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Progression and application of CRISPR-Cas genomic editors

Yang, Li, Tang, Jing, Ma, Xuelei, Lin, Yuan, Ma, Guorong, Shan, Minghai, Wang, Libin, Yang, Yanhui·2021·Methods

Abstract

Base editing technology is an efficient tool for genome editing, particularly in the correction of base mutations. Diverse base editing systems were developed according to the dCas9 or nCas9 linked with different deaminase or reverse transcriptase in the editors, including ABEs, CBEs, PEs and dual-functional of base editor (such as CGBE1, A&C-BEmax, ACBE, etc.). Currently, Base editing technology has been widely applied to various fields such as microorganisms, plants, animals and medicine for basic research and therapeutics. Here, we reviewed the advancement of base editing technology. We also discussed the application of base editors in different areas in the future.

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Research works printed but not linked: 94

  1. Chakraborty, 2014, A CRISPR/Cas9-based system for reprogramming cell lineage specification, Stem Cell Rep., 3, 940, 10.1016/j.stemcr.2014.09.013 · DOI
  2. Zheng, 2014, Precise gene deletion and replacement using the CRISPR/Cas9 system in human cells, Biotechniques, 57, 115, 10.2144/000114196 · DOI
  3. Bhattacharya, 2015, CRISPR/Cas9: An inexpensive, efficient loss of function tool to screen human disease genes in Xenopus, Dev. Biol., 408, 196, 10.1016/j.ydbio.2015.11.003 · DOI
  4. Bakondi, 2016, In Vivo CRISPR/Cas9 Gene Editing Corrects Retinal Dystrophy in the S334ter-3 Rat Model of Autosomal Dominant Retinitis Pigmentosa, Molecular therapy : the journal of the American Society of Gene Therapy., 24, 556, 10.1038/mt.2015.220 · DOI
  5. Albadri, 2017, Genome editing using CRISPR/Cas9-based knock-in approaches in zebrafish, Methods, 15, 77, 10.1016/j.ymeth.2017.03.005 · DOI
  6. Kunze, 2018, Synthetic AAV/CRISPR vectors for blocking HIV-1 expression in persistently infected astrocytes, Glia., 66, 413, 10.1002/glia.23254 · DOI
  7. Chen W, McKenna A, Schreiber J, Haeussler M, Yin Y, Agarwal V, Noble WS, Shendure J. Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair. Nucleic acids research. 2019 Jun 5; https://doi.org/10.1093/nar/gkz487. · DOI
  8. Cong, 2013, Multiplex genome engineering using CRISPR/Cas systems, Science, 339, 819, 10.1126/science.1231143 · DOI · Paper page
  9. Ran, 2013, Genome engineering using the CRISPR-Cas9 system, Nat. Protoc., 8, 2281, 10.1038/nprot.2013.143 · DOI · Paper page
  10. Zhang, 2020, Multiplex precise base editing in cynomolgus monkeys, Nat. Commun., 11, 2325, 10.1038/s41467-020-16173-0 · DOI
  11. Yeh WH, Shubina-Oleinik O, Levy JM, Pan B, Newby GA, Wornow M, Burt R, Chen JC, Holt JR, Liu DR. In vivo base editing restores sensory transduction and transiently improves auditory function in a mouse model of recessive deafness. Sci Transl Med. 2020 Jun 3; 12(546)https://doi.org/10.1126/scitranslmed.aay9101. · DOI
  12. Plosky, 2016, CRISPR-Mediated Base Editing without DNA Double-Strand Breaks, Mol. Cell, 62, 477, 10.1016/j.molcel.2016.05.006 · DOI
  13. Hampton, 2020, DNA Prime Editing: A New CRISPR-Based Method to Correct Most Disease-Causing Mutations, JAMA, 323, 405, 10.1001/jama.2019.21827 · DOI
