Adikusuma F, Piltz S, Corbett MA, Turvey M, McColl SR, Helbig KJ, Beard MR, Hughes J, Pomerantz RT, Thomas PQ (2018) Large deletions induced by Cas9 cleavage. Nature 560:E8–E9
Aida T, Chiyo K, Usami T, Ishikubo H, Imahashi R, Wada Y, Tanaka KF, Sakuma T, Yamamoto T, Tanaka K (2015) Cloning-free CRISPR/Cas system facilitates functional cassette knock-in in mice. Genome Biol 16:87
Aida T, Nakade S, Sakuma T, Izu Y, Oishi A, Mochida K, Ishikubo H, Usami T, Aizawa H, Yamamoto T et al (2016) Gene cassette knock-in in mammalian cells and zygotes by enhanced MMEJ. BMC Genomics 17:979
Aird EJ, Lovendahl KN, St Martin A, Harris RS, Gordon WR (2018) Increasing Cas9-mediated homology-directed repair efficiency through covalent tethering of DNA repair template. Commun Biol 1:54
Alanis-Lobato G, Zohren J, Mccarthy A, Fogarty NME, Kubikova N, Hardman E, Greco M, Wells D, Turner JMA, Niakan KK (2020) Frequent loss-of-heterozygosity in CRISPR-Cas9-edited early human embryos. bioRxiv.
Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, Chen PJ, Wilson C, Newby GA, Raguram A et al (2019) Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576(7785):149–157
Anzalone AV, Koblan LW, Liu DR (2020) Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors. Nat Biotechnol 38:824–844
Bak RO, Porteus MH (2017) CRISPR-Mediated Integration of Large Gene Cassettes Using AAV Donor Vectors. Cell Rep 20:750–756
Baltimore D, Berg P, Botchan M, Carroll D, Charo RA, Church G, Corn JE, Daley GQ, Doudna JA, Fenner M et al (2015) Biotechnology. A prudent path forward for genomic engineering and germline gene modification. Science 348:36–38
Bedell VM, Wang Y, Campbell JM, Poshusta TL, Starker CG, Krug RG 2nd, Tan W, Penheiter SG, Ma AC, Leung AY et al (2012) In vivo genome editing using a high-efficiency TALEN system. Nature 491:114–118
Bennardo N, Cheng A, Huang N, Stark JM (2008) Alternative-NHEJ is a mechanistically distinct pathway of mammalian chromosome break repair. PLoS Genet 4:
Bothmer A, Phadke T, Barrera LA, Margulies CM, Lee CS, Buquicchio F, Moss S, Abdulkerim HS, Selleck W, Jayaram H et al (2017) Characterization of the interplay between DNA repair and CRISPR/Cas9-induced DNA lesions at an endogenous locus. Nat Commun 8:13905
Canaj H, Hussmann JA, Li H, Beckman KA, Goodrich L, Cho NH, Li YJ, Santos DA, McGeever A, Stewart EM et al (2019) Deep profiling reveals substantial heterogeneity of integration outcomes in CRISPR knock-in experiments. BioRxiv.
Carlson-Stevermer J, Abdeen AA, Kohlenberg L, Goedland M, Molugu K, Lou M, Saha K (2017) Assembly of CRISPR ribonucleoproteins with biotinylated oligonucleotides via an RNA aptamer for precise gene editing. Nat Commun 8:1711
Ceccaldi R, Rondinelli B, D’Andrea AD (2016) Repair pathway choices and consequences at the double-strand break. Trends Cell Biol 26:52–64
Chang HHY, Pannunzio NR, Adachi N, Lieber MR (2017) Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nat Rev Mol Cell Biol 18:495–506
Chen F, Pruett-Miller SM, Huang Y, Gjoka M, Duda K, Taunton J, Collingwood TN, Frodin M, Davis GD (2011) High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases. Nat Methods 8:753–755
Chen JS, Dagdas YS, Kleinstiver BP, Welch MM, Sousa AA, Harrington LB, Sternberg SH, Joung JK, Yildiz A, Doudna JA (2017) Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. Nature 550:407–410
Chen S, Sun S, Moonen D, Lee C, Lee AY, Schaffer DV, He L (2019) CRISPR-READI: Efficient Generation of Knockin Mice by CRISPR RNP Electroporation and AAV Donor Infection. Cell Rep 27(3780–3789):
Chen Y, Zhi S, Liu W, Wen J, Hu S, Cao T, Sun H, Li Y, Huang L, Liu Y et al (2020) Development of highly efficient dual-AAV split adenosine base editor for in vivo gene therapy. Small Methods 4(9):2000309
Choulika A, Perrin A, Dujon B, Nicolas JF (1995) Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae. Mol Cell Biol 15:1968–1973
Chu VT, Weber T, Wefers B, Wurst W, Sander S, Rajewsky K, Kuhn R (2015) Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat Biotechnol 33:543–548
Codner GF, Mianne J, Caulder A, Loeffler J, Fell R, King R, Allan AJ, Mackenzie M, Pike FJ, McCabe CV et al (2018) Application of long single-stranded DNA donors in genome editing: generation and validation of mouse mutants. BMC Biol 16:70
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA et al (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823
Cornu TI, Mussolino C, Cathomen T (2017) Refining strategies to translate genome editing to the clinic. Nat Med 23:415–423
