Google Scholar]
  61. 61. 
    Kim D, Bae S, Park J, Kim E, Kim S et al. 2015. Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat. Methods 12:3237–43
    [Google Scholar]
  62. 62. 
    Kim D, Luk K, Wolfe SA, Kim J-S. 2019. Evaluating and enhancing target specificity of gene-editing nucleases and deaminases. Annu. Rev. Biochem. 88:191–220
    [Google Scholar]
  63. 63. 
    Kim D, Kim D, Lee G, Cho S-I, Kim J-S. 2019. Genome-wide target specificity of CRISPR RNA-guided adenine base editors. Nat. Biotechnol. 37:4430–35
    [Google Scholar]
  64. 64. 
    Kim D, Lim K, Kim S-T, Yoon S, Kim K et al. 2017. Genome-wide target specificities of CRISPR RNA-guided programmable deaminases. Nat. Biotechnol. 35:5475–80
    [Google Scholar]
  65. 65. 
    Kim S, Kim D, Cho SW, Kim J, Kim J-S 2014. Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res 24:61012–19
    [Google Scholar]
  66. 66. 
    Kim YB, Komor AC, Levy JM, Packer MS, Zhao KT, Liu DR. 2017. Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions. Nat. Biotechnol. 35:4371–76
    [Google Scholar]
  67. 67. 
    Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT et al. 2016. High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529:7587490–95
    [Google Scholar]
  68. 68. 
    Klemm SL, Shipony Z, Greenleaf WJ. 2019. Chromatin accessibility and the regulatory epigenome. Nat. Rev. Genet. 20:4207–20
    [Google Scholar]
  69. 69. 
    Koblan LW, Doman JL, Wilson C, Levy JM, Tay T et al. 2018. Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. Nat. Biotechnol. 36:9843–46
    [Google Scholar]
  70. 70. 
    Koblan LW, Erdos MR, Wilson C, Cabral WA, Levy JM et al. 2021. In vivo base editing rescues Hutchinson-Gilford progeria syndrome in mice. Nature 589:7843608–14
    [Google Scholar]
  71. 71. 
    Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. 2016. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533:7603420–24
    [Google Scholar]
  72. 72. 
    Komor AC, Zhao KT, Packer MS, Gaudelli NM, Waterbury AL 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. 3:8eaao4774
    [Google Scholar]
  73. 73. 
    Konermann S, Lotfy P, Brideau NJ, Oki J, Shokhirev MN, Hsu PD. 2018. Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors. Cell 173:3665–676.e14
    [Google Scholar]
  74. 74. 
    Kulcsár PI, Tálas A, Huszár K, Ligeti Z, Tóth E et al. 2017. Crossing enhanced and high fidelity SpCas9 nucleases to optimize specificity and cleavage. Genome Biol 18:1190
    [Google Scholar]
  75. 75. 
    Kuscu C, Arslan S, Singh R, Thorpe J, Adli M 2014. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat. Biotechnol. 32:7677–83
    [Google Scholar]
  76. 76. 
    Kushawah G, Hernandez-Huertas L, Abugattas-Nuñez del Prado J, Martinez-Morales JR, DeVore ML et al. 2020. CRISPR-Cas13d induces efficient mRNA knockdown in animal embryos. Dev. Cell 54:6805–817.e7
    [Google Scholar]
  77. 77. 
    Lee JK, Jeong E, Lee J, Jung M, Shin E et al. 2018. Directed evolution of CRISPR-Cas9 to increase its specificity. Nat. Commun. 9:13048
    [Google Scholar]
  78. 78. 
    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. 6:29eaba1773
    [Google Scholar]
  79. 79. 
    Li J-F, Norville JE, Aach J, McCormack M, Zhang D et al. 2013. Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat. Biotechnol. 31:8688–91
    [Google Scholar]
  80. 80. 
    Li L, Hu S, Chen X. 2018. Non-viral delivery systems for CRISPR/Cas9-based genome editing: challenges and opportunities. Biomaterials 171:207–18
    [Google Scholar]
  81. 81. 
    Li S, Li X, Xue W, Zhang L, Yang L-Z et al. 2021. Screening for functional circular RNAs using the CRISPR–Cas13 system. Nat. Methods 18:151–59
    [Google Scholar]
  82. 82. 
    Liang P, Xie X, Zhi S, Sun H, Zhang X et al. 2019. Genome-wide profiling of adenine base editor specificity by EndoV-seq. Nat. Commun. 10:167
    [Google Scholar]
  83. 83. 