  14. Landrum, 2016, ClinVar: public archive of interpretations of clinically relevant variants, Nucleic Acids Res., 44, D862, 10.1093/nar/gkv1222 · DOI · Paper page
  15. Kuscu, 2016, CRISPR-Cas9-AID base editor is a powerful gain-of-function screening tool, Nat. Methods, 13, 983, 10.1038/nmeth.4076 · DOI
  16. Liang, 2017, Effective gene editing by high-fidelity base editor 2 in mouse zygotes, Protein & Cell., 8, 601, 10.1007/s13238-017-0418-2 · DOI
  17. Yang, 2017, APOBEC: From mutator to editor, Journal of Genetics and genomics = Yi chuan xue bao, 44, 423, 10.1016/j.jgg.2017.04.009 · DOI
  18. Kurt, 2021, CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells, Nat. Biotechnol., 39, 41, 10.1038/s41587-020-0609-x · DOI · Paper page
  19. Zhang, 2020, Dual base editor catalyzes both cytosine and adenine base conversions in human cells, Nat. Biotechnol., 38, 856, 10.1038/s41587-020-0527-y · DOI
  20. Xie, 2020, ACBE, a new base editor for simultaneous C-to-T and A-to-G substitutions in mammalian systems, BMC Biol., 18, 131, 10.1186/s12915-020-00866-5 · DOI
  21. Komor, 2016, Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage, Nature, 533, 420, 10.1038/nature17946 · DOI · Paper page
  22. Zhou, 2019, Programmable Base Editing of the Sheep Genome Revealed No Genome-Wide Off-Target Mutations, Front. Genet., 10, 215, 10.3389/fgene.2019.00215 · DOI
  23. Zhang, 2017, Programmable base editing of zebrafish genome using a modified CRISPR-Cas9 system, Nat. Commun., 8, 118, 10.1038/s41467-017-00175-6 · DOI
  24. Li, 2020, Programmable base editing of mutated TERT promoter inhibits brain tumour growth, Nat. Cell Biol., 22, 282, 10.1038/s41556-020-0471-6 · DOI
  25. Gaudelli, 2017, Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage, Nature, 551, 464, 10.1038/nature24644 · DOI · Paper page
  26. Hua, 2019, Expanding the base editing scope in rice by using Cas9 variants, Plant Biotechnol. J., 17, 499, 10.1111/pbi.12993 · DOI
  27. Anzalone, 2019, Search-and-replace genome editing without double-strand breaks or donor DNA, Nature, 576, 149, 10.1038/s41586-019-1711-4 · DOI · Paper page
  28. Wang, 2017, Enhanced base editing by co-expression of free uracil DNA glycosylase inhibitor, Cell Res., 27, 1289, 10.1038/cr.2017.111 · DOI
  29. A.C. Komor, K.T. Zhao, Packer MS. Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity. 2017; 3(8):eaao4774. https://doi.org/10.1126/sciadv.aao4774. · DOI · Paper page
  30. Lee S, Ding N, Sun Y, Yuan T, Li J, Yuan Q, Liu L, Yang J, Wang Q, Kolomeisky AB, Hilton IB, Zuo E, Gao X. Single C-to-T substitution using engineered APOBEC3G-nCas9 base editors with minimum genome- and transcriptome-wide off-target effects. Science advances. 2020 Jul; 6(29):eaba1773. https://doi.org/10.1126/sciadv.aba1773. · DOI
  31. Grunewald, 2019, CRISPR DNA base editors with reduced RNA off-target and self-editing activities, Nat. Biotechnol., 37, 1041, 10.1038/s41587-019-0236-6 · DOI
  32. Zhou, 2019, Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis, Nature, 571, 275, 10.1038/s41586-019-1314-0 · DOI · Paper page
  33. Rees, 2019, Analysis and minimization of cellular RNA editing by DNA adenine base editors, Sci. Adv., 5, eaax5717, 10.1126/sciadv.aax5717 · DOI
  34. Huang, 2019, Developing ABEmax-NG with Precise Targeting and Expanded Editing Scope to Model Pathogenic Splice Site Mutations In Vivo, iScience., 31, 640, 10.1016/j.isci.2019.05.008 · DOI
