Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 2011;471(7340):602–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339(6121):819–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, et al. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol. 2014;32:670–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337(6096):816–21.
Article
CAS
PubMed
Google Scholar
Kearns NA, Pham H, Tabak B, Genga RM, Silverstein NJ, Garber M, Maehr R. Functional annotation of native enhancers with a Cas9-histone demethylase fusion. Nat Methods. 2015;12(5):401–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Han J, Zhang J, Chen L, Shen B, Zhou J, Hu B, Du Y, Tate PH, Huang X, Zhang W. Efficient in vivo deletion of a large imprinted lncRNA by CRISPR/Cas9. RNA Biol. 2014;11(7):829–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bassett AR, Azzam G, Wheatley L, Tibbit C, Rajakumar T, McGowan S, Stanger N, Ewels PA, Taylor S, Ponting CP, et al. Understanding functional miRNA-target interactions in vivo by site-specific genome engineering. Nat Commun. 2014;5:4640.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liao HK, Gu Y, Diaz A, Marlett J, Takahashi Y, Li M, Suzuki K, Xu R, Hishida T, Chang CJ, et al. Use of the CRISPR/Cas9 system as an intracellular defense against HIV-1 infection in human cells. Nat Commun. 2015;6:6413.
Article
CAS
PubMed
Google Scholar
Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell. 2013;155(7):1479–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li J, Zhang BB, Ren YG, Gu SY, Xiang YH, Du JL. Intron targeting-mediated and endogenous gene integrity-maintaining knockin in zebrafish using the CRISPR/Cas9 system. Cell Res. 2015;25(5):634–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell. 2013;153(4):910–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wagner JC, Platt RJ, Goldfless SJ, Zhang F, Niles JC. Efficient CRISPR-Cas9-mediated genome editing in Plasmodium falciparum. Nat Methods. 2014;11(9):915–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vinayak S, Pawlowic MC, Sateriale A, Brooks CF, Studstill CJ, Bar-Peled Y, Cipriano MJ, Striepen B. Genetic modification of the diarrhoeal pathogen Cryptosporidium parvum. Nature. 2015;523:477–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sasaki H, Yoshida K, Hozumi A, Sasakura Y. CRISPR/Cas9-mediated gene knockout in the ascidian Ciona intestinalis. Dev Growth Differ. 2014;56(7):499–510.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C, Qiu JL. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Biotechnol. 2014;32(9):947–51.
Article
CAS
PubMed
Google Scholar
Zhou H, Liu B, Weeks DP, Spalding MH, Yang B. Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice. Nucleic Acids Res. 2014;42(17):10903–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brooks C, Nekrasov V, Lippman ZB, Van Eck J. Efficient gene editing in tomato in the first generation using the clustered regularly interspaced short palindromic repeats/CRISPR-associated9 system. Plant Physiol. 2014;166(3):1292–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wei W, Xin H, Roy B, Dai J, Miao Y, Gao G. Heritable genome editing with CRISPR/Cas9 in the silkworm, Bombyx mori. PLoS One. 2014;9(7):e101210.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shen Z, Zhang X, Chai Y, Zhu Z, Yi P, Feng G, Li W, Ou G. Conditional knockouts generated by engineered CRISPR-Cas9 endonuclease reveal the roles of coronin in C. elegans neural development. Dev Cell. 2014;30(5):625–36.
Article
CAS
PubMed
Google Scholar
Gilles AF, Schinko JB, Averof M. Efficient CRISPR-mediated gene targeting and transgene replacement in the beetle Tribolium castaneum. Development. 2015;142:2832–9.
Article
CAS
PubMed
Google Scholar
Square T, Romasek M, Jandzik D, Cattell MV, Klymkowsky M, Medeiros DM. CRISPR/Cas9-mediated mutagenesis in the sea lamprey, Petromyzon marinus: a powerful tool for understanding ancestral gene functions in vertebrates. Development. 2015;142:4180–7.
Article
CAS
PubMed
Google Scholar
Liu D, Wang ZX, Xiao A, Zhang YT, Li WY, Zu Y, Yao SH, Lin S, Zhang B. Efficient gene targeting in zebrafish mediated by a zebrafish-codon-optimized Cas9 and evaluation of off-targeting effect. J Genet Genomics. 2014;41(1):43–6.
Article
CAS
PubMed
Google Scholar
Edvardsen RB, Leininger S, Kleppe L, Skaftnesmo KO, Wargelius A. Targeted mutagenesis in Atlantic salmon (Salmo salar L.) using the CRISPR/Cas9 system induces complete knockout individuals in the F0 generation. PLoS One. 2014;9(9):e108622.