    Lin L, Liu Y, Xu F, Huang J, Daugaard TF et al. 2018. Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases. GigaScience 7:31–19
    [Google Scholar]
  84. 84. 
    Liu L, Li X, Ma J, Li Z, You L et al. 2017. The molecular architecture for RNA-guided RNA cleavage by Cas13a. Cell 170:4714–26.e10
    [Google Scholar]
  85. 85. 
    Liu L, Li X, Wang J, Wang M, Chen P et al. 2017. Two distant catalytic sites are responsible for C2c2 RNase activities. Cell 168:1–2121–34.e12
    [Google Scholar]
  86. 86. 
    Liu Y, Li X, He S, Huang S, Li C et al. 2020. Efficient generation of mouse models with the prime editing system. Cell Discov 6:27
    [Google Scholar]
  87. 87. 
    Liu Y, Mao S, Huang S, Li Y, Chen Y et al. 2020. REPAIRx, a specific yet highly efficient programmable A > I RNA base editor. EMBO J 39:22e104748
    [Google Scholar]
  88. 88. 
    Liu Y, Zhou C, Huang S, Dang L, Wei Y et al. 2020. A Cas-embedding strategy for minimizing off-target effects of DNA base editors. Nat. Commun. 11:16073
    [Google Scholar]
  89. 89. 
    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 13:121029–35
    [Google Scholar]
  90. 90. 
    Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M et al. 2013. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 31:9833–38
    [Google Scholar]
  91. 91. 
    Mali P, Yang L, Esvelt KM, Aach J, Guell M et al. 2013. RNA-guided human genome engineering via Cas9. Science 339:6121823–26
    [Google Scholar]
  92. 92. 
    Meeske AJ, Nakandakari-Higa S, Marraffini LA. 2019. Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage. Nature 570:7760241–45
    [Google Scholar]
  93. 93. 
    Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N et al. 2020. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583:7818699–710
    [Google Scholar]
  94. 94. 
    Nakamura M, Gao Y, Dominguez AA, Qi LS. 2021. CRISPR technologies for precise epigenome editing. Nat. Cell Biol. 23:111–22
    [Google Scholar]
  95. 95. 
    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 353:6305aaf8729
    [Google Scholar]
  96. 96. 
    Nishimasu H, Cong L, Yan WX, Ran FA, Zetsche B et al. 2015. Crystal structure of Staphylococcus aureus Cas9. Cell 162:51113–26
    [Google Scholar]
  97. 97. 
    Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata S et al. 2014. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156:5935–49
    [Google Scholar]
  98. 98. 
    Nishimasu H, Shi X, Ishiguro S, Gao L, Hirano S et al. 2018. Engineered CRISPR-Cas9 nuclease with expanded targeting space. Science 361:64081259–62
    [Google Scholar]
  99. 99. 
    Pan C, Sretenovic S, Qi Y 2021. CRISPR/dCas-mediated transcriptional and epigenetic regulation in plants. Curr. Opin. Plant Biol. 60:101980
    [Google Scholar]
  100. 100. 
    Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR 2013. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat. Biotechnol. 31:9839–43
    [Google Scholar]
  101. 101. 
    Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS et al. 2013. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152:51173–83
    [Google Scholar]
  102. 102. 
    Ramakrishna S, Kwaku Dad A-B, Beloor J, Gopalappa R, Lee S-K, Kim H 2014. Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA. Genome Res 24:61020–27
    [Google Scholar]
  103. 103. 
    Ran FA, Hsu PD, Lin C-Y, Gootenberg JS, Konermann S et al. 2013. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154:61380–89
    [Google Scholar]
  104. 104. 
    Rees HA, Komor AC, Yeh W-H, 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. 8:115790
    [Google Scholar]
  105. 105. 
    Rees HA, Liu DR. 2018. Base editing: precision chemistry on the genome and transcriptome of living cells. Nat. Rev. Genet. 19:12770–88
    [Google Scholar]
  106. 106. 
    Rees HA, Wilson C, Doman JL, Liu DR. 2019. Analysis and minimization of cellular RNA editing by DNA adenine base editors. Sci. Adv. 5:5eaax5717
    [Google Scholar]
  107. 107. 
    Richter MF, Zhao KT, Eton E, Lapinaite A, Newby GA et al. 2020. Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity. Nat. Biotechnol. 38:7883–91
    [Google Scholar]
  108. 108. 
    Saunderson EA, Stepper P, Gomm JJ, Hoa L, Morgan A et al. 2017. Hit-and-run epigenetic editing prevents senescence entry in primary breast cells from healthy donors. Nat. Commun. 8:11450
    [Google Scholar]
  109. 109. 