  35. Koblan, 2018, Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction, Nat. Biotechnol., 36, 843, 10.1038/nbt.4172 · DOI · Paper page
  36. Rees, 2018, Base editing: precision chemistry on the genome and transcriptome of living cells, Nat. Rev. Genet., 19, 770, 10.1038/s41576-018-0059-1 · DOI · Paper page
  37. Kim YB, Komor AC, Levy JM. Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions. 2017 Apr; 35(4):371-376. https://doi.org/10.1038/nbt.3803. · DOI · Paper page
  38. Song, 2020, Adenine base editing in an adult mouse model of tyrosinaemia, Nat. Biomed. Eng., 4, 125, 10.1038/s41551-019-0357-8 · DOI · Paper page
  39. Doman, 2020, Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors, Nat. Biotechnol., 38, 620, 10.1038/s41587-020-0414-6 · DOI · Paper page
  40. Gaudelli, 2020, Directed evolution of adenine base editors with increased activity and therapeutic application, Nat. Biotechnol., 38, 892, 10.1038/s41587-020-0491-6 · DOI
  41. Wu, 2019, Progress in the application of CRISPR: From gene to base editing, Med. Res. Rev., 39, 665, 10.1002/med.21537 · DOI
  42. Li, 2020, Docking sites inside Cas9 for adenine base editing diversification and RNA off-target elimination, Nat Commun., 11, 5827, 10.1038/s41467-020-19730-9 · DOI
  43. Li, 2020, Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors, Nat. Biotechnol., 38, 875, 10.1038/s41587-019-0393-7 · DOI
  44. Sakata, 2020, Base editors for simultaneous introduction of C-to-T and A-to-G mutations, Nat. Biotechnol., 38, 865, 10.1038/s41587-020-0509-0 · DOI
  45. Zuo, 2020, A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects, Nat. Methods, 17, 600, 10.1038/s41592-020-0832-x · DOI
  46. Negishi, 2019, An adenine base editor with expanded targeting scope using SpCas9-NGv1 in rice, Plant Biotechnol. J., 17, 1476, 10.1111/pbi.13120 · DOI · Paper page
  47. Rees, 2017, Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery, Nat. Commun., 6, 15790, 10.1038/ncomms15790 · DOI · Paper page
  48. Liu, 2018, Highly efficient RNA-guided base editing in rabbit, Nat. Commun., 9, 2717, 10.1038/s41467-018-05232-2 · DOI
  49. Levy, 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, 10.1038/s41551-019-0501-5 · DOI
  50. Qiao, 2009, Hydrodynamic limb vein injection of adeno-associated virus serotype 8 vector carrying canine myostatin propeptide gene into normal dogs enhances muscle growth, Hum Gene Ther., 20, 1, 10.1089/hum.2008.135 · DOI
  51. Hua, 2020, Simplified adenine base editors improve adenine base editing efficiency in rice, Plant Biotechnol. J., 18, 770, 10.1111/pbi.13244 · DOI · Paper page
  52. Miller, 2020, Continuous evolution of SpCas9 variants compatible with non-G PAMs, Nat. Biotechnol., 38, 471, 10.1038/s41587-020-0412-8 · DOI
  53. Nguyen Tran, 2020, Engineering domain-inlaid SaCas9 adenine base editors with reduced RNA off-targets and increased on-target DNA editing, Nat. Commun., 11, 4871, 10.1038/s41467-020-18715-y · DOI
  54. Liang, 2019, Genome-wide profiling of adenine base editor specificity by EndoV-seq, Nat. Commun., 10, 67, 10.1038/s41467-018-07988-z · DOI · Paper page
  55. Liu, 2019, Expanded targeting scope and enhanced base editing efficiency in rabbit using optimized xCas9(3.7). Cellular and molecular life sciences, CMLS., 76, 4155, 10.1007/s00018-019-03110-8 · DOI