De Ravin SS, Li L, Wu X, Choi U, Allen C, Koontz S, Lee J, Theobald-Whiting N, Chu J, Garofalo M et al (2017) CRISPR-Cas9 gene repair of hematopoietic stem cells from patients with X-linked chronic granulomatous disease. Sci Transl Med 9:eaah3480
Dever DP, Bak RO, Reinisch A, Camarena J, Washington G, Nicolas CE, Pavel-Dinu M, Saxena N, Wilkens AB, Mantri S et al (2016) CRISPR/Cas9 beta-globin gene targeting in human haematopoietic stem cells. Nature 539:384–389
DeWitt MA, Magis W, Bray NL, Wang T, Berman JR, Urbinati F, Heo SJ, Mitros T, Munoz DP, Boffelli D et al (2016) Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells. Sci Transl Med 8:
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 38:620–628
Doudna JA (2020) The promise and challenge of therapeutic genome editing. Nature 578:229–236
Egli D, Zuccaro MV, Kosicki M, Church GM, Bradley A, Jasin M (2018) Inter-homologue repair in fertilized human eggs? Nature 560:E5–E7
Gaj T, Gersbach CA, Barbas CF 3rd (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31:397–405
Gaj T, Staahl BT, Rodrigues GMC, Limsirichai P, Ekman FK, Doudna JA, Schaffer DV (2017) Targeted gene knock-in by homology-directed genome editing using Cas9 ribonucleoprotein and AAV donor delivery. Nucleic Acids Res 45:
Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR (2017) Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage. Nature 551:464–471
Ge XA, Hunter CP (2019) Efficient homologous recombination in mice using long single stranded DNA and CRISPR Cas9 nickase. G3 (Bethesda) 9:281–286
Grunewald J, Zhou R, Garcia SP, Iyer S, Lareau CA, Aryee MJ, Joung JK (2019a) Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors. Nature 569:433–437
Grunewald J, Zhou R, Iyer S, Lareau CA, Garcia SP, Aryee MJ, Joung JK (2019b) CRISPR DNA base editors with reduced RNA off-target and self-editing activities. Nat Biotechnol 37:1041–1048
Gu B, Posfai E, Rossant J (2018) Efficient generation of targeted large insertions by microinjection into two-cell-stage mouse embryos. Nat Biotechnol 36:632–637
Gurumurthy CB, O’Brien AR, Quadros RM, Adams J Jr, Alcaide P, Ayabe S, Ballard J, Batra SK, Beauchamp MC, Becker KA et al (2019) Reproducibility of CRISPR-Cas9 methods for generation of conditional mouse alleles: a multi-center evaluation. Genome Biol 20:171
Hendel A, Kildebeck EJ, Fine EJ, Clark J, Punjya N, Sebastiano V, Bao G, Porteus MH (2014) Quantifying genome-editing outcomes at endogenous loci with SMRT sequencing. Cell Rep 7:293–305
Hisano Y, Sakuma T, Nakade S, Ohga R, Ota S, Okamoto H, Yamamoto T, Kawahara A (2015) Precise in-frame integration of exogenous DNA mediated by CRISPR/Cas9 system in zebrafish. Sci Rep 5:8841
Iyer S, Mir A, Vega-Badillo J, Roscoe BP, Ibraheim R, Zhu LHJ, Lee JY, Liu PP, Luk K, Mintzer E et al (2019) Efficient homology-directed repair with circular ssDNA donors. bioRxiv.
Jiang F, Taylor DW, Chen JS, Kornfeld JE, Zhou K, Thompson AJ, Nogales E, Doudna JA (2016) Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage. Science 351:867–871
Jin S, Zong Y, Gao Q, Zhu Z, Wang Y, Qin P, Liang C, Wang D, Qiu JL, Zhang F et al (2019) Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice. Science 364:292–295
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 337:816–821
Kan Y, Ruis B, Takasugi T, Hendrickson EA (2017) Mechanisms of precise genome editing using oligonucleotide donors. Genome Res 27:1099–1111
Kim D, Lim K, Kim ST, Yoon SH, Kim K, Ryu SM, Kim JS (2017a) Genome-wide target specificities of CRISPR RNA-guided programmable deaminases. Nat Biotechnol 35:475–480
Kim K, Ryu SM, Kim ST, Baek G, Kim D, Lim K, Chung E, Kim S, Kim JS (2017b) Highly efficient RNA-guided base editing in mouse embryos. Nat Biotechnol 35:435–437
Kim YB, Komor AC, Levy JM, Packer MS, Zhao KT, Liu DR (2017c) Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions. Nat Biotechnol 35:371–376
Kim D, Kim DE, Lee G, Cho SI, Kim JS (2019) Genome-wide target specificity of CRISPR RNA-guided adenine base editors. Nat Biotechnol 37:430–435
Klompe SE, Vo PLH, Halpin-Healy TS, Sternberg SH (2019) Transposon-encoded CRISPR-Cas systems direct RNA-guided DNA integration. Nature 571:219–225
Kohama Y, Higo S, Masumura Y, Shiba M, Kondo T, Ishizu T, Higo T, Nakamura S, Kameda S, Tabata T et al (2020) Adeno-associated virus-mediated gene delivery promotes S-phase entry-independent precise targeted integration in cardiomyocytes. Sci Rep 10:15348
Comments (0)