    Schoger E, Carroll KJ, Iyer LM, McAnally JR, Tan W et al. 2020. CRISPR-mediated activation of endogenous gene expression in the postnatal heart. Circ. Res. 126:16–24
    [Google Scholar]
  110. 110. 
    Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F 2016. Rationally engineered Cas9 nucleases with improved specificity. Science 351:626884–88
    [Google Scholar]
  111. 111. 
    Slaymaker IM, Mesa P, Kellner MJ, Kannan S, Brignole E et al. 2019. High-resolution structure of Cas13b and biochemical characterization of RNA targeting and cleavage. Cell Rep 26:133741–51.e5
    [Google Scholar]
  112. 112. 
    Smargon AA, Cox DBT, Pyzocha NK, Zheng K, Slaymaker IM et al. 2017. Cas13b is a type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx28. Mol. Cell 65:4618–30.e7
    [Google Scholar]
  113. 113. 
    Stemmer M, Thumberger T, del Sol Keyer M, Wittbrodt J, Mateo JL 2015. CCTop: an intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PLOS ONE 10:4e0124633 Correction. 2017. PLOS ONE 12(4):e0176619
    [Google Scholar]
  114. 114. 
    Stuart T, Satija R. 2019. Integrative single-cell analysis. Nat. Rev. Genet. 20:5257–72
    [Google Scholar]
  115. 115. 
    Suh S, Choi EH, Leinonen H, Foik AT, Newby GA et al. 2021. Restoration of visual function in adult mice with an inherited retinal disease via adenine base editing. Nat. Biomed. Eng. 5:2169–78
    [Google Scholar]
  116. 116. 
    Sürün D, Schneider A, Mircetic J, Neumann K, Lansing F et al. 2020. Efficient generation and correction of mutations in human iPS cells utilizing mRNAs of CRISPR base editors and prime editors. Genes 11:5511
    [Google Scholar]
  117. 117. 
    Tang X, Liu G, Zhou J, Ren Q, You Q et al. 2018. A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice. Genome Biol 19:184
    [Google Scholar]
  118. 118. 
    Thakore PI, D'Ippolito AM, Song L, Safi A, Shivakumar NK et al. 2015. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat. Methods 12:121143–49
    [Google Scholar]
  119. 119. 
    Tsai SQ, Joung JK. 2016. Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases. Nat. Rev. Genet. 17:5300–12
    [Google Scholar]
  120. 120. 
    Tsai SQ, Nguyen NT, Malagon-Lopez J, Topkar VV, Aryee MJ, Joung JK. 2017. CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR–Cas9 nuclease off-targets. Nat. Methods 14:6607–14
    [Google Scholar]
  121. 121. 
    Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V et al. 2014. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat. Biotechnol. 32:6569–76
    [Google Scholar]
  122. 122. 
    Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV et al. 2015. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat. Biotechnol. 33:2187–97
    [Google Scholar]
  123. 123. 
    Tycko J, Myer VE, Hsu PD. 2016. Methods for optimizing CRISPR-Cas9 genome editing specificity. Mol. Cell 63:3355–70
    [Google Scholar]
  124. 124. 
    Tycko J, Wainberg M, Marinov GK, Ursu O, Hess GT et al. 2019. Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements. Nat. Commun. 10:14063
    [Google Scholar]
  125. 125. 
    Vakulskas CA, Dever DP, Rettig GR, Turk R, Jacobi AM et al. 2018. A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells. Nat. Med. 24:81216–24
    [Google Scholar]
  126. 126. 
    Villiger L, Rothgangl T, Witzigmann D, Oka R, Lin PJC et al. 2021. In vivo cytidine base editing of hepatocytes without detectable off-target mutations in RNA and DNA. Nat. Biomed. Eng. 5:2179–89
    [Google Scholar]
  127. 127. 
    Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW et al. 2013. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153:4910–18
    [Google Scholar]
  128. 128. 
    Wang Q, Liu X, Zhou J, Yang C, Wang G et al. 2019. The CRISPR-Cas13a gene-editing system induces collateral cleavage of RNA in glioma cells. Adv. Sci. 6:201901299
    [Google Scholar]
  129. 129. 
    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. 36:10946–49
    [Google Scholar]
  130. 130. 
    Wessels H-H, Méndez-Mancilla A, Guo X, Legut M, Daniloski Z, Sanjana NE 2020. Massively parallel Cas13 screens reveal principles for guide RNA design. Nat. Biotechnol. 38:6722–27
    [Google Scholar]
  131. 131. 
