Mojica FJ, Diez-Villasenor C, Soria E, Juez G. Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol Microbiol. 2000;36(1):244–6.
Article
CAS
PubMed
Google Scholar
Pourcel C, Salvignol G, Vergnaud G. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology. 2005;151(Pt 3):653–63.
CAS
PubMed
Google Scholar
Jansen R, van Embden JDA, Gaastra W, Schouls L. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol. 2002;43(6):1565–75.
Article
CAS
PubMed
Google Scholar
Groenen PM, Bunschoten AE, van Soolingen D, van Embden JD. Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method. Mol Microbiol. 1993;10(5):1057.
Article
CAS
PubMed
Google Scholar
Sola C, Filliol I, Legrand E, Lesjean S, Locht C, Rastogi N. Genotyping of the Mycobacterium tuberculosis complex using MIRUs: association with VNTR and spoligotyping for molecular epidemiology and evolutionary genetics. Infect Genet Evol. 2003;3(2):125–33.
Article
CAS
PubMed
Google Scholar
van Embden JD, van Gorkom T, Kremer K, Jansen R, van Der Zeijst BA, Schouls LM. Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria. J Bacteriol. 2000;182(9):2393–401.
Article
PubMed
PubMed Central
Google Scholar
Grissa I, Vergnaud G, Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics. 2007;8(1):172.
Article
PubMed
PubMed Central
CAS
Google Scholar
Koonin EV, Makarova KS, Zhang F. Diversity, classification and evolution of CRISPR-Cas systems. Curr Opin Microbiol. 2017;37:67–78.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell. 2014;156(5):935–49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gasiunas G, Barrangou R, Horvath P, Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A. 2012;109(39):E2579–86.
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.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jiang F, Taylor DW, Chen JS, Kornfeld JE, Zhou K, Thompson AJ, Nogales E, Doudna JA. Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage. Science. 2016;351(6275):867.
Article
CAS
PubMed
PubMed Central
Google Scholar
Leenay RT, Maksimchuk KR, Slotkowski RA, Agrawal RN, Gomaa AA, Briner AE, Barrangou R, Beisel CL. Identifying and visualizing functional PAM diversity across CRISPR-Cas systems. Mol Cell. 2016;62(1):137–47.
Article
CAS
PubMed
PubMed Central
Google Scholar
Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJJ, Charpentier E, Haft DH. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol. 2015;13(11):722–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shou J, Li J, Liu Y, Wu Q. Precise and predictable CRISPR chromosomal rearrangements reveal principles of Cas9-mediated nucleotide insertion. Mol Cell. 2018;71:498–509.
Article
CAS
PubMed
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
Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science. 2013;339(6121):823.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cox DBT, Platt RJ, Zhang F. Therapeutic genome editing: prospects and challenges. Nat Med. 2015;21(2):121–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Niu D, Wei HJ, Lin L, George H, Wang T, Lee IH, Zhao HY, Wang Y, Kan Y, Shrock E, et al. Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science. 2017;357(6357):1303.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yuen KS, Chan CP, Kok KH, Jin DY. Mutagenesis and genome engineering of Epstein-Barr virus in cultured human cells by CRISPR/Cas9. Methods Mol Biol. 2017;1498:23–31.
Article
CAS
PubMed
Google Scholar
Wang D, Wang XW, Peng XC, Xiang Y, Song SB, Wang YY, Chen L, Xin VW, Lyu YN, Ji J, et al. CRISPR/Cas9 genome editing technology significantly accelerated herpes simplex virus research. Cancer Gene Ther. 2018;25(5–6):93–105.
Article
CAS
PubMed
Google Scholar
Burby PE, Simmons LA. CRISPR/Cas9 editing of the Bacillus subtilis genome. Bio Protoc. 2017;7(8):e2272.
