Homology-based repair induced by CRISPR-Cas nucleases in mammalian embryo genome editing

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

CAS  Article  Google Scholar 

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

Article  Google Scholar 

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

Article  Google Scholar 

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

Article  Google Scholar 

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

CAS  Article  Google Scholar 

Anzalone AV, Koblan LW, Liu DR (2020) Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors. Nat Biotechnol 38:824–844

CAS  Article  Google Scholar 

Bak RO, Porteus MH (2017) CRISPR-Mediated Integration of Large Gene Cassettes Using AAV Donor Vectors. Cell Rep 20:750–756

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

Bennardo N, Cheng A, Huang N, Stark JM (2008) Alternative-NHEJ is a mechanistically distinct pathway of mammalian chromosome break repair. PLoS Genet 4:

Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

Article  Google Scholar 

Ceccaldi R, Rondinelli B, D’Andrea AD (2016) Repair pathway choices and consequences at the double-strand break. Trends Cell Biol 26:52–64

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

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):

Google Scholar 

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

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

Article  Google Scholar 

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

CAS  Article  Google Scholar 

Cornu TI, Mussolino C, Cathomen T (2017) Refining strategies to translate genome editing to the clinic. Nat Med 23:415–423

CAS  Article  Google Scholar 

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

Article  Google Scholar 

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

CAS  Article  Google Scholar 

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:

Article  Google Scholar 

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

CAS  Article  Google Scholar 

Doudna JA (2020) The promise and challenge of therapeutic genome editing. Nature 578:229–236

CAS  Article  Google Scholar 

Egli D, Zuccaro MV, Kosicki M, Church GM, Bradley A, Jasin M (2018) Inter-homologue repair in fertilized human eggs? Nature 560:E5–E7

CAS  Article  Google Scholar 

Gaj T, Gersbach CA, Barbas CF 3rd (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31:397–405

CAS  Article  Google Scholar 

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:

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

CAS  Google Scholar 

Kan Y, Ruis B, Takasugi T, Hendrickson EA (2017) Mechanisms of precise genome editing using oligonucleotide donors. Genome Res 27:1099–1111

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

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

CAS  Article  Google Scholar 

Klompe SE, Vo PLH, Halpin-Healy TS, Sternberg SH (2019) Transposon-encoded CRISPR-Cas systems direct RNA-guided DNA integration. Nature 571:219–225

CAS  Article  Google Scholar 

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

CAS  Article 

Comments (0)

No login
gif