Skip to main content Accessibility help

Development of CRISPR-Cas systems for genome editing and beyond

  • F. Zhang (a1) (a2) (a3)


The development of clustered regularly interspaced short-palindromic repeat (CRISPR)-Cas systems for genome editing has transformed the way life science research is conducted and holds enormous potential for the treatment of disease as well as for many aspects of biotechnology. Here, I provide a personal perspective on the development of CRISPR-Cas9 for genome editing within the broader context of the field and discuss our work to discover novel Cas effectors and develop them into additional molecular tools. The initial demonstration of Cas9-mediated genome editing launched the development of many other technologies, enabled new lines of biological inquiry, and motivated a deeper examination of natural CRISPR-Cas systems, including the discovery of new types of CRISPR-Cas systems. These new discoveries in turn spurred further technological developments. I review these exciting discoveries and technologies as well as provide an overview of the broad array of applications of these technologies in basic research and in the improvement of human health. It is clear that we are only just beginning to unravel the potential within microbial diversity, and it is quite likely that we will continue to discover other exciting phenomena, some of which it may be possible to repurpose as molecular technologies. The transformation of mysterious natural phenomena to powerful tools, however, takes a collective effort to discover, characterize, and engineer them, and it has been a privilege to join the numerous researchers who have contributed to this transformation of CRISPR-Cas systems.

  • View HTML
    • Send article to Kindle

      To send this article to your Kindle, first ensure is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle.

      Note you can select to send to either the or variations. ‘’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

      Find out more about the Kindle Personal Document Service.

      Development of CRISPR-Cas systems for genome editing and beyond
      Available formats

      Send article to Dropbox

      To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Dropbox.

      Development of CRISPR-Cas systems for genome editing and beyond
      Available formats

      Send article to Google Drive

      To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Google Drive.

      Development of CRISPR-Cas systems for genome editing and beyond
      Available formats


This is an Open Access article, distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives licence (, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is unaltered and is properly cited. The written permission of Cambridge University Press must be obtained for commercial re-use or in order to create a derivative work.

Corresponding author

Author for correspondence: F. Zhang, E-mail:


Hide All
Abudayyeh, OO, Gootenberg, JS, Konermann, S, Joung, J, Slaymaker, IM, Cox, DBT, Shmakov, S, Makarova, KS, Semenova, E, Minakhin, L, Severinov, K, Regev, A, Lander, ES, Koonin, EV and Zhang, F (2016) C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353, aaf5573.
Abudayyeh, OO, Gootenberg, JS, Essletzbichler, P, Han, S, Joung, J, Belanto, JJ, Verdine, V, Cox, DBT, Kellner, MJ, Regev, A, Lander, ES, Voytas, DF, Ting, AY and Zhang, F (2017) RNA targeting with CRISPR–Cas13. Nature 550, 280284.
Adamson, B, Norman, TM, Jost, M, Cho, MY, Nuñez, JK, Chen, Y, Villalta, JE, Gilbert, LA, Horlbeck, MA, Hein, MY, Pak, RA, Gray, AN, Gross, CA, Dixit, A, Parnas, O, Regev, A and Weissman, JS (2016) A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response. Cell 167, 18671882.
Adikusuma, F, Piltz, S, Corbett, MA, Turvey, M, Mccoll, SR, Helbig, KJ, Beard, MR, Hughes, J, Pomerantz, RT and Thomas, PQ (2018) Large deletions induced by Cas9 cleavage. Nature 560, E8E9.
Aguirre, AJ, Meyers, RM, Weir, BA, Vazquez, F, Zhang, CZ, Ben-David, U, Cook, A, Ha, G, Harrington, WF, Doshi, MB, Kost-Alimova, M, Gill, S, Xu, H, Ali, LD, Jiang, G, Pantel, S, Lee, Y, Goodale, A, Cherniack, AD, Oh, C, Kryukov, G, Cowley, GS, Garraway, LA, Stegmaier, K, Roberts, CW, Golub, TR, Meyerson, M, Root, DE, Tsherniak, A and Hahn, WC (2016) Genomic copy number dictates a gene-independent cell response to CRISPR/Cas9 targeting. Cancer Discovery 6, 914929.
Akbari, OS, Bellen, HJ, Bier, E, Bullock, SL, Burt, A, Church, GM, Cook, KR, Duchek, P, Edwards, OR, Esvelt, KM, Gantz, VM, Golic, KG, Gratz, SJ, Harrison, MM, Hayes, KR, James, AA, Kaufman, TC, Knoblich, J, Malik, HS, Matthews, KA, O'connor-Giles, KM, Parks, AL, Perrimon, N, Port, F, Russell, S, Ueda, R and Wildonger, J (2015) BIOSAFETY. Safeguarding gene drive experiments in the laboratory. Science 349, 927929.
Akcakaya, P, Bobbin, ML, Guo, JA, Malagon-Lopez, J, Clement, K, Garcia, SP, Fellows, MD, Porritt, MJ, Firth, MA, Carreras, A, Baccega, T, Seeliger, F, Bjursell, M, Tsai, SQ, Nguyen, NT, Nitsch, R, Mayr, LM, Pinello, L, Bohlooly, YM, Aryee, MJ, Maresca, M and Joung, JK (2018) In vivo CRISPR editing with no detectable genome-wide off-target mutations. Nature 561, 416419.
ALLERGAN (2019) Single Ascending Dose Study in Participants With LCA10. Identifier: NCT03872479 (
Aman, R, Ali, Z, Butt, H, Mahas, A, Aljedaani, F, Khan, MZ, Ding, S and Mahfouz, M (2018) RNA virus interference via CRISPR/Cas13a system in plants. Genome Biology 19, 1.
Anders, C, Niewoehner, O, Duerst, A and Jinek, M (2014) Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513, 569573.
Bae, S, Park, J and Kim, JS (2014) Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 14731475.
Baltimore, D, Berg, P, Botchan, M, Carroll, D, Charo, RA, Church, G, Corn, JE, Daley, GQ, Doudna, JA, Fenner, M, Greely, HT, Jinek, M, Martin, GS, Penhoet, E, Puck, J, Sternberg, SH, Weissman, JS and Yamamoto, KR (2015) Biotechnology. A prudent path forward for genomic engineering and germline gene modification. Science 348, 3638.
Barrangou, R and Horvath, P (2017) A decade of discovery: CRISPR functions and applications. Nature Microbiology 2, 17092.
Barrangou, R, Fremaux, C, Deveau, H, Richards, M, Boyaval, P, Moineau, S, Romero, DA and Horvath, P (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 17091712.
Bastakoty, D and Young, PP (2016) Wnt/beta-catenin pathway in tissue injury: roles in pathology and therapeutic opportunities for regeneration. FASEB Journal 30, 32713284.
Benler, S, Cobian-Guemes, AG, Mcnair, K, Hung, SH, Levi, K, Edwards, R and Rohwer, F (2018) A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage. Microbiome 6, 191.
Bewg, WP, Ci, D and Tsai, CJ (2018) Genome editing in trees: from multiple repair pathways to long-term stability. Frontiers in Plant Science 9, 1732.
Bikard, D, Jiang, W, Samai, P, Hochschild, A, Zhang, F and Marraffini, LA (2013) Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Research 41, 74297437.
Bikard, D, Euler, CW, Jiang, W, Nussenzweig, PM, Goldberg, GW, Duportet, X, Fischetti, VA and Marraffini, LA (2014) Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. Nature Biotechnology 32, 11461150.
Birling, MC, Herault, Y and Pavlovic, G (2017) Modeling human disease in rodents by CRISPR/Cas9 genome editing. Mamm Genome 28, 291301.
Blanc-Mathieu, R, Krasovec, M, Hebrard, M, Yau, S, Desgranges, E, Martin, J, Schackwitz, W, Kuo, A, Salin, G, Donnadieu, C, Desdevises, Y, Sanchez-Ferandin, S, Moreau, H, Rivals, E, Grigoriev, IV, Grimsley, N, Eyre-Walker, A and Piganeau, G (2017) Population genomics of picophytoplankton unveils novel chromosome hypervariability. Science Advances 3, e1700239.
Boch, J, Scholze, H, Schornack, S, Landgraf, A, Hahn, S, Kay, S, Lahaye, T, Nickstadt, A and Bonas, U (2009) Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326, 15091512.
Bolotin, A, Quinquis, B, Sorokin, A and Ehrlich, SD (2005) Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology (Reading England) 151(Pt 8), 25512561.
Boyden, ES, Zhang, F, Bamberg, E, Nagel, G and Deisseroth, K (2005) Millisecond-timescale, genetically targeted optical control of neural activity. Nature Neuroscience 8, 12631268.
Brooks, C, Nekrasov, V, Lippman, ZB and Van Eck, J (2014) Efficient gene editing in tomato in the first generation using the clustered regularly interspaced short palindromic repeats/CRISPR-associated9 system. Plant Physiology 166, 12921297.
Brouns, SJ, Jore, MM, Lundgren, M, Westra, ER, Slijkhuis, RJ, Snijders, AP, Dickman, MJ, Makarova, KS, Koonin, EV and Van Der Oost, J (2008) Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960964.
Burstein, D, Harrington, LB, Strutt, SC, Probst, AJ, Anantharaman, K, Thomas, BC, Doudna, JA and Banfield, JF (2017) New CRISPR-Cas systems from uncultivated microbes. Nature 542, 237241.
Cameron, P, Fuller, CK, Donohoue, PD, Jones, BN, Thompson, MS, Carter, MM, Gradia, S, Vidal, B, Garner, E, Slorach, EM, Lau, E, Banh, LM, Lied, AM, Edwards, LS, Settle, AH, Capurso, D, Llaca, V, Deschamps, S, Cigan, M, Young, JK and May, AP (2017) Mapping the genomic landscape of CRISPR-Cas9 cleavage. Nature Methods 14, 600606.
Canny, MD, Moatti, N, Wan, LCK, Fradet-Turcotte, A, Krasner, D, Mateos-Gomez, PA, Zimmermann, M, Orthwein, A, Juang, YC, Zhang, W, Noordermeer, SM, Seclen, E, Wilson, MD, Vorobyov, A, Munro, M, Ernst, A, Ng, TF, Cho, T, Cannon, PM, Sidhu, SS, Sicheri, F and Durocher, D (2018) Inhibition of 53BP1 favors homology-dependent DNA repair and increases CRISPR-Cas9 genome-editing efficiency. Nature Biotechnology 36, 95102.
Canver, MC, Smith, EC, Sher, F, Pinello, L, Sanjana, NE, Shalem, O, Chen, DD, Schupp, PG, Vinjamur, DS, Garcia, SP, Luc, S, Kurita, R, Nakamura, Y, Fujiwara, Y, Maeda, T, Yuan, G-C, Zhang, F, Orkin, SH and Bauer, DE (2015) BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature 527, 192197.
Carroll, D (2012) A CRISPR approach to gene targeting. Molecular Therapy 20, 16581660.
Casini, A, Olivieri, M, Petris, G, Montagna, C, Reginato, G, Maule, G, Lorenzin, F, Prandi, D, Romanel, A, Demichelis, F, Inga, A and Cereseto, A (2018) A highly specific SpCas9 variant is identified by in vivo screening in yeast. Nature Biotechnology 36, 265271.
Charlesworth, CT, Deshpande, PS, Dever, DP, Camarena, J, Lemgart, VT, Cromer, MK, Vakulskas, CA, Collingwood, MA, Zhang, L, Bode, NM, Behlke, MA, Dejene, B, Cieniewicz, B, Romano, R, Lesch, BJ, Gomez-Ospina, N, Mantri, S, Pavel-Dinu, M, Weinberg, KI and Porteus, MH (2019) Identification of preexisting adaptive immunity to Cas9 proteins in humans. Nature Medicine 25, 249254.
Chatterjee, P, Jakimo, N and Jacobson, JM (2018) Minimal PAM specificity of a highly similar SpCas9 ortholog. Science Advances 4, eaau0766.
Chen, B, Gilbert, LA, Cimini, BA, Schnitzbauer, J, Zhang, W, Li, GW, Park, J, Blackburn, EH, Weissman, JS, Qi, LS and Huang, B (2013) Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155, 14791491.
Chen, S, Sanjana, NE, Zheng, K, Shalem, O, Lee, K, Shi, X, Scott, DA, Song, J, Pan, JQ, Weissleder, R, Lee, H, Zhang, F and Sharp, PA (2015a) Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell 160, 12461260.
Chen, Y, Zheng, Y, Kang, Y, Yang, W, Niu, Y, Guo, X, Tu, Z, Si, C, Wang, H, Xing, R, Pu, X, Yang, SH, Li, S, Ji, W and Li, XJ (2015b) Functional disruption of the dystrophin gene in rhesus monkey using CRISPR/Cas9. Human Molecular Genetics 24, 37643774.