Article
PubMed
PubMed Central
Google Scholar
Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol. 2013;31(3):233–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jiang Y, Chen B, Duan CL, Sun BB, Yang JJ, Yang S. Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system. Appl Environ Microbiol. 2015;81(7):2506–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Selle K, Barrangou R. Harnessing CRISPR-Cas systems for bacterial genome editing. Trends Microbiol. 2015;23(4):225–32.
Article
CAS
PubMed
Google Scholar
Horwitz AA, Walter JM, Schubert MG, Kung SH, Hawkins K, Platt DM, Hernday AD, Mahatdejkul-Meadows T, Szeto W, Chandran SS, et al. Efficient multiplexed integration of synergistic alleles and metabolic pathways in yeasts via CRISPR-Cas. Cell Syst. 2015;1(1):88–96.
Article
CAS
PubMed
Google Scholar
Jacobs JZ, Ciccaglione KM, Tournier V, Zaratiegui M. Implementation of the CRISPR-Cas9 system in fission yeast. Nat Commun. 2014;5:5344.
Article
CAS
PubMed
Google Scholar
Jakociunas T, Jensen MK, Keasling JD. CRISPR/Cas9 advances engineering of microbial cell factories. Metab Eng. 2016;34:44–59.
Article
CAS
PubMed
Google Scholar
Schwartz CM, Hussain MS, Blenner M, Wheeldon I. Synthetic RNA polymerase III promoters facilitate high-efficiency CRISPR-Cas9-mediated genome editing in Yarrowia lipolytica. ACS Synth Biol. 2016;5(4):356–9.
Article
CAS
PubMed
Google Scholar
Vyas VK, Barrasa MI, Fink GR. A Candida albicans CRISPR system permits genetic engineering of essential genes and gene families. Sci Adv. 2015;1(3):e1500248.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wang Y, Wei D, Zhu X, Pan J, Zhang P, Huo L, Zhu X. A ‘suicide’ CRISPR-Cas9 system to promote gene deletion and restoration by electroporation in Cryptococcus neoformans. Sci Rep. 2016;6:31145.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weninger A, Hatzl AM, Schmid C, Vogl T, Glieder A. Combinatorial optimization of CRISPR/Cas9 expression enables precision genome engineering in the methylotrophic yeast Pichia pastoris. J Biotechnol. 2016;235:139–49.
Article
CAS
PubMed
Google Scholar
Feng Z, Zhang B, Ding W, Liu X, Yang DL, Wei P, Cao F, Zhu S, Zhang F, Mao Y, et al. Efficient genome editing in plants using a CRISPR/Cas system. Cell Res. 2013;23(10):1229–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gao X, Li F, Li M, Kianinejad AS, Dever JK, Wheeler TA, Li Z, He P, Shan L. Cotton GhBAK1 mediates Verticillium wilt resistance and cell death. J Integr Plant Biol. 2013;55(7):586–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li JF, Norville JE, Aach J, McCormack M, Zhang D, Bush J, Church GM, Sheen J. Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol. 2013;31(8):688–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nekrasov V, Staskawicz B, Weigel D, Jones JD, Kamoun S. Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nat Biotechnol. 2013;31(8):691–3.
Article
CAS
PubMed
Google Scholar
Xie K, Yang Y. RNA-guided genome editing in plants using a CRISPR-Cas system. Mol Plant. 2013;6(6):1975–83.
Article
CAS
PubMed
Google Scholar
Chen C, Fenk LA, de Bono M. Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Res. 2013;41(20):e193.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bassett AR, Liu JL. CRISPR/Cas9 and genome editing in Drosophila. J Genet Genomics. 2014;41(1):7–19.
Article
CAS
PubMed
Google Scholar
Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, Joung JK. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol. 2013;31(3):227–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guo X, Zhang T, Hu Z, Zhang Y, Shi Z, Wang Q, Cui Y, Wang F, Zhao H, Chen Y. Efficient RNA/Cas9-mediated genome editing in Xenopus tropicalis. Development. 2014;141(3):707–14.