Article
CAS
PubMed
PubMed Central
Google Scholar
Whitworth KM, Lee K, Benne JA, Beaton BP, Spate LD, Murphy SL, Samuel MS, Mao J, O’Gorman C, Walters EM, et al. Use of the CRISPR/Cas9 system to produce genetically engineered pigs from in vitro-derived oocytes and embryos. Biol Reprod. 2014;91(3):78.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shao Y, Guan Y, Wang L, Qiu Z, Liu M, Chen Y, Wu L, Li Y, Ma X, Liu M, et al. CRISPR/Cas-mediated genome editing in the rat via direct injection of one-cell embryos. Nat Protoc. 2014;9(10):2493–512.
Article
CAS
PubMed
Google Scholar
Ni W, Qiao J, Hu S, Zhao X, Regouski M, Yang M, Polejaeva IA, Chen C. Efficient gene knockout in goats using CRISPR/Cas9 system. PLoS One. 2014;9(9):e106718.
Article
CAS
PubMed
PubMed Central
Google Scholar
Honda A, Hirose M, Sankai T, Yasmin L, Yuzawa K, Honsho K, Izu H, Iguchi A, Ikawa M, Ogura A. Single-step generation of rabbits carrying a targeted allele of the tyrosinase gene using CRISPR/Cas9. Exp Anim. 2015;64(1):31–7.
Article
CAS
PubMed
Google Scholar
Peng J, Zhou Y, Zhu S, Wei W. High-throughput screens in mammalian cells using the CRISPR-Cas9 system. FEBS J. 2015;282(11):2089–96.
Article
CAS
PubMed
Google Scholar
Lane AB, Strzelecka M, Ettinger A, Grenfell AW, Wittmann T, Heald R. Enzymatically generated CRISPR libraries for genome labeling and screening. Dev Cell. 2015;34(3):373–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schmidt T, Schmid-Burgk JL, Hornung V. Synthesis of an arrayed sgRNA library targeting the human genome. Sci Rep. 2015;5:14987.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vidigal JA, Ventura A. Rapid and efficient one-step generation of paired gRNA CRISPR-Cas9 libraries. Nat Commun. 2015;6:8083.
Article
CAS
PubMed
PubMed Central
Google Scholar
Canver MC, Smith EC, Sher F, Pinello L, Sanjana NE, Shalem O, Chen DD, Schupp PG, Vinjamur DS, Garcia SP, et al. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature. 2015;527:192–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Köferle A, Stricker SH, Beck S. Brave new epigenomes: the dawn of epigenetic engineering. Genome Med. 2015;7(1):59.
Article
PubMed Central
Google Scholar
Sambrook J, Russell DW. Isolation of DNA fragments from polyacrylamide gels by the crush and soak method. CSH Protoc. 2006;2006:1.
Google Scholar
Gibson DG, Young L, Chuang RY, Venter JC, Hutchison 3rd CA, Smith HO. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 2009;6(5):343–5.
Article
CAS
PubMed
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17(1):10.
Article
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gilks WR, Richardson S, Spiegelhalter DJ. Markov chain Monte Carlo in practice. Boca Raton: Chapman & Hall; 1998.
Google Scholar
Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, Gonzales AP, Li Z, Peterson RT, Yeh JR, et al. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature. 2015;523(7561):481–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Esvelt KM, Mali P, Braff JL, Moosburner M, Yaung SJ, Church GM. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods. 2013;10(11):1116–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ran FA, Cong L, Yan WX, Scott DA, Gootenberg JS, Kriz AJ, Zetsche B, Shalem O, Wu X, Makarova KS, et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature. 2015;520(7546):186–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cuatrecasas P, Fuchs S, Anfinsen CB. Catalytic properties and specificity of the extracellular nuclease of Staphylococcus aureus. J Biol Chem. 1967;242(7):1541–7.
CAS
PubMed
Google Scholar
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860–921.
Article
CAS
PubMed
Google Scholar
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002;420(6915):520–62.
Article
CAS
PubMed
Google Scholar
Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 2013;31(9):827–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang L, Guell M, Niu D, George H, Lesha E, Grishin D, Aach J, Shrock E, Xu W, Poci J, et al. Genome-wide inactivation of porcine endogenous retroviruses (PERVs). Science. 2015;163:759–71.
Google Scholar
Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015;163:759–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Encode, Project, Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57–74.
Article
CAS
Google Scholar
Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science. 2014;343(6166):80–4.
Article
CAS
PubMed
Google Scholar