Chen, B, Hu, J, Almeida, R, Liu, H, Balakrishnan, S, Covill-Cooke, C, Lim, WA and Huang, B (2016) Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci. Nucleic Acids Research 44, e75e75.
Chen, JS, Dagdas, YS, Kleinstiver, BP, Welch, MM, Sousa, AA, Harrington, LB, Sternberg, SH, Joung, JK, Yildiz, A and Doudna, JA (2017) Enhanced proofreading governs CRISPR–Cas9 targeting accuracy. Nature 550, 407410.
Chen, JS, Ma, E, Harrington, LB, Da Costa, M, Tian, X, Palefsky, JM and Doudna, JA (2018) CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 360, 436439.
Cho, SW, Kim, S, Kim, JM and Kim, JS (2013) Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nature Biotechnology 31, 230232.
Cho, SW, Kim, S, Kim, Y, Kweon, J, Kim, HS, Bae, S and Kim, JS (2014) Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Research 24, 132141.
Chylinski, K, Makarova, KS, Charpentier, E and Koonin, EV (2014) Classification and evolution of type II CRISPR-Cas systems. Nucleic Acids Research 42, 60916105.
Citorik, RJ, Mimee, M and Lu, TK (2014) Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nature Biotechnology 32, 11411145.
Concordet, JP and Haeussler, M (2018) CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. Nucleic Acids Research 46, W242W245.
Cong, L, Ran, FA, Cox, D, Lin, SL, Barretto, R, Habib, N, Hsu, PD, Wu, XB, Jiang, WY, Marraffini, LA and Zhang, F (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819823.
Courtier-Orgogozo, V, Morizot, B and Boete, C (2017) Agricultural pest control with CRISPR-based gene drive: time for public debate: should we use gene drive for pest control? EMBO Reports 18, 878880.
Cox, DB, Platt, RJ and Zhang, F (2015) Therapeutic genome editing: prospects and challenges. Nature Medicine 21, 121131.
Cox, DBT, Gootenberg, JS, Abudayyeh, OO, Franklin, B, Kellner, MJ, Joung, J and Zhang, F (2017) RNA editing with CRISPR-Cas13. Science 550, eaaq0180.
Cromwell, CR, Sung, K, Park, J, Krysler, AR, Jovel, J, Kim, SK and Hubbard, BP (2018) Incorporation of bridged nucleic acids into CRISPR RNAs improves Cas9 endonuclease specificity. Nature Communications 9, 1448.
Crosetto, N, Mitra, A, Silva, MJ, Bienko, M, Dojer, N, Wang, Q, Karaca, E, Chiarle, R, Skrzypczak, M, Ginalski, K, Pasero, P, Rowicka, M and Dikic, I (2013) Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nature Methods 10, 361366.
Dahlman, JE, Abudayyeh, OO, Joung, J, Gootenberg, JS, Zhang, F and Konermann, S (2015) Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease. Nature Biotechnology 33, 11591161.
Davis, KM, Pattanayak, V, Thompson, DB, Zuris, JA and Liu, DR (2015) Small molecule–triggered Cas9 protein with improved genome-editing specificity. Nature Chemical Biology 11, 316318.
Deltcheva, E, Chylinski, K, Sharma, CM, Gonzales, K, Chao, Y, Pirzada, ZA, Eckert, MR, Vogel, J and Charpentier, E (2011) CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471, 602607.
Deng, W, Henriet, S and Chourrout, D (2018) Prevalence of mutation-prone microhomology-mediated end joining in a chordate lacking the c-NHEJ DNA repair pathway. Current Biology 28, 33373341 e3334.
Deveau, H, Barrangou, R, Garneau, JE, Labonte, J, Fremaux, C, Boyaval, P, Romero, DA, Horvath, P and Moineau, S (2008) Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. Journal of Bacteriology 190, 13901400.
Dever, DP, Bak, RO, Reinisch, A, Camarena, J, Washington, G, Nicolas, CE, Pavel-Dinu, M, Saxena, N, Wilkens, AB, Mantri, S, Uchida, N, Hendel, A, Narla, A, Majeti, R, Weinberg, KI and Porteus, MH (2016) CRISPR/cas9 beta-globin gene targeting in human haematopoietic stem cells. Nature 539, 384389.
Dicarlo, JE, Norville, JE, Mali, P, Rios, X, Aach, J and Church, GM (2013) Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Research 41, gkt135gk4343.
Dixit, A, Parnas, O, Li, B, Chen, J, Fulco, CP, Jerby-Arnon, L, Marjanovic, ND, Dionne, D, Burks, T, Raychowdhury, R, Adamson, B, Norman, TM, Lander, ES, Weissman, JS, Friedman, N and Regev, A (2016) Perturb-Seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell 167, 18531866.
Doench, JG (2017) Am I ready for CRISPR? A user's guide to genetic screens. Nature Publishing Group 19, 6780.
Doench, JG, Hartenian, E, Graham, DB, Tothova, Z, Hegde, M, Smith, I, Sullender, M, Ebert, BL, Xavier, RJ and Root, DE (2014) Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nature Biotechnology 32, 12621267.
Doench, JG, Fusi, N, Sullender, M, Hegde, M, Vaimberg, EW, Donovan, KF, Smith, I, Tothova, Z, Wilen, C, Orchard, R, Virgin, HW, Listgarten, J and Root, DE (2016) Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nature Biotechnology 34, 184191.
Doetschman, T, Gregg, RG, Maeda, N, Hooper, ML, Melton, DW, Thompson, S and Smithies, O (1987) Targetted correction of a mutant HPRT gene in mouse embryonic stem cells. Nature 330, 576578.
Dong, D, Ren, K, Qiu, X, Zheng, J, Guo, M, Guan, X, Liu, H, Li, N, Zhang, B, Yang, D, Ma, C, Wang, S, Wu, D, Ma, Y, Fan, S, Wang, J, Gao, N and Huang, Z (2016) The crystal structure of Cpf1 in complex with CRISPR RNA. Nature 532, 522526.
Donovan, KF, Hegde, M, Sullender, M, Vaimberg, EW, Johannessen, CM, Root, DE and Doench, JG (2017) Creation of novel protein variants with CRISPR/Cas9-mediated mutagenesis: turning a screening by-product into a discovery tool. PLoS One 12, e0170445.
Doron, S, Melamed, S, Ofir, G, Leavitt, A, Lopatina, A, Keren, M, Amitai, G and Sorek, R (2018) Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359, eaar4120.
Doudna, JA and Charpentier, E (2014) Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346, 1258096.
Doulatov, S, Hodes, A, Dai, L, Mandhana, N, Liu, M, Deora, R, Simons, RW, Zimmerly, S and Miller, JF (2004) Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements. Nature 431, 476481.
Dow, LE, Fisher, J, O'rourke, KP, Muley, A, Kastenhuber, ER, Livshits, G, Tschaharganeh, DF, Socci, ND and Lowe, SW (2015) Inducible in vivo genome editing with CRISPR-Cas9. Nature Biotechnology 33, 390394.
Duan, J, Lu, G, Hong, Y, Hu, Q, Mai, X, Guo, J, Si, X, Wang, F and Zhang, Y (2018) Live imaging and tracking of genome regions in CRISPR/dCas9 knock-in mice. Genome Biology 19, 192.
East-Seletsky, A, O'connell, MR, Knight, SC, Burstein, D, Cate, JHD, Tjian, R and Doudna, JA (2016) Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature 538, 270273.
Egli, D, Zuccaro, MV, Kosicki, M, Church, GM, Bradley, A and Jasin, M (2018) Inter-homologue repair in fertilized human eggs? Nature 560, E5E7.
Esvelt, KM, Mali, P, Braff, JL, Moosburner, M, Yaung, SJ and Church, GM (2013) Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nature 10, 11161121.
Eyquem, J, Mansilla-Soto, J, Giavridis, T, Van Der Stegen, SJ, Hamieh, M, Cunanan, KM, Odak, A, Gonen, M and Sadelain, M (2017) Targeting a CAR to the TRAC locus with CRISPR/Cas9 enhances tumour rejection. Nature 543, 113117.
Fellmann, C, Gowen, BG, Lin, PC, Doudna, JA and Corn, JE (2017) Cornerstones of CRISPR-Cas in drug discovery and therapy. Nature Reviews Drug Discovery 16, 89100.
Feng, Z, Zhang, B, Ding, W, Liu, X, Yang, DL, Wei, P, Cao, F, Zhu, S, Zhang, F, Mao, Y and Zhu, JK (2013) Efficient genome editing in plants using a CRISPR/Cas system. Cell Research 23, 12291232.
Finn, JD, Smith, AR, Patel, MC, Shaw, L, Youniss, MR, Van Heteren, J, Dirstine, T, Ciullo, C, Lescarbeau, R, Seitzer, J, Shah, RR, Shah, A, Ling, D, Growe, J, Pink, M, Rohde, E, Wood, KM, Salomon, WE, Harrington, WF, Dombrowski, C, Strapps, WR, Chang, Y and Morrissey, DV (2018) A single administration of CRISPR/Cas9 lipid nanoparticles achieves robust and persistentiIn vivo genome editing. Cell Reports 22, 22272235.
Fogarty, NME, Mccarthy, A, Snijders, KE, Powell, BE, Kubikova, N, Blakeley, P, Lea, R, Elder, K, Wamaitha, SE, Kim, D, Maciulyte, V, Kleinjung, J, Kim, JS, Wells, D, Vallier, L, Bertero, A, Turner, JMA and Niakan, KK (2017) Genome editing reveals a role for OCT4 in human embryogenesis. Nature 550, 6773.
Fonfara, I, Le Rhun, A, Chylinski, K, Makarova, KS, Lécrivain, A-L, Bzdrenga, J, Koonin, EV and Charpentier, E (2014) Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Research 42, 25772590.
Fonfara, I, Richter, H, Bratovič, M, Le Rhun, A and Charpentier, E (2016) The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature 532, 517521.