Article
CAS
PubMed
Google Scholar
Bai Y, He L, Li P, Xu K, Shao S, Ren C, Liu Z, Wei Z, Zhang Z. Efficient genome editing in chicken DF-1 cells using the CRISPR/Cas9 system. G3 (Bethesda). 2016;6(4):917–23.
Article
CAS
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
Crispo M, Mulet AP, Tesson L, Barrera N, Cuadro F, dos Santos-Neto PC, Nguyen TH, Creneguy A, Brusselle L, Anegon I, Menchaca A. Efficient generation of myostatin knock-out sheep using CRISPR/Cas9 technology and microinjection into zygotes. PLoS ONE. 2015;10(8):e0136690.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang S, Ren S, Bai R, Xiao P, Zhou Q, Zhou Y, Zhou Z, Niu Y, Ji W, Chen Y. No off-target mutations in functional genome regions of a CRISPR/Cas9-generated monkey model of muscular dystrophy. J Biol Chem. 2018;293(30):11654–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hou Z, Zhang Y, Propson NE, Howden SE, Chu LF, Sontheimer EJ, Thomson JA. Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc Natl Acad Sci U S A. 2013;110(39):15644–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hu W, Kaminski R, Yang F, Zhang Y, Cosentino L, Li F, Luo B, Alvarez-Carbonell D, Garcia-Mesa Y, Karn J, et al. RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection. Proc Natl Acad Sci. 2014;111(31):11461–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Khalili K, Kaminski R, Gordon J, Cosentino L, Hu W. Genome editing strategies: potential tools for eradicating HIV-1/AIDS. J Neurovirol. 2015;21(3):310–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kaminski R, Chen Y, Fischer T, Tedaldi E, Napoli A, Zhang Y, Karn J, Hu W, Khalili K. Elimination of HIV-1 genomes from human T-lymphoid cells by CRISPR/Cas9 gene editing. Sci Rep. 2016;6:22555.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kaminski R, Bella R, Yin C, Otte J, Ferrante P, Gendelman HE, Li H, Booze R, Gordon J, Hu W, et al. Excision of HIV-1 DNA by gene editing: a proof-of-concept in vivo study. Gene Ther. 2016;23(8–9):690–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nelson CE, Hakim CH, Ousterout DG, Thakore PI, Moreb EA, Castellanos Rivera RM, Madhavan S, Pan X, Ran FA, Yan WX, et al. In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy. Science. 2016;351(6271):403–7.
Article
CAS
PubMed
Google Scholar
Carroll KJ, Makarewich CA, McAnally J, Anderson DM, Zentilin L, Liu N, Giacca M, Bassel-Duby R, Olson EN. A mouse model for adult cardiac-specific gene deletion with CRISPR/Cas9. Proc Natl Acad Sci U S A. 2016;113(2):338–43.
Article
CAS
PubMed
Google Scholar
Sander JD, Joung JK. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol. 2014;32(4):347–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lei Y, Zhang X, Su J, Jeong M, Gundry MC, Huang YH, Zhou Y, Li W, Goodell MA. Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein. Nat Commun. 2017;8:16026.
Article
CAS
PubMed
PubMed Central
Google Scholar
Choudhury SR, Cui Y, Lubecka K, Stefanska B, Irudayaraj J. CRISPR-dCas9 mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter. Oncotarget. 2016;7:46545–56.
PubMed
PubMed Central
Google Scholar
Gu W, Crawford ED, O’Donovan BD, Wilson MR, Chow ED, Retallack H, DeRisi JL. Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biol. 2016;17:41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shin G, Grimes SM, Lee H, Lau BT, Xia LC, Ji HP. CRISPR-Cas9-targeted fragmentation and selective sequencing enable massively parallel microsatellite analysis. Nat Commun. 2017;8:14291.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Q, Zhang BB, Xu XH, Long FF, Wang JK. CRISPR-typing PCR (ctPCR), a new Cas9-based DNA detection method. bioRxiv. 2017. https://doi.org/10.1101/236588.