  56. Jiang, 2018, BE-PLUS: a new base editing tool with broadened editing window and enhanced fidelity, Cell Res., 28, 855, 10.1038/s41422-018-0052-4 · DOI
  57. Pausch, 2020, CRISPR-CasPhi from huge phages is a hypercompact genome editor, Science, 369, 333, 10.1126/science.abb1400 · DOI
  58. Tan, 2019, Engineering of high-precision base editors for site-specific single nucleotide replacement, Nat. Commun., 10, 439, 10.1038/s41467-018-08034-8 · DOI
  59. Wang, 2021, Microbial Base Editing: A Powerful Emerging Technology for Microbial Genome Engineering, Trends Biotechnol., 39, 165, 10.1016/j.tibtech.2020.06.010 · DOI
  60. Liu, 2017, Development of a CRISPR/Cas9 genome editing toolbox for Corynebacterium glutamicum, Microb. Cell Fact., 16, 205, 10.1186/s12934-017-0815-5 · DOI
  61. Yang, 2020, Genome editing systems across yeast species, Curr. Opin. Biotechnol., 1, 255, 10.1016/j.copbio.2020.08.011 · DOI
  62. Wei, 2019, Mycobacterium tuberculosis type III-A CRISPR/Cas system crRNA and its maturation have atypical features, FASEB journal : official publication of the Federation of American Societies for Experimental Biology., 33, 1496, 10.1096/fj.201800557RR · DOI
  63. Miki, 2021, CRISPR/Cas9-Based Genome Editing Toolbox for Arabidopsis thaliana, Methods Mol. Biol., 2200, 121, 10.1007/978-1-0716-0880-7_5 · DOI
  64. Yarra, 2020, CRISPR/Cas mediated base editing: a practical approach for genome editing in oil palm, 3 Biotech, 10, 306, 10.1007/s13205-020-02302-5 · DOI
  65. Kang, 2018, Precision genome engineering through adenine base editing in plants, Nat. Plants., 4, 427, 10.1038/s41477-018-0178-x · DOI
  66. Lu, 2017, Precise Editing of a Target Base in the Rice Genome Using a Modified CRISPR/Cas9 System, Molecular plant., 10, 523, 10.1016/j.molp.2016.11.013 · DOI
  67. Packer, 2017, Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion, Nat. Biotechnol., 35, 438, 10.1038/nbt.3811 · DOI
  68. Hua, 2018, Precise A.T to G.C Base Editing in the Rice Genome, Molecular plant., 11, 627, 10.1016/j.molp.2018.02.007 · DOI
  69. Hua, 2020, Precision genome engineering in rice using prime editing system, Plant Biotechnol. J., 18, 2167, 10.1111/pbi.13395 · DOI
  70. Lu, 2021, Precise Genome Modification in Tomato Using an Improved Prime Editing System, Plant Biotechnol. J., 19, 415, 10.1111/pbi.13497 · DOI
  71. Xu, 2020, Versatile Nucleotides Substitution in Plant Using an Improved Prime Editing System, Molecular plant., 13, 675, 10.1016/j.molp.2020.03.012 · DOI
  72. Liu, 2020, Precise base editing with CC context-specificity using engineered human APOBEC3G-nCas9 fusions, BMC Biol., 18, 111, 10.1186/s12915-020-00849-6 · DOI
  73. Qi, 2020, Base Editing Mediated Generation of Point Mutations Into Human Pluripotent Stem Cells for Modeling Disease, Front. Cell Dev. Biol., 8, 10.3389/fcell.2020.590581 · DOI
  74. Qin, 2018, Precise A*T to G*C base editing in the zebrafish genome, BMC Biol., 16, 139, 10.1186/s12915-018-0609-1 · DOI
  75. Liu, 2019, Efficient and precise base editing in rabbits using human APOBEC3A-nCas9 fusions, Cell Discov., 5, 31, 10.1038/s41421-019-0099-5 · DOI
  76. Xie, 2019, Efficient base editing for multiple genes and loci in pigs using base editors, Nat. Commun., 10, 2852, 10.1038/s41467-019-10421-8 · DOI
  77. Zhou, 2020, Highly efficient generation of sheep with a defined FecB(B) mutation via adenine base editing, Genet Sel Evol., 52, 35, 10.1186/s12711-020-00554-6 · DOI