Frieda, KL, Linton, JM, Hormoz, S, Choi, J, Chow, KK, Singer, ZS, Budde, MW, Elowitz, MB and Cai, L (2017) Synthetic recording and in situ readout of lineage information in single cells. Nature 541, 107111.
Friedland, AE, Tzur, YB, Esvelt, KM, Colaiácovo, MP, Church, GM and Calarco, JA (2013) Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nature Methods 10, 741743.
Frock, RL, Hu, J, Meyers, RM, Ho, YJ, Kii, E and Alt, FW (2015) Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nature Biotechnology 33, 179186.
Fulco, CP, Munschauer, M, Anyoha, R, Munson, G, Grossman, SR, Perez, EM, Kane, M, Cleary, B, Lander, ES and Engreitz, JM (2016) Systematic mapping of functional enhancer-promoter connections with CRISPR interference. Science 354, 769773.
Fu, Y, Foden, JA, Khayter, C, Maeder, ML, Reyon, D, Joung, JK and Sander, JD (2013) High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nature Biotechnology 31, 822826.
Fu, Y, Sander, JD, Reyon, D, Cascio, VM and Joung, JK (2014) Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nature Biotechnology 32, 279284.
Gantz, VM, Jasinskiene, N, Tatarenkova, O, Fazekas, A, Macias, VM, Bier, E and James, AA (2015) Highly efficient Cas9-mediated gene drive for population modification of the malaria vector mosquito Anopheles stephensi. Proceedings of the National Academy of Sciences 112, E6736E6743.
Gao, C (2018) The future of CRISPR technologies in agriculture. Nature Reviews Molecular Cell Biology 19, 275276.
Gao, L, Cox, DBT, Yan, WX, Manteiga, JC, Schneider, MW, Yamano, T, Nishimasu, H, Nureki, O, Crosetto, N and Zhang, F (2017) Engineered Cpf1 variants with altered PAM specificities. Nature Biotechnology 163, 759.
Garcia-Doval, C and Jinek, M (2017) Molecular architectures and mechanisms of class 2 CRISPR-associated nucleases. Current Opinion in Structural Biology 47, 157166.
Garneau, JE, Dupuis, ME, Villion, M, Romero, DA, Barrangou, R, Boyaval, P, Fremaux, C, Horvath, P, Magadan, AH and Moineau, S (2010) The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 6771.
Gasiunas, G, Barrangou, R, Horvath, P and Siksnys, V (2012) Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proceedings of the National Academy of Sciences of the United States of America 109, E2579E2586.
Gasperini, M, Hill, AJ, Mcfaline-Figueroa, JL, Martin, B, Kim, S, Zhang, MD, Jackson, D, Leith, A, Schreiber, J, Noble, WS, Trapnell, C, Ahituv, N and Shendure, J (2019) A genome-wide framework for mapping gene regulation via cellular genetic screens. Cell 176, 377390.
Gaudelli, NM, Komor, AC, Rees, HA, Packer, MS, Badran, AH, Bryson, DI and Liu, DR (2017) Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 551, 464471.
Ge, Y, Gomez, NC, Adam, RC, Nikolova, M, Yang, H, Verma, A, Lu, CP, Polak, L, Yuan, S, Elemento, O and Fuchs, E (2017) Stem cell lineage infidelity drives wound repair and cancer. Cell 169, 636650.
Ghorbal, M, Gorman, M, Macpherson, CR, Martins, RM, Scherf, A and Lopez-Rubio, J-J (2014) Genome editing in the human malaria parasite plasmodium falciparum using the CRISPR-Cas9 system. Nature Biotechnology 32, 819821.
Giannoukos, G, Ciulla, DM, Marco, E, Abdulkerim, HS, Barrera, LA, Bothmer, A, Dhanapal, V, Gloskowski, SW, Jayaram, H, Maeder, ML, Skor, MN, Wang, T, Myer, VE and Wilson, CJ (2018) UDitas, a genome editing detection method for indels and genome rearrangements. BMC Genomics 19, 212.
Gilbert, LA, Larson, MH, Morsut, L, Liu, Z, Brar, GA, Torres, SE, Stern-Ginossar, N, Brandman, O, Whitehead, EH, Doudna, JA, Lim, WA, Weissman, JS and Qi, LS (2013) CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154, 442451.
Gilbert, LA, Horlbeck, MA, Adamson, B, Villalta, JE, Chen, Y, Whitehead, EH, Guimaraes, C, Panning, B, Ploegh, HL, Bassik, MC, Qi, LS, Kampmann, M and Weissman, JS (2014) Genome-Scale CRISPR-mediated control of gene repression and activation. Cell 159, 647661.
Gootenberg, JS, Abudayyeh, OO, Lee, JW, Essletzbichler, P, Dy, AJ, Joung, J, Verdine, V, Donghia, N, Daringer, NM, Freije, CA, Myhrvold, C, Bhattacharyya, RP, Livny, J, Regev, A, Koonin, EV, Hung, DT, Sabeti, PC, Collins, JJ and Zhang, F (2017) Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356, 438442.
Gootenberg, JS, Abudayyeh, OO, Kellner, MJ, Joung, J, Collins, JJ and Zhang, F (2018) Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 360, 439444.
Gratz, SJ, Cummings, AM, Nguyen, JN, Hamm, DC, Donohue, LK, Harrison, MM, Wildonger, J and O'connor-Giles, KM (2013) Genome engineering of drosophila with the CRISPR RNA-guided Cas9 nuclease. Genetics 194, 10291035.
Grunewald, J, Zhou, R, Garcia, SP, Iyer, S, Lareau, CA, Aryee, MJ and Joung, JK (2019) Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors. Nature 569, 433437.
Grunwald, HA, Gantz, VM, Poplawski, G, Xu, XS, Bier, E and Cooper, KL (2019) Super-Mendelian inheritance mediated by CRISPR-Cas9 in the female mouse germline. Nature 566, 105109.
Guilinger, JP, Thompson, DB and Liu, DR (2014) Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nature Biotechnology 32, 577582.
Guo, X, Chitale, P and Sanjana, NE (2017) Target discovery for precision medicine using high-throughput genome engineering. Advances in Experimental Medicine and Biology 1016, 123145.
Gu, W, Crawford, ED, O'donovan, BD, Wilson, MR, Chow, ED, Retallack, H and Derisi, JL (2016) Depletion of abundant sequences by hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biology 17, 41.
Hajian, R, Balderston, S, Tran, T, Deboer, T, Etienne, J, Sandhu, M, Wauford, NA, Chung, J-Y, Nokes, J, Athaiya, M, Paredes, J, Peytavi, R, Goldsmith, B, Murthy, N, Conboy, IM and Aran, K (2019) Detection of unamplified target genes via CRISPR–Cas9 immobilized on a graphene field-effect transistor. Nature Biomedical Engineering.
Hale, CR, Zhao, P, Olson, S, Duff, MO, Graveley, BR, Wells, L, Terns, RM and Terns, MP (2009) RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139, 945956.
Halperin, SO, Tou, CJ, Wong, EB, Modavi, C, Schaffer, DV and Dueber, JE (2018) CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window. Nature 560, 248252.
Hammond, A, Galizi, R, Kyrou, K, Simoni, A, Siniscalchi, C, Katsanos, D, Gribble, M, Baker, D, Marois, E, Russell, S, Burt, A, Windbichler, N, Crisanti, A and Nolan, T (2015) A CRISPR-Cas9 gene drive system targeting female reproduction in the malaria mosquito vector Anopheles gambiae. Nature Biotechnology 34, 7883.
Han, BW, Herrin, BR, Cooper, MD and Wilson, IA (2008) Antigen recognition by variable lymphocyte receptors. Science 321, 18341837.
Han, K, Jeng, EE, Hess, GT, Morgens, DW, Li, A and Bassik, MC (2017) Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions. Nature Biotechnology 35, 463474.
Han, R, Li, L, Ugalde, AP, Tal, A, Manber, Z, Barbera, EP, Chiara, VD, Elkon, R and Agami, R (2018) Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence. Genome Biology 19, 118.
Harrington, LB, Burstein, D, Chen, JS, Paez-Espino, D, Ma, E, Witte, IP, Cofsky, JC, Kyrpides, NC, Banfield, JF and Doudna, JA (2018) Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science 362, 839842.
Hart, T and Moffat, J (2016) BAGEL: a computational framework for identifying essential genes from pooled library screens. BMC Bioinformatics 17, 164.
Hart, T, Chandrashekhar, M, Aregger, M, Steinhart, Z, Brown, KR, Macleod, G, Mis, M, Zimmermann, M, Fradet-Turcotte, A, Sun, S, Mero, P, Dirks, P, Sidhu, S, Roth, FP, Rissland, OS, Durocher, D, Angers, S and Moffat, J (2015) High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell 163, 15151526.
Hart, T, Tong, AHY, Chan, K, Van Leeuwen, J, Seetharaman, A, Aregger, M, Chandrashekhar, M, Hustedt, N, Seth, S, Noonan, A, Habsid, A, Sizova, O, Nedyalkova, L, Climie, R, Tworzyanski, L, Lawson, K, Sartori, MA, Alibeh, S, Tieu, D, Masud, S, Mero, P, Weiss, A, Brown, KR, Usaj, M, Billmann, M, Rahman, M, Constanzo, M, Myers, CL, Andrews, BJ, Boone, C, Durocher, D and Moffat, J (2017) Evaluation and design of genome-wide CRISPR/SpCas9 knockout screens. G3 (Bethesda) 7, 27192727.
Heigwer, F, Zhan, T, Breinig, M, Winter, J, Brugemann, D, Leible, S and Boutros, M (2016) CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries. Genome Biology 17, 55.
Heler, R, Samai, P, Modell, JW, Weiner, C, Goldberg, GW, Bikard, D and Marraffini, LA (2015) Cas9 specifies functional viral targets during CRISPR-Cas adaptation. Nature 519, 199202.