Article
Google Scholar
Jia CQ, Huai C, Ding J, Hu L, Su B, Chen HY, Lu DR. New applications of CRISPR/Cas9 system on mutant DNA detection. Gene. 2018;641:55–62.
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, Huang B. 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
Ma HH, Tu LC, Naseri A, Huisman M, Zhang SJ, Grunwald D, Pederson T. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol. 2016;34:528.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sampson TR, Saroj SD, Llewellyn AC, Tzeng YL, Weiss DS. A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature. 2013;497(7448):254–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Price AA, Sampson TR, Ratner HK, Grakoui A, Weiss DS. Cas9-mediated targeting of viral RNA in eukaryotic cells. Proc Natl Acad Sci U S A. 2015;112(19):6164–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sampson TR, Weiss DS. Exploiting CRISPR/Cas systems for biotechnology. BioEssays. 2014;36(1):34–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Green J, Hu J. Editing plants for virus resistance using CRISPR-Cas. Acta Virol. 2017;61(2):138–42.
Article
CAS
PubMed
Google Scholar
Chen F, Ding X, Feng Y, Seebeck T, Jiang Y, Davis GD. Targeted activation of diverse CRISPR-Cas systems for mammalian genome editing via proximal CRISPR targeting. Nat Commun. 2017;8:14958.
Article
CAS
PubMed
PubMed Central
Google Scholar
O’Connell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature. 2014;516(7530):263–6.
Article
PubMed
PubMed Central
CAS
Google Scholar
Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013;152(5):1173–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nelles DA, Fang MY, O’Connell MR, Xu JL, Markmiller SJ, Doudna JA, Yeo GW. Programmable RNA tracking in live cells with CRISPR/Cas9. Cell. 2016;165(2):488–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rau K, Rentmeister A. CRISPR/Cas9: a new tool for RNA imaging in live cells. ChemBioChem. 2016;17(18):1682–4.
Article
CAS
PubMed
Google Scholar
Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM. Cas9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol. 2013;31(9):833–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, Trevino AE, Scott DA, Inoue A, Matoba S, Zhang Y, et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell. 2013;154(6):1380–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fu Y, Reyon D, Joung JK. Targeted genome editing in human cells using CRISPR/Cas nucleases and truncated guide RNAs. Methods Enzymol. 2014;546:21–45.
Article
CAS
PubMed
Google Scholar
Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, Goodwin MJ, Aryee MJ, Joung JK. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat Biotechnol. 2014;32(6):569–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F. Rationally engineered Cas9 nucleases with improved specificity. Science. 2016;351(6268):84–8.
Article
CAS
PubMed
Google Scholar
Hu JH, Miller SM, Geurts MH, Tang WX, Chen LW, Sun N, Zeina CM, Gao X, Rees HA, Lin Z, et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature. 2018;556(7699):57–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen Y, Liu X, Zhang Y, Wang H, Ying H, Liu M, Li D, Lui KO, Ding Q. A self-restricted CRISPR system to reduce off-target effects. Mol Ther. 2016;24(9):1508–10.
Article
CAS
PubMed
PubMed Central
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(3):759–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, et al. Crystal structure of Cpf1 in complex with guide RNA and target DNA. Cell. 2016;165(4):949–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fonfara I, Richter H, Bratovic M, Le Rhun A, Charpentier E. The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature. 2016;532(7600):517–21.
Article
CAS
PubMed
Google Scholar
Swarts DC, van der Oost J, Jinek M. Structural basis for guide RNA processing and seed-dependent DNA targeting by CRISPR-Cas12a. Mol Cell. 2017;66(2):221–233. e4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim D, Kim J, Hur JK, Been KW, Yoon SH, Kim JS. Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells. Nat Biotechnol. 2016;34(8):863–8.