    Wienert B, Wyman SK, Richardson CD, Yeh CD, Akcakaya P et al. 2019. Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq. Science 364:6437286–89
    [Google Scholar]
  132. 132. 
    Willi M, Smith HE, Wang C, Liu C, Hennighausen L. 2018. Mutation frequency is not increased in CRISPR-Cas9-edited mice. Nat. Methods 15:10756–58
    [Google Scholar]
  133. 133. 
    Wright AV, Sternberg SH, Taylor DW, Staahl BT, Bardales JA et al. 2015. Rational design of a split-Cas9 enzyme complex. PNAS 112:102984–89
    [Google Scholar]
  134. 134. 
    Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD et al. 2014. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat. Biotechnol. 32:7670–76
    [Google Scholar]
  135. 135. 
    Xu C, Zhou Y, Xiao Q, He B, Geng G et al. 2021. Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes. Nat. Methods 18:5499–506
    [Google Scholar]
  136. 136. 
    Xu W, Song W, Yang Y, Wu Y, Lv X et al. 2019. Multiplex nucleotide editing by high-fidelity Cas9 variants with improved efficiency in rice. BMC Plant Biol 19:1511
    [Google Scholar]
  137. 137. 
    Yan WX, Mirzazadeh R, Garnerone S, Scott D, Schneider MW et al. 2017. BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks. Nat. Commun. 8:15058
    [Google Scholar]
  138. 138. 
    Yeo NC, Chavez A, Lance-Byrne A, Chan Y, Menn D et al. 2018. An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat. Methods 15:8611–16
    [Google Scholar]
  139. 139. 
    Yin H, Song C-Q, Suresh S, Kwan S-Y, Wu Q et al. 2018. Partial DNA-guided Cas9 enables genome editing with reduced off-target activity. Nat. Chem. Biol. 14:3311–16
    [Google Scholar]
  140. 140. 
    Yu Y, Leete TC, Born DA, Young L, Barrera LA et al. 2020. Cytosine base editors with minimized unguided DNA and RNA off-target events and high on-target activity. Nat. Commun. 11:12052
    [Google Scholar]
  141. 141. 
    Zetsche B, Volz SE, Zhang F. 2015. A split-Cas9 architecture for inducible genome editing and transcription modulation. Nat. Biotechnol. 33:2139–42
    [Google Scholar]
  142. 142. 
    Zhang B, Ye Y, Ye W, Perčulija V, Jiang H et al. 2019. Two HEPN domains dictate CRISPR RNA maturation and target cleavage in Cas13d. Nat. Commun. 10:12544
    [Google Scholar]
  143. 143. 
    Zhang C, Konermann S, Brideau NJ, Lotfy P, Wu X et al. 2018. Structural basis for the RNA-guided ribonuclease activity of CRISPR-Cas13d. Cell 175:1212–23.e17
    [Google Scholar]
  144. 144. 
    Zhao X, Liu L, Lang J, Cheng K, Wang Y et al. 2018. A CRISPR-Cas13a system for efficient and specific therapeutic targeting of mutant KRAS for pancreatic cancer treatment. Cancer Lett 431:171–81
    [Google Scholar]
  145. 145. 
    Zhao Y, Yang X, Zhou G, Zhang T 2020. Engineering plant virus resistance: from RNA silencing to genome editing strategies. Plant Biotechnol. J. 18:2328–36
    [Google Scholar]
  146. 146. 
    Zhou C, Hu X, Tang C, Liu W, Wang S et al. 2020. CasRx-mediated RNA targeting prevents choroidal neovascularization in a mouse model of age-related macular degeneration. Natl. Sci. Rev. 7:5835–37
    [Google Scholar]
  147. 147. 
    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 571:7764275–78
    [Google Scholar]
  148. 148. 
    Zhou H, Su J, Hu X, Zhou C, Li H et al. 2020. Glia-to-neuron conversion by CRISPR-CasRx alleviates symptoms of neurological disease in mice. Cell 181:3590–603.e16
    [Google Scholar]
  149. 149. 
    Zong Y, Song Q, Li C, Jin S, Zhang D et al. 2018. Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A. Nat. Biotechnol. 36:10950–53
    [Google Scholar]
  150. 150. 
    Zuo E, Sun Y, Wei W, Yuan T, Ying W et al. 2019. Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science 364:6437289–92
    [Google Scholar]
  151. 151. 
    Zuo E, Sun Y, Yuan T, He B, Zhou C et al. 2020. A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects. Nat. Methods 17:6600–4
    [Google Scholar]
/content/journals/10.1146/annurev-genet-071719-030438
Loading
/content/journals/10.1146/annurev-genet-071719-030438
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error