Hess, GT, Fresard, L, Han, K, Lee, CH, Li, A, Cimprich, KA, Montgomery, SB and Bassik, MC (2016) Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells. Nature Methods 13, 10361042.
Hess, GT, Tycko, J, Yao, D and Bassik, MC (2017) Methods and applications of CRISPR-mediated base editing in eukaryotic genomes. Molecular Cell 68, 2643.
Hilton, IB, D'ippolito, AM, Vockley, CM, Thakore, PI, Crawford, GE, Reddy, TE and Gersbach, CA (2015) Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nature Biotechnology 33, 510517.
Hirano, H, Gootenberg, JS, Horii, T, Abudayyeh, OO, Kimura, M, Hsu, PD, Nakane, T, Ishitani, R, Hatada, I, Zhang, F, Nishimasu, H and Nureki, O (2016) Structure and engineering of Francisella novicida Cas9. Cell 164, 950961.
Horlbeck, MA, Gilbert, LA, Villalta, JE, Adamson, B, Pak, RA, Chen, Y, Fields, AP, Park, CY, Corn, JE, Kampmann, M and Weissman, JS (2016) Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. Elife 5, e19760.
Horlbeck, MA, Xu, A, Wang, M, Bennett, NK, Park, CY, Bogdanoff, D, Adamson, B, Chow, ED, Kampmann, M, Peterson, TR, Nakamura, K, Fischbach, MA, Weissman, JS and Gilbert, LA (2018) Mapping the genetic landscape of human cells. Cell 174, 953967.
Horvath, P, Romero, DA, Coute-Monvoisin, AC, Richards, M, Deveau, H, Moineau, S, Boyaval, P, Fremaux, C and Barrangou, R (2008) Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. Journal of Bacteriology 190, 14011412.
Horvath, P, Coute-Monvoisin, AC, Romero, DA, Boyaval, P, Fremaux, C and Barrangou, R (2009) Comparative analysis of CRISPR loci in lactic acid bacteria genomes. International Journal of Food Microbiology 131, 6270.
Hotta, A and Yamanaka, S (2015) From genomics to gene therapy: induced pluripotent stem cells meet genome editing. Annual Review of Genetics 49, 4770.
Hou, Z, Zhang, Y, Propson, NE, Howden, SE, Chu, LF, Sontheimer, EJ and Thomson, JA (2013) Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proceedings of the National Academy of Sciences of the United States of America 110, 1564415649.
Hsu, PD, Scott, DA, Weinstein, JA, Ran, FA, Konermann, S, Agarwala, V, Li, Y, Fine, EJ, Wu, X, Shalem, O, Cradick, TJ, Marraffini, LA, Bao, G and Zhang, F (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nature Biotechnology 31, 827832.
Hsu, PD, Lander, ES and Zhang, F (2014) Development and applications of CRISPR-Cas9 for genome engineering. Cell 157, 12621278.
Hua, K, Tao, X and Zhu, JK (2019) Expanding the base editing scope in rice by using Cas9 variants. Plant Biotechnology Journal 17, 499504.
Hu, W, Kaminski, R, Yang, F, Zhang, Y, Cosentino, L, Li, F, Luo, B, Alvarez-Carbonell, D, Garcia-Mesa, Y, Karn, J, Mo, X and Khalili, K (2014) RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection. Proceedings of the National Academy of Sciences of the United States of America 111, 1146111466.
Hu, JH, Miller, SM, Geurts, MH, Tang, W, Chen, L, Sun, N, Zeina, CM, Gao, X, Rees, HA, Lin, Z and Liu, DR (2018) Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature 556, 5763.
Hwang, WY, Fu, Y, Reyon, D, Maeder, ML, Tsai, SQ, Sander, JD, Peterson, RT, Yeh, JR and Joung, JK (2013) Efficient genome editing in zebrafish using a CRISPR-Cas system. Nature Biotechnology 31, 227229.
Ibraheim, R, Song, CQ, Mir, A, Amrani, N, Xue, W and Sontheimer, EJ (2018) All-in-one adeno-associated virus delivery and genome editing by Neisseria meningitidis Cas9 in vivo. Genome Biology 19, 137.
Ipsaro, JJ, Shen, C, Arai, E, Xu, Y, Kinney, JB, Joshua-Tor, L, Vakoc, CR and Shi, J (2017) Rapid generation of drug-resistance alleles at endogenous loci using CRISPR-Cas9 indel mutagenesis. PLoS One 12, e0172177.
Ishino, Y, Shinagawa, H, Makino, K, Amemura, M and Nakata, A (1987) Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. Journal of Bacteriology 169, 54295433.
Ishino, Y, Krupovic, M and Forterre, P (2018) History of CRISPR-Cas from encounter with a mysterious repeated sequence to genome editing technology. Journal of Bacteriology 200, e00580.
Jackson, RN and Wiedenheft, B (2015) A conserved structural chassis for mounting Versatile CRISPR RNA-guided immune responses. Molecular Cell 58, 722728.
Jacob, F (1977) Evolution and tinkering. Science 196, 11611166.
Jain, IH, Zazzeron, L, Goli, R, Alexa, K, Schatzman-Bone, S, Dhillon, H, Goldberger, O, Peng, J, Shalem, O, Sanjana, NE, Zhang, F, Goessling, W, Zapol, WM and Mootha, VK (2016) Hypoxia as a therapy for mitochondrial disease. Science 352, 5461.
Jaitin, DA, Weiner, A, Yofe, I, Lara-Astiaso, D, Keren-Shaul, H, David, E, Salame, TM, Tanay, A, Van Oudenaarden, A and Amit, I (2016) Dissecting immune circuits by linking CRISPR-pooled screens with single-cell RNA-Seq. Cell 167, 18831896.
Jansen, R, Embden, JD, Gaastra, W and Schouls, LM (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Molecular Microbiology 43, 15651575.
Jiang, F and Doudna, JA (2017) CRISPR-Cas9 Structures and mechanisms. Annual Review of Biophysics 46, 505529.
Jiang, W, Zhou, H, Bi, H, Fromm, M, Yang, B and Weeks, DP (2013) Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Research 41, e188e188.
Jinek, M, Chylinski, K, Fonfara, I, Hauer, M, Doudna, JA and Charpentier, E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816821.
Jinek, M, East, A, Cheng, A, Lin, S, Ma, E and Doudna, J (2013) RNA-programmed genome editing in human cells. Elife 2, e00471.
Jinek, M, Jiang, F, Taylor, DW, Sternberg, SH, Kaya, E, Ma, E, Anders, C, Hauer, M, Zhou, K, Lin, S, Kaplan, M, Iavarone, AT, Charpentier, E, Nogales, E and Doudna, JA (2014) Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343, 12479971247997.
Jin, S, Zong, Y, Gao, Q, Zhu, Z, Wang, Y, Qin, P, Liang, C, Wang, D, Qiu, J-L, Zhang, F and Gao, C (2019) Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice. Science 364, 292295.
Jost, M and Weissman, JS (2018) CRISPR approaches to small molecule target identification. ACS Chemical Biology 13, 366375.
Joung, JK and Sander, JD (2013) TALENs: a widely applicable technology for targeted genome editing. Nature Reviews Molecular Cell Biology 14, 4955.
Joung, J, Engreitz, JM, Konermann, S, Abudayyeh, OO, Verdine, VK, Aguet, F, Gootenberg, JS, Sanjana, NE, Wright, JB, Fulco, CP, Tseng, Y-Y, Yoon, CH, Boehm, JS, Lander, ES and Zhang, F (2017) Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood. Nature 548, 343346.
Kalhor, R, Mali, P and Church, GM (2017) Rapidly evolving homing CRISPR barcodes. Nature Methods 14, 195200.
Kang, BC, Yun, JY, Kim, ST, Shin, Y, Ryu, J, Choi, M, Woo, JW and Kim, JS (2018) Precision genome engineering through adenine base editing in plants. Nat Plants 4, 427431.
Kan, Y, Ruis, B, Takasugi, T and Hendrickson, EA (2017) Mechanisms of precise genome editing using oligonucleotide donors. Genome Research 27, 10991111.
Karvelis, T, Gasiunas, G, Young, J, Bigelyte, G, Silanskas, A, Cigan, M and Siksnys, V (2015) Rapid characterization of CRISPR-Cas9 protospacer adjacent motif sequence elements. Genome Biology 16, 253.
Kearns, NA, Pham, H, Tabak, B, Genga, RM, Silverstein, NJ, Garber, M and Maehr, R (2015) Functional annotation of native enhancers with a Cas9–histone demethylase fusion. Nature Methods 12, 401403.
Kim, H and Kim, JS (2014) A guide to genome engineering with programmable nucleases. Nature Reviews Genetics 15, 321334.
Kim, D, Bae, S, Park, J, Kim, E, Kim, S, Yu, HR, Hwang, J, Kim, J-I and Kim, J-S (2015) Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nature Methods 12, 237243.
Kim, E, Koo, T, Park, SW, Kim, D, Kim, K, Cho, HY, Song, DW, Lee, KJ, Jung, MH, Kim, S, Kim, JH, Kim, JH and Kim, JS (2017a) In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni. Nature Communications 8, 14500.
Kim, H, Kim, S-T, Ryu, J, Kang, B-C, Kim, J-S and Kim, S-G (2017b) CRISPR/Cpf1-mediated DNA-free plant genome editing. Nature Communications 8, 14406.
Kim, D, Kim, DE, Lee, G, Cho, SI and Kim, JS (2019) Genome-wide target specificity of CRISPR RNA-guided adenine base editors. Nature Biotechnology 37, 430435.
Klann, TS, Black, JB, Chellappan, M, Safi, A, Song, L, Hilton, IB, Crawford, GE, Reddy, TE and Gersbach, CA (2017) CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome. Nature Biotechnology 35, 561568.
Kleinstiver, BP, Prew, MS, Tsai, SQ, Nguyen, NT, Topkar, VV, Zheng, Z and Joung, JK (2015a) Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition. Nature Biotechnology 33, 12931298.