Article
CAS
PubMed
Google Scholar
Endo A, Masafumi M, Kaya H, Toki S. Efficient targeted mutagenesis of rice and tobacco genomes using Cpf1 from Francisella novicida. Sci Rep. 2016;6:38169.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hu X, Wang C, Liu Q, Fu Y, Wang K. Targeted mutagenesis in rice using CRISPR-Cpf1 system. J Genet Genomics. 2017;44(1):71–3.
Article
PubMed
Google Scholar
Wang M, Mao Y, Lu Y, Tao X, Zhu JK. Multiplex gene editing in rice using the CRISPR-Cpf1 system. Mol Plant. 2017;10(7):1011–3.
Article
CAS
PubMed
Google Scholar
Xu R, Qin R, Li H, Li D, Li L, Wei P, Yang J. Generation of targeted mutant rice using a CRISPR-Cpf1 system. Plant Biotechnol J. 2017;15(6):713–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yin X, Biswal AK, Dionora J, Perdigon KM, Balahadia CP, Mazumdar S, Chater C, Lin HC, Coe RA, Kretzschmar T, et al. CRISPR-Cas9 and CRISPR-Cpf1 mediated targeting of a stomatal developmental gene EPFL9 in rice. Plant Cell Rep. 2017;36(5):745–57.
Article
CAS
PubMed
Google Scholar
Ungerer J, Pakrasi HB. Cpf1 is a versatile tool for CRISPR genome editing across diverse species of Cyanobacteria. Sci Rep. 2016;6:39681.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hur JK, Kim K, Been KW, Baek G, Ye S, Hur JW, Ryu SM, Lee YS, Kim JS. Targeted mutagenesis in mice by electroporation of Cpf1 ribonucleoproteins. Nat Biotechnol. 2016;34(8):807–8.
Article
CAS
PubMed
Google Scholar
Kim Y, Cheong SA, Lee JG, Lee SW, Lee MS, Baek IJ, Sung YH. Generation of knockout mice by Cpf1-mediated gene targeting. Nat Biotechnol. 2016;34(8):808–10.
Article
CAS
PubMed
Google Scholar
Watkinschow DE, Varshney GK, Garrett LJ, Chen Z, Jimenez EA, Rivas C, Bishop KS, Sood R, Harper UL, Pavan WJ. Highly efficient Cpf1-mediated gene targeting in mice following high concentration pronuclear injection. G3 Genes. 2017;7(2):719–22.
CAS
Google Scholar
Yu Z, Long C, Hui L, Mcanally JR, Baskin KK, Shelton JM, Basselduby R, Olson EN. CRISPR-Cpf1 correction of muscular dystrophy mutations in human cardiomyocytes and mice. Sci Adv. 2017;3(4):e1602814.
Article
CAS
Google Scholar
Verwaal R, Buiting-Wiessenhaan N, Dalhuijsen S, Roubos JA. CRISPR/Cpf1 enables fast and simple genome editing of Saccharomyces cerevisiae. Yeast. 2017;35:201–11.
Article
PubMed
CAS
Google Scholar
Jiang Y, Qian F, Yang J, Liu Y, Dong F, Xu C, Sun B, Chen B, Xu X, Li Y, et al. CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum. Nat Commun. 2017;8:15179.
Article
PubMed
PubMed Central
Google Scholar
Ma S, Liu Y, Liu Y, Chang J, Zhang T, Wang X, Shi R, Lu W, Xia X, Zhao P, et al. An integrated CRISPR Bombyx mori genome editing system with improved efficiency and expanded target sites. Insect Biochem Mol Biol. 2017;83:13–20.
Article
CAS
PubMed
Google Scholar
Gardner MJ, Shallom SJ, Carlton JM, Salzberg SL, Nene V, Shoaibi A, Ciecko A, Lynn J, Rizzo M, Weaver B. Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature. 2002;419(6906):531–4.
Article
CAS
PubMed
Google Scholar
Hanson RD, Ley TJ. A-T-rich scaffold attachment regions flank the hematopoietic serine protease genes clustered on chromosome 14q11.2. Blood. 1992;79(3):610–8.