  78. Li, 2019, Base pair editing in goat: nonsense codon introgression into FGF5 results in longer hair, The FEBS J., 286, 4675, 10.1111/febs.14983 · DOI
  79. Liang, 2017, Correction of beta-thalassemia mutant by base editor in human embryos, Protein & cell., 8, 811, 10.1007/s13238-017-0475-6 · DOI
  80. Li, 2017, Highly efficient and precise base editing in discarded human tripronuclear embryos, Protein & cell., 8, 776, 10.1007/s13238-017-0458-7 · DOI
  81. Winter, 2019, Targeted exon skipping with AAV-mediated split adenine base editors, Cell Discov., 5, 41, 10.1038/s41421-019-0109-7 · DOI
  82. Liu, 2020, Efficient generation of mouse models with the prime editing system, Cell Discov., 6, 27, 10.1038/s41421-020-0165-z · DOI
  83. Ryu, 2018, Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy, Nat. Biotechnol., 36, 536, 10.1038/nbt.4148 · DOI
  84. Suh, 2021, Restoration of visual function in adult mice with an inherited retinal disease via adenine base editing, Nat. Biomed. Eng., 5, 169, 10.1038/s41551-020-00632-6 · DOI
  85. Liang, 2020, AcrIIA5 Suppresses Base Editors and Reduces Their Off-Target Effects, Cells., 9, 10.3390/cells9081786 · DOI
  86. Zhang, 2020, Increasing the efficiency and targeting range of cytidine base editors through fusion of a single-stranded DNA-binding protein domain, Nat. Cell Biol., 22, 740, 10.1038/s41556-020-0518-8 · DOI
  87. Cheng, 2021, Base editing with high efficiency in allotetraploid oilseed rape by A3A-PBE system, Plant Biotechnol. J., 19, 87, 10.1111/pbi.13444 · DOI
  88. Wu, 2019, Increasing Cytosine Base Editing Scope and Efficiency With Engineered Cas9-PmCDA1 Fusions and the Modified sgRNA in Rice, Front. Genet., 10, 379, 10.3389/fgene.2019.00379 · DOI
  89. LeBlanc, 2018, Increased efficiency of targeted mutagenesis by CRISPR/Cas9 in plants using heat stress, The Plant journal : for cell and molecular biology., 93, 377, 10.1111/tpj.13782 · DOI
  90. Huang, 2019, Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors, Nat. Biotechnol., 37, 626, 10.1038/s41587-019-0134-y · DOI
  91. Tanaka, 2018, In vivo targeted single-nucleotide editing in zebrafish, Sci. Rep., 8, 11423, 10.1038/s41598-018-29794-9 · DOI
  92. Carrington, 2020, BE4max and AncBE4max Are Efficient in Germline Conversion of C: G to T: A Base Pairs in Zebrafish, Cells., 9, 10.3390/cells9071690 · DOI
  93. Lee, 2020, Highly elevated base excision repair pathway in primordial germ cells causes low base editing activity in chickens, FASEB journal : official publication of the Federation of American Societies for Experimental Biology., 34, 15907, 10.1096/fj.202001065RRR · DOI
  94. Komatsu, 2020, Production of Herbicide-Sensitive Strain to Prevent Volunteer Rice Infestation Using a CRISPR-Cas9 Cytidine Deaminase Fusion, Front. Plant Sci., 11, 925, 10.3389/fpls.2020.00925 · DOI

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Metadata

Authors
Yang, L., Tang, J., Ma, X., Lin, Y., Ma, G., Shan, M., Wang, L., & Yang, Y.
Venue
Methods
Publisher
Elsevier BV
Published
2021-10
Volume
194
Pages
65-74
ISSN
1046-2023
Cited by
10
References
6
Language
en
Funders
  • Chinese Academy of Sciences (XAB2019AW11)
  • National Natural Science Foundation of China (81202567, 81560604, 81860470)

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