Kleinstiver, BP, Prew, MS, Tsai, SQ, Topkar, VV, Nguyen, NT, Zheng, Z, Gonzales, APW, Li, Z, Peterson, RT, Yeh, J-RJ, Aryee, MJ and Joung, JK (2015b) Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523, 481485.
Kleinstiver, BP, Pattanayak, V, Prew, MS, Tsai, SQ, Nguyen, NT, Zheng, Z and Joung, JK (2016a) High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529, 490495.
Kleinstiver, BP, Tsai, SQ, Prew, MS, Nguyen, NT, Welch, MM, Lopez, JM, Mccaw, ZR, Aryee, MJ and Joung, JK (2016b) Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells. Nature Biotechnology 34, 869874.
Kleinstiver, BP, Sousa, AA, Walton, RT, Tak, YE, Hsu, JY, Clement, K, Welch, MM, Horng, JE, Malagon-Lopez, J, Scarfo, I, Maus, MV, Pinello, L, Aryee, MJ and Joung, JK (2019) Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nature Biotechnology 37, 276282.
Knight, SC, Xie, L, Deng, W, Guglielmi, B, Witkowsky, LB, Bosanac, L, Zhang, ET, El Beheiry, M, Masson, JB, Dahan, M, Liu, Z, Doudna, JA and Tjian, R (2015) Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science 350, 823826.
Knott, GJ, East-Seletsky, A, Cofsky, JC, Holton, JM, Charles, E, O'connell, MR and Doudna, JA (2017) Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme. Nature Structural &Molecular Biology 24, 825833.
Kocak, DD, Josephs, EA, Bhandarkar, V, Adkar, SS, Kwon, JB and Gersbach, CA (2019) Increasing the specificity of CRISPR systems with engineered RNA secondary structures. Nature Biotechnology.
Koike-Yusa, H, Li, Y, Tan, EP, Velasco-Herrera Mdel, C and Yusa, K (2014) Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nature Biotechnology 32, 267273.
Komor, AC, Kim, YB, Packer, MS, Zuris, JA and Liu, DR (2016) Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420424.
Konermann, S, Brigham, MD, Trevino, AE, Hsu, PD, Heidenreich, M, Cong, L, Platt, RJ, Scott, DA, Church, GM and Zhang, F (2013) Optical control of mammalian endogenous transcription and epigenetic states. Nature 500, 472476.
Konermann, S, Brigham, MD, Trevino, AE, Joung, J, Abudayyeh, OO, Barcena, C, Hsu, PD, Habib, N, Gootenberg, JS, Nishimasu, H, Nureki, O and Zhang, F (2014) Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517, 583588.
Konermann, S, Lotfy, P, Brideau, NJ, Oki, J, Shokhirev, MN and Hsu, PD (2018) Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors. Cell 173, 665676.
Koonin, EV and Makarova, KS (2017) Mobile genetic elements and evolution of CRISPR-Cas systems: all the way there and back. Genome Biology and Evolution 9, 28122825.
Kosicki, M, Tomberg, K and Bradley, A (2018) Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements. Nature Biotechnology 36, 765771.
Labun, K, Montague, TG, Gagnon, JA, Thyme, SB and Valen, E (2016) CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. Nucleic Acids Research 44, W272W276.
Lander, ES, Baylis, F, Zhang, F, Charpentier, E, Berg, P, Bourgain, C, Friedrich, B, Joung, JK, Li, J, Liu, D, Naldini, L, Nie, JB, Qiu, R, Schoene-Seifert, B, Shao, F, Terry, S, Wei, W and Winnacker, EL (2019) Adopt a moratorium on heritable genome editing. Nature 567, 165168.
Lee, CM, Cradick, TJ and Bao, G (2016) The Neisseria meningitidis CRISPR-Cas9 system enables specific genome editing in mammalian cells. Molecular Therapy 24, 645654.
Lee, JK, Jeong, E, Lee, J, Jung, M, Shin, E, Kim, Y-H, Lee, K, Jung, I, Kim, D, Kim, S and Kim, J-S (2018) Directed evolution of CRISPR-Cas9 to increase its specificity. Nature Communications 9, 3048.
Lemay, ML, Horvath, P and Moineau, S (2017) The CRISPR-Cas app goes viral. Current Opinion in Microbiology 37, 103109.
Liang, Z, Zhang, K, Chen, K and Gao, C (2014) Targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system. Journal of Genetics and Genomics=Yi chuan xue bao 41, 6368.
Liang, P, Xu, Y, Zhang, X, Ding, C, Huang, R, Zhang, Z, Lv, J, Xie, X, Chen, Y, Li, Y, Sun, Y, Bai, Y, Songyang, Z, Ma, W, Zhou, C and Huang, J (2015) CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes. Protein Cell 6, 363372.
Liang, Z, Chen, K, Li, T, Zhang, Y, Wang, Y, Zhao, Q, Liu, J, Zhang, H, Liu, C, Ran, Y and Gao, C (2017) Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. Nature Communications 8, 14261.
Liao, HK, Hatanaka, F, Araoka, T, Reddy, P, Wu, MZ, Sui, Y, Yamauchi, T, Sakurai, M, O'keefe, DD, Nunez-Delicado, E, Guillen, P, Campistol, JM, Wu, CJ, Lu, LF, Esteban, CR and Izpisua Belmonte, JC (2017) In vivo target gene activation via CRISPR/Cas9-mediated trans-epigenetic modulation. Cell 171, 14951507.
Link, KH and Breaker, RR (2009) Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches. Gene Therapy 16, 11891201.
Lin, S, Staahl, BT, Alla, RK and Doudna, JA (2014) Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. Elife 3, e04766.
Listgarten, J, Weinstein, M, Kleinstiver, BP, Sousa, AA, Joung, JK, Crawford, J, Gao, K, Hoang, L, Elibol, M, Doench, JG and Fusi, N (2018) Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs. Nature Biomedical Engineering 2, 3847.
Liu, KI, Ramli, MNB, Woo, CWA, Wang, Y, Zhao, T, Zhang, X, Yim, GRD, Chong, BY, Gowher, A, Chua, MZH, Jung, J, Lee, JHJ and Tan, MH (2016a) A chemical-inducible CRISPR-Cas9 system for rapid control of genome editing. Nature Chemical Biology 12, 980987.
Liu, XS, Wu, H, Ji, X, Stelzer, Y, Wu, X, Czauderna, S, Shu, J, Dadon, D, Young, RA and Jaenisch, R (2016b) Editing DNA methylation in the mammalian genome. Cell 167, 233247.
Liu, L, Li, X, Ma, J, Li, Z, You, L, Wang, J, Wang, M, Zhang, X and Wang, Y (2017 a) The molecular architecture for RNA-guided RNA cleavage by Cas13a. Cell 170, 714726.
Liu, L, Li, X, Wang, J, Wang, M, Chen, P, Yin, M, Li, J, Sheng, G and Wang, Y (2017 b) Two distant catalytic sites are responsible for C2c2 RNase activities. Cell 168, 121134.
Liu, SJ, Horlbeck, MA, Cho, SW, Birk, HS, Malatesta, M, He, D, Attenello, FJ, Villalta, JE, Cho, MY, Chen, Y, Mandegar, MA, Olvera, MP, Gilbert, LA, Conklin, BR, Chang, HY, Weissman, JS and Lim, DA (2017c) CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science 355, eaah7111.
Liu, N, Lee, CH, Swigut, T, Grow, E, Gu, B, Bassik, MC and Wysocka, J (2018a) Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators. Nature 553, 228232.
Liu, XS, Wu, H, Krzisch, M, Wu, X, Graef, J, Muffat, J, Hnisz, D, Li, CH, Yuan, B, Xu, C, Li, Y, Vershkov, D, Cacace, A, Young, RA and Jaenisch, R (2018b) Rescue of Fragile X syndrome neurons by DNA methylation editing of the FMR1 gene. Cell 172, 979992.
Liu, Y, Yu, C, Daley, TP, Wang, F, Cao, WS, Bhate, S, Lin, X, Still, C 2nd, Liu, H, Zhao, D, Wang, H, Xie, XS, Ding, S, Wong, WH, Wernig, M and Qi, LS (2018c) CRISPR activation screens systematically identify factors that drive neuronal fate and reprogramming. Cell Stem Cell 23, 758771.
Liu, Z, Lu, Z, Yang, G, Huang, S, Li, G, Feng, S, Liu, Y, Li, J, Yu, W, Zhang, Y, Chen, J, Sun, Q and Huang, X (2018d) Efficient generation of mouse models of human diseases via ABE- and BE-mediated base editing. Nature Communications 9, 2338.
Liu, J-J, Orlova, N, Oakes, BL, Ma, E, Spinner, HB, Baney, KLM, Chuck, J, Tan, D, Knott, GJ, Harrington, LB, Al-Shayeb, B, Wagner, A, Brötzmann, J, Staahl, BT, Taylor, KL, Desmarais, J, Nogales, E and Doudna, JA (2019) Casx enzymes comprise a distinct family of RNA-guided genome editors. Nature 566, 218223.
Li, J-F, Norville, JE, Aach, J, Mccormack, M, Zhang, D, Bush, J, Church, GM and Sheen, J (2013) Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nature Biotechnology 31, 688691.
Li, W, Xu, H, Xiao, T, Cong, L, Love, MI, Zhang, F, Irizarry, RA, Liu, JS, Brown, M and Liu, XS (2014) MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biology 15, 554.
Li, X, Fan, D, Zhang, W, Liu, G, Zhang, L, Zhao, L, Fang, X, Chen, L, Dong, Y, Chen, Y, Ding, Y, Zhao, R, Feng, M, Zhu, Y, Feng, Y, Jiang, X, Zhu, D, Xiang, H, Feng, X, Li, S, Wang, J, Zhang, G, Kronforst, MR and Wang, W (2015) Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies. Nature Communications 6, 8212.
Li, M, Au, LYC, Douglah, D, Chong, A, White, BJ, Ferree, PM and Akbari, OS (2017) Generation of heritable germline mutations in the jewel wasp Nasonia vitripennis using CRISPR/Cas9. Scientific Reports 7, 901.
Li, C, Zong, Y, Wang, Y, Jin, S, Zhang, D, Song, Q, Zhang, R and Gao, C (2018a) Expanded base editing in rice and wheat using a Cas9-adenosine deaminase fusion. Genome Biology 19, 59.
Li, S-Y, Cheng, Q-X, Wang, J-M, Li, X-Y, Zhang, Z-L, Gao, S, Cao, R-B, Zhao, G-P and Wang, J (2018b) CRISPR-Cas12a-assisted nucleic acid detection. Cell Discovery 4, 20.