CAS
PubMed
Google Scholar
Zetsche B, Heidenreich M, Mohanraju P, Fedorova I, Kneppers J, DeGennaro EM, Winblad N, Choudhury SR, Abudayyeh OO, Gootenberg JS, et al. Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. Nat Biotechnol. 2017;35(1):31–4.
Article
CAS
PubMed
Google Scholar
Zhong G, Wang H, Li Y, Tran MH, Farzan M. Cpf1 proteins excise CRISPR RNAs from mRNA transcripts in mammalian cells. Nat Chem Biol. 2017;13(8):839–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Begemann MB, Gray BN, January E, Gordon GC, He Y, Liu H, Wu X, Brutnell TP, Mockler TC, Oufattole M. Precise insertion and guided editing of higher plant genomes using Cpf1 CRISPR nucleases. Sci Rep. 2017;7(1):11606.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kim HK, Song M, Lee J, Menon AV, Jung S, Kang YM, Choi JW, Woo E, Koh HC, Nam JW, et al. In vivo high-throughput profiling of CRISPR-Cpf1 activity. Nat Methods. 2017;14(2):153–9.
Article
CAS
PubMed
Google Scholar
Kleinstiver BP, Tsai SQ, Prew MS, Nguyen NT, Welch MM, Lopez JM, McCaw ZR, Aryee MJ, Joung JK. Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells. Nat Biotechnol. 2016;34(8):869–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Port F, Bullock SL. Augmenting CRISPR applications in Drosophila with tRNA-flanked sgRNAs. Nat Methods. 2016;13(10):852–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova KS, Wolf YI, et al. Diversity and evolution of Class 2 CRISPR-Cas systems. Nat Rev Microbiol. 2017;15(3):169–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Biol Direct. 2013;8:15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grynberg M, Erlandsen H, Godzik A. HEPN: a common domain in bacterial drug resistance and human neurodegenerative proteins. Trends Biochem Sci. 2003;28(5):224–6.
Article
CAS
PubMed
Google Scholar
East-Seletsky A, O’Connell MR, Knight SC, Burstein D, Cate Jamie HD, Tjian R, Doudna JA. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature. 2016;538:270–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu L, Li XY, Ma J, Li ZQ, You LL, Wang JY, Wang M, Zhang XZ, Wang YL. The molecular architecture for RNA-guided RNA cleavage by Cas13a. Cell. 2017;170(4):714–726.e10.
Article
CAS
PubMed
Google Scholar
Liu L, Li X, Wang J, Wang M, Chen P, Yin M, Li J, Sheng G, Wang YL. Two distant catalytic sites are responsible for C2c2 RNase activities. Cell. 2017;168(1–2):121–134.e12.
Article
CAS
PubMed
Google Scholar
Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS, Semenova E, Minakhin L, Joung J, Konermann S, Severinov K, et al. Discovery and functional characterization of diverse Class 2 CRISPR-Cas systems. Mol Cell. 2015;60(3):385–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Majumdar S, Zhao P, Pfister NT, Compton M, Olson S, Glover CV 3rd, Wells L, Graveley BR, Terns RM, Terns MP. Three CRISPR-Cas immune effector complexes coexist in Pyrococcus furiosus. RNA. 2015;21(6):1147–58.
Article
CAS
PubMed
PubMed Central
Google Scholar
Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, Shmakov S, Makarova KS, Semenova E, Minakhin L, et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016;353(6299):aaf5573.
Article
PubMed
PubMed Central
CAS
Google Scholar
East-Seletsky A, O’Connell MR, Burstein D, Knott GJ, Doudna JA. RNA targeting by functionally orthogonal Type VI-A CRISPR-Cas enzymes. Mol Cell. 2017;66(3):373–383.e3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 2017;356(6336):438–42.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gootenberg JS, Abudayyeh OO, Kellner MJ, Joung J, Collins JJ, Zhang F. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science. 2018;360:439–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen JS, Ma E, Harrington LB, Da Costa M, Tian X, Palefsky JM, Doudna JA. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science. 2018. https://doi.org/10.1126/science.aar6245.
Article
PubMed
PubMed Central
Google Scholar
Murovec J, Pirc Z, Yang B. New variants of CRISPR RNA-guided genome editing enzymes. Plant Biotechnol J. 2017;15(8):917–26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Aman R, Ali Z, Butt H, Mahas A, Aljedaani F, Khan MZ, Ding S, Mahfouz M. RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol. 2018;19(1):1.
Article
PubMed
PubMed Central
Google Scholar
Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J, Belanto JJ, Verdine V, Cox DBT, Kellner MJ, Regev A, et al. RNA targeting with CRISPR-Cas13. Nature. 2017;550(7675):280–4.
Article
PubMed
PubMed Central
CAS
Google Scholar
Cox DB, Gootenberg JS, Abudayyeh OO, Franklin B, Kellner MJ, Joung J, Zhang F. RNA editing with CRISPR-Cas13. Science. 2017;358(6366):1019–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Smargon AA, Cox DB, Pyzocha NK, Zheng K, Slaymaker IM, Gootenberg JS, Abudayyeh OA, Essletzbichler P, Shmakov S, Makarova KS, et al. Cas13b is a Type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx28. Mol Cell. 2017;65(4):618–630.e7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barrangou R, Gersbach CA. Expanding the CRISPR toolbox: targeting RNA with Cas13b. Mol Cell. 2017;65(4):582–4.
Article
CAS
PubMed
Google Scholar
Ali Z, Mahas A, Mahfouz M. CRISPR/Cas13 as a tool for RNA interference. Trends Plant Sci. 2018;23(5):374–8.
Article
CAS
PubMed
Google Scholar
Makarova KS, Zhang F, Koonin EV. SnapShot: class 2 CRISPR-Cas systems. Cell. 2017;168(1–2):328.e1.
Google Scholar
Munoz DM, Cassiani PJ, Li L, Billy E, Korn JM, Jones MD, Golji J, Ruddy DA, Yu K, McAllister G, et al. CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions. Cancer Discov. 2016;6:900–13.
Article
CAS
PubMed
Google Scholar
Aguirre AJ, Meyers RM, Weir BA, Vazquez F, Zhang CZ, Ben-David U, Cook A, Ha G, Harrington WF, Doshi MB, et al. Genomic copy number dictates a gene-independent cell response to CRISPR/Cas9 targeting. Cancer Discov. 2016;6:914–29.
Article
CAS
PubMed
PubMed Central
Google Scholar
Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533:420–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature. 2017;551(7681):464–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Charlesworth CT, Deshpande PS, Dever DP, Dejene B, Gomez-Ospina N, Mantri S, Pavel-Dinu M, Camarena J, Weinberg KI, Porteus MH. Identification of pre-existing adaptive immunity to Cas9 proteins in humans. BioRxiv. 2018. https://doi.org/10.1101/243345.
Article
Google Scholar
Kim H, Kim ST, Ryu J, Kang BC, Kim JS, Kim SG. CRISPR/Cpf1-mediated DNA-free plant genome editing. Nat Commun. 2017;8:14406.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yan WX, Chong S, Zhang H, Makarova KS, Koonin EV, Cheng DR, Scott DA. Cas13d is a compact RNA-targeting Type VI CRISPR effector positively modulated by a WYL-domain-containing accessory protein. Mol cell. 2018;70(2):327–339.e5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Konermann S, Lotfy P, Brideau NJ, Oki J, Shokhirev MN, Hsu PD. Transcriptome engineering with RNA-targeting Type VI-D CRISPR effectors. Cell. 2018;173(3):665–676.e14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Puschnik AS, Majzoub K, Ooi YS, Carette JE. A CRISPR toolbox to study virus-host interactions. Nat Rev Microbiol. 2017;15(6):351–64.
Article
CAS
PubMed
PubMed Central
Google Scholar