Li, X, Wang, Y, Liu, Y, Yang, B, Wang, X, Wei, J, Lu, Z, Zhang, Y, Wu, J, Huang, X, Yang, L and Chen, J (2018c) Base editing with a Cpf1-cytidine deaminase fusion. Nature Biotechnology 36, 324327.
Loenen, WA, Dryden, DT, Raleigh, EA, Wilson, GG and Murray, NE (2014) Highlights of the DNA cutters: a short history of the restriction enzymes. Nucleic Acids Research 42, 319.
Long, C, Amoasii, L, Mireault, AA, Mcanally, JR, Li, H, Sanchez-Ortiz, E, Bhattacharyya, S, Shelton, JM, Bassel-Duby, R and Olson, EN (2016) Postnatal genome editing partially restores dystrophin expression in a mouse model of muscular dystrophy. Science 351, 400403.
Lunshof, J (2015) Regulate gene editing in wild animals. Nature 521, 127.
Maddalo, D, Manchado, E, Concepcion, CP, Bonetti, C, Vidigal, JA, Han, YC, Ogrodowski, P, Crippa, A, Rekhtman, N, De Stanchina, E, Lowe, SW and Ventura, A (2014) In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system. Nature 516, 423427.
Maeder, ML, Linder, SJ, Cascio, VM, Fu, Y, Ho, QH and Joung, JK (2013) CRISPR RNA-guided activation of endogenous human genes. Nature Methods 10, 977979.
Maeder, ML, Stefanidakis, M, Wilson, CJ, Baral, R, Barrera, LA, Bounoutas, GS, Bumcrot, D, Chao, H, Ciulla, DM, Dasilva, JA, Dass, A, Dhanapal, V, Fennell, TJ, Friedland, AE, Giannoukos, G, Gloskowski, SW, Glucksmann, A, Gotta, GM, Jayaram, H, Haskett, SJ, Hopkins, B, Horng, JE, Joshi, S, Marco, E, Mepani, R, Reyon, D, Ta, T, Tabbaa, DG, Samuelsson, SJ, Shen, S, Skor, MN, Stetkiewicz, P, Wang, T, Yudkoff, C, Myer, VE, Albright, CF and Jiang, H (2019) Development of a gene-editing approach to restore vision loss in Leber congenital amaurosis type 10. Nature Medicine 25, 229233.
Makarova, KS, Aravind, L, Grishin, NV, Rogozin, IB and Koonin, EV (2002) A DNA repair system specific for thermophilic archaea and bacteria predicted by genomic context analysis. Nucleic Acids Research 30, 482496.
Makarova, KS, Grishin, NV, Shabalina, SA, Wolf, YI and Koonin, EV (2006) A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biology Direct 1, 7.
Makarova, KS, Haft, DH, Barrangou, R, Brouns, SJJ, Charpentier, E, Horvath, P, Moineau, S, Mojica, FJM, Wolf, YI, Yakunin, AF, Van Der Oost, J and Koonin, EV (2011) Evolution and classification of the CRISPR–Cas systems. Nature Reviews Microbiology 9, 467477.
Makarova, KS, Wolf, YI, Alkhnbashi, OS, Costa, F, Shah, SA, Saunders, SJ, Barrangou, R, Brouns, SJJ, Charpentier, E, Haft, DH, Horvath, P, Moineau, S, Mojica, FJM, Terns, RM, Terns, MP, White, MF, Yakunin, AF, Garrett, RA, Van Der Oost, J, Backofen, R and Koonin, EV (2015) An updated evolutionary classification of CRISPR-Cas systems. Nature Reviews Microbiology 13, 722736.
Mali, P, Aach, J, Stranges, PB, Esvelt, KM, Moosburner, M, Kosuri, S, Yang, L and Church, GM (2013a) CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nature Biotechnology 31, 833838.
Mali, P, Yang, LH, Esvelt, KM, Aach, J, Guell, M, Dicarlo, JE, Norville, JE and Church, GM (2013b) RNA-guided Human genome engineering via Cas9. Science 339, 823826.
Mandal, PK, Ferreira, LM, Collins, R, Meissner, TB, Boutwell, CL, Friesen, M, Vrbanac, V, Garrison, BS, Stortchevoi, A, Bryder, D, Musunuru, K, Brand, H, Tager, AM, Allen, TM, Talkowski, ME, Rossi, DJ and Cowan, CA (2014) Efficient ablation of genes in human hematopoietic stem and effector cells using CRISPR/Cas9. Cell Stem Cell 15, 643652.
Mandegar, MA, Huebsch, N, Frolov, EB, Shin, E, Truong, A, Olvera, MP, Chan, AH, Miyaoka, Y, Holmes, K, Spencer, CI, Judge, LM, Gordon, DE, Eskildsen, TV, Villalta, JE, Horlbeck, MA, Gilbert, LA, Krogan, NJ, Sheikh, SP, Weissman, JS, Qi, LS, So, PL and Conklin, BR (2016) CRISPR interference efficiently induces specific and reversible gene silencing in human iPSCs. Cell Stem Cell 18, 541553.
Manguso, RT, Pope, HW, Zimmer, MD, Brown, FD, Yates, KB, Miller, BC, Collins, NB, Bi, K, Lafleur, MW, Juneja, VR, Weiss, SA, Lo, J, Fisher, DE, Miao, D, Van Allen, E, Root, DE, Sharpe, AH, Doench, JG and Haining, WN (2017) In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target. Nature 547, 413418.
Mao, Y, Zhang, H, Xu, N, Zhang, B, Gou, F and Zhu, JK (2013) Application of the CRISPR-Cas system for efficient genome engineering in plants. Molecular Plant 6, 20082011.
Marceau, CD, Puschnik, AS, Majzoub, K, Ooi, YS, Brewer, SM, Fuchs, G, Swaminathan, K, Mata, MA, Elias, JE, Sarnow, P and Carette, JE (2016) Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens. Nature 535, 159163.
Marino, ND, Zhang, JY, Borges, AL, Sousa, AA, Leon, LM, Rauch, BJ, Walton, RT, Berry, JD, Joung, JK, Kleinstiver, BP and Bondy-Denomy, J (2018) Discovery of widespread type I and type V CRISPR-Cas inhibitors. Science 362, 240242.
Marraffini, LA (2015) CRISPR-Cas immunity in prokaryotes. Nature 526, 5561.
Marraffini, LA and Sontheimer, EJ (2008) CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322, 18431845.
Martin, A, Serano, JM, Jarvis, E, Bruce, HS, Wang, J, Ray, S, Barker, CA, O'connell, LC and Patel, NH (2016) CRISPR/cas9 mutagenesis reveals versatile roles of Hox genes in crustacean limb specification and evolution. Current Biology: CB 26, 1426.
Maruyama, T, Dougan, SK, Truttmann, MC, Bilate, AM, Ingram, JR and Ploegh, HL (2015) Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nature Biotechnology 33, 538542.
Mastroianni, M, Watanabe, K, White, TB, Zhuang, F, Vernon, J, Matsuura, M, Wallingford, J and Lambowitz, AM (2008) Group II intron-based gene targeting reactions in eukaryotes. PLoS One 3, e3121.
Ma, H, Naseri, A, Reyes-Gutierrez, P, Wolfe, SA, Zhang, S and Pederson, T (2015) Multicolor CRISPR labeling of chromosomal loci in human cells. Proceedings of the National Academy of Sciences of the United States of America 112, 30023007.
Ma, H, Tu, LC, Naseri, A, Huisman, M, Zhang, S, Grunwald, D and Pederson, T (2016a) CRISPR-Cas9 nuclear dynamics and target recognition in living cells. Journal of Cell Biology 214, 529537.
Ma, H, Tu, LC, Naseri, A, Huisman, M, Zhang, S, Grunwald, D and Pederson, T (2016b) Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nature Biotechnology 34, 528530.
Ma, H, Marti-Gutierrez, N, Park, SW, Wu, J, Lee, Y, Suzuki, K, Koski, A, Ji, D, Hayama, T, Ahmed, R, Darby, H, Van Dyken, C, Li, Y, Kang, E, Park, AR, Kim, D, Kim, ST, Gong, J, Gu, Y, Xu, X, Battaglia, D, Krieg, SA, Lee, DM, Wu, DH, Wolf, DP, Heitner, SB, Belmonte, JCI, Amato, P, Kim, JS, Kaul, S and Mitalipov, S (2017) Correction of a pathogenic gene mutation in human embryos. Nature 548, 413419.
Ma, H, Marti-Gutierrez, N, Park, SW, Wu, J, Hayama, T, Darby, H, Van Dyken, C, Li, Y, Koski, A, Liang, D, Suzuki, K, Gu, Y, Gong, J, Xu, X, Ahmed, R, Lee, Y, Kang, E, Ji, D, Park, AR, Kim, D, Kim, ST, Heitner, SB, Battaglia, D, Krieg, SA, Lee, DM, Wu, DH, Wolf, DP, Amato, P, Kaul, S, Belmonte, JCI, Kim, JS and Mitalipov, S (2018) Ma et al. Reply. Nature 560, E10E23.
Mckenna, A, Findlay, GM, Gagnon, JA, Horwitz, MS, Schier, AF and Shendure, J (2016) Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science 353, aaf7907.
Meeske, AJ and Marraffini, LA (2018) RNA guide complementarity prevents self-targeting in type VI CRISPR systems. Molecular Cell 71, 791801.
Meier, JA, Zhang, F and Sanjana, NE (2017) GUIDES: sgRNA design for loss-of-function screens. Nature Methods 14, 831832.
Miyaoka, Y, Berman, JR, Cooper, SB, Mayerl, SJ, Chan, AH, Zhang, B, Karlin-Neumann, GA and Conklin, BR (2016) Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing. Scientific Reports 6, 23549.
Miyaoka, Y, Mayerl, SJ, Chan, AH and Conklin, BR (2018) Detection and quantification of HDR and NHEJ induced by genome editing at endogenous gene loci using droplet digital PCR. Methods in Molecular Biology 1768, 349362.
Mojica, FJ and Rodriguez-Valera, F (2016) The discovery of CRISPR in archaea and bacteria. FEBS Journal 283, 31623169.
Mojica, FJ, Diez-Villasenor, C, Garcia-Martinez, J and Soria, E (2005) Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. Journal of Molecular Evolution 60, 174182.
Mojica, FJ, Diez-Villasenor, C, Garcia-Martinez, J and Almendros, C (2009) Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology (Reading England) 155(Pt 3), 733740.
Moreno-Mateos, MA, Fernandez, JP, Rouet, R, Vejnar, CE, Lane, MA, Mis, E, Khokha, MK, Doudna, JA and Giraldez, AJ (2017) CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing. Nature Communications 8, 2024.
Morgan, SL, Mariano, NC, Bermudez, A, Arruda, NL, Wu, F, Luo, Y, Shankar, G, Jia, L, Chen, H, Hu, JF, Hoffman, AR, Huang, CC, Pitteri, SJ and Wang, KC (2017) Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping. Nature Communications 8, 15993.
Morgens, DW, Wainberg, M, Boyle, EA, Ursu, O, Araya, CL, Tsui, CK, Haney, MS, Hess, GT, Han, K, Jeng, EE, Li, A, Snyder, MP, Greenleaf, WJ, Kundaje, A and Bassik, MC (2017) Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens. Nature Communications 8, 15178.
Moscou, MJ and Bogdanove, AJ (2009) A simple cipher governs DNA recognition by TAL effectors. Science 326, 1501.
Munoz, DM, Cassiani, PJ, Li, L, Billy, E, Korn, JM, Jones, MD, Golji, J, Ruddy, DA, Yu, K, Mcallister, G, Deweck, A, Abramowski, D, Wan, J, Shirley, MD, Neshat, SY, Rakiec, D, De Beaumont, R, Weber, O, Kauffmann, A, Mcdonald, ER 3rd, Keen, N, Hofmann, F, Sellers, WR, Schmelzle, T, Stegmeier, F and Schlabach, MR (2016) CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions. Cancer Discovery 6, 900913.
Myers, SA, Wright, J, Peckner, R, Kalish, BT, Zhang, F and Carr, SA (2018) Discovery of proteins associated with a predefined genomic locus via dCas9-APEX-mediated proximity labeling. Nature Methods 15, 437439.
Myhrvold, C, Freije, CA, Gootenberg, JS, Abudayyeh, OO, Metsky, HC, Durbin, AF, Kellner, MJ, Tan, AL, Paul, LM, Parham, LA, Garcia, KF, Barnes, KG, Chak, B, Mondini, A, Nogueira, ML, Isern, S, Michael, SF, Lorenzana, I, Yozwiak, NL, Macinnis, BL, Bosch, I, Gehrke, L, Zhang, F and Sabeti, PC (2018) Field-deployable viral diagnostics using CRISPR-Cas13. Science 360, 444448.
Nakamura, M, Srinivasan, P, Chavez, M, Carter, MA, Dominguez, AA, La Russa, M, Lau, MB, Abbott, TR, Xu, X, Zhao, D, Gao, Y, Kipniss, NH, Smolke, CD, Bondy-Denomy, J and Qi, LS (2019) Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells. Nature Communications 10, 194.
Nakayama, T, Fish, MB, Fisher, M, Oomen-Hajagos, J, Thomsen, GH and Grainger, RM (2013) Simple and efficient CRISPR/Cas9-mediated targeted mutagenesis in Xenopus tropicalis. Genesis (New York N.Y. : 2000) 51, 835843.
Nelles, DA, Fang, MY, O'connell, MR, Xu, JL, Markmiller, SJ, Doudna, JA and Yeo, GW (2016) Programmable RNA tracking in live cells with CRISPR/Cas9. Cell 165, 488496.
Nelson, CE, Hakim, CH, Ousterout, DG, Thakore, PI, Moreb, EA, Rivera, RMC, Madhavan, S, Pan, X, Ran, FA, Yan, WX, Asokan, A, Zhang, F, Duan, D and Gersbach, CA (2016) In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy. Science 351, 403407.
Nelson, CE, Wu, Y, Gemberling, MP, Oliver, ML, Waller, MA, Bohning, JD, Robinson-Hamm, JN, Bulaklak, K, Castellanos Rivera, RM, Collier, JH, Asokan, A and Gersbach, CA (2019) Long-term evaluation of AAV-CRISPR genome editing for Duchenne muscular dystrophy. Nature Medicine 25, 427432.
Nguyen, DP, Miyaoka, Y, Gilbert, LA, Mayerl, SJ, Lee, BH, Weissman, JS, Conklin, BR and Wells, JA (2016) Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity. Nature Communications 7, 12009.
Nihongaki, Y, Kawano, F, Nakajima, T and Sato, M (2015) Photoactivatable CRISPR-Cas9 for optogenetic genome editing. Nature Biotechnology 33, 755760.
Nishida, K, Arazoe, T, Yachie, N, Banno, S, Kakimoto, M, Tabata, M, Mochizuki, M, Miyabe, A, Araki, M, Hara, KY, Shimatani, Z and Kondo, A (2016) Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science 353, aaf8729aaf8729.
Nishimasu, H, Ran, FA, Hsu, PD, Konermann, S, Shehata, SI, Dohmae, N, Ishitani, R, Zhang, F and Nureki, O (2014) Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156, 935949.
Nishimasu, H, Cong, L, Yan, WX, Ran, FA, Zetsche, B, Li, Y, Kurabayashi, A, Ishitani, R, Zhang, F and Nureki, O (2015) Crystal structure of Staphylococcus aureus Cas9. Cell 162, 11131126.
Nishimasu, H, Shi, X, Ishiguro, S, Gao, L, Hirano, S, Okazaki, S, Noda, T, Abudayyeh, OO, Gootenberg, JS, Mori, H, Oura, S, Holmes, B, Tanaka, M, Seki, M, Hirano, H, Aburatani, H, Ishitani, R, Ikawa, M, Yachie, N, Zhang, F and Nureki, O (2018) Engineered CRISPR-Cas9 nuclease with expanded targeting space. Science 361, 12591262.
Nissim, L, Perli, SD, Fridkin, A, Perez-Pinera, P and Lu, TK (2014) Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. Molecular Cell 54, 698710.
Niu, Y, Shen, B, Cui, Y, Chen, Y, Wang, J, Wang, L, Kang, Y, Zhao, X, Si, W, Li, W, Xiang, AP, Zhou, J, Guo, X, Bi, Y, Si, C, Hu, B, Dong, G, Wang, H, Zhou, Z, Li, T, Tan, T, Pu, X, Wang, F, Ji, S, Zhou, Q, Huang, X, Ji, W and Sha, J (2014) Generation of gene-modified Cynomolgus monkey via Cas9/RNA-mediated gene targeting in one-cell embryos. Cell 156, 836843.
Niu, D, Wei, HJ, Lin, L, George, H, Wang, T, Lee, IH, Zhao, HY, Wang, Y, Kan, Y, Shrock, E, Lesha, E, Wang, G, Luo, Y, Qing, Y, Jiao, D, Zhao, H, Zhou, X, Wang, S, Wei, H, Guell, M, Church, GM and Yang, L (2017) Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science 357, 13031307.
Noordermeer, SM, Adam, S, Setiaputra, D, Barazas, M, Pettitt, SJ, Ling, AK, Olivieri, M, Álvarez-Quilón, A, Moatti, N, Zimmermann, M, Annunziato, S, Krastev, DB, Song, F, Brandsma, I, Frankum, J, Brough, R, Sherker, A, Landry, S, Szilard, RK, Munro, MM, Mcewan, A, De Rugy, TG, Lin, Z-Y, Hart, T, Moffat, J, Gingras, A-C, Martin, A, Van Attikum, H, Jonkers, J, Lord, CJ, Rottenberg, S and Durocher, D (2018) The shieldin complex mediates 53BP1-dependent DNA repair. Nature 560, 117121.
Nunez, JK, Harrington, LB, Kranzusch, PJ, Engelman, AN and Doudna, JA (2015) Foreign DNA capture during CRISPR-Cas adaptive immunity. Nature 527, 535538.
Nymark, M, Sharma, AK, Sparstad, T, Bones, AM and Winge, P (2016) A CRISPR/Cas9 system adapted for gene editing in marine algae. Scientific Reports 6, 24951.
Paquet, D, Kwart, D, Chen, A, Sproul, A, Jacob, S, Teo, S, Olsen, KM, Gregg, A, Noggle, S and Tessier-Lavigne, M (2016) Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9. Nature 533, 125129.
Pardee, K, Green, AA, Takahashi, MK, Braff, D, Lambert, G, Lee, JW, Ferrante, T, Ma, D, Donghia, N, Fan, M, Daringer, NM, Bosch, I, Dudley, DM, O'connor, DH, Gehrke, L and Collins, JJ (2016) Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell 165, 12551266.
Park, RJ, Wang, T, Koundakjian, D, Hultquist, JF, Lamothe-Molina, P, Monel, B, Schumann, K, Yu, H, Krupzcak, KM, Garcia-Beltran, W, Piechocka-Trocha, A, Krogan, NJ, Marson, A, Sabatini, DM, Lander, ES, Hacohen, N and Walker, BD (2017) A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors. Nature Genetics 49, 193203.
Parnas, O, Jovanovic, M, Eisenhaure, TM, Herbst, RH, Dixit, A, Ye, CJ, Przybylski, D, Platt, RJ, Tirosh, I, Sanjana, NE, Shalem, O, Satija, R, Raychowdhury, R, Mertins, P, Carr, SA, Zhang, F, Hacohen, N and Regev, A (2015) A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks. Cell 162, 675686.
Patel, SJ, Sanjana, NE, Kishton, RJ, Eidizadeh, A, Vodnala, SK, Cam, M, Gartner, JJ, Jia, L, Steinberg, SM, Yamamoto, TN, Merchant, AS, Mehta, GU, Chichura, A, Shalem, O, Tran, E, Eil, R, Sukumar, M, Guijarro, EP, Day, CP, Robbins, P, Feldman, S, Merlino, G, Zhang, F and Restifo, NP (2017) Identification of essential genes for cancer immunotherapy. Nature 548, 537542.
Pattanayak, V, Lin, S, Guilinger, JP, Ma, E, Doudna, JA and Liu, DR (2013) High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nature Biotechnology 31, 839843.
Pawluk, A, Amrani, N, Zhang, Y, Garcia, B, Hidalgo-Reyes, Y, Lee, J, Edraki, A, Shah, M, Sontheimer, EJ, Maxwell, KL and Davidson, AR (2016) Naturally occurring off-switches for CRISPR-Cas9. Cell 167, 18291838.
Perez-Pinera, P, Kocak, DD, Vockley, CM, Adler, AF, Kabadi, AM, Polstein, LR, Thakore, PI, Glass, KA, Ousterout, DG, Leong, KW, Guilak, F, Crawford, GE, Reddy, TE and Gersbach, CA (2013) RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nature Methods 10, 973976.
Perli, SD, Cui, CH and Lu, TK (2016) Continuous genetic recording with self-targeting CRISPR-Cas in human cells. Science 353, aag0511.
Pinello, L, Canver, MC, Hoban, MD, Orkin, SH, Kohn, DB, Bauer, DE and Yuan, GC (2016) Analyzing CRISPR genome-editing experiments with CRISPResso. Nature Biotechnology 34, 695697.
Platt, RJ, Chen, S, Zhou, Y, Yim, MJ, Swiech, L, Kempton, HR, Dahlman, JE, Parnas, O, Eisenhaure, TM, Jovanovic, M, Graham, DB, Jhunjhunwala, S, Heidenreich, M, Xavier, RJ, Langer, R, Anderson, DG, Hacohen, N, Regev, A, Feng, G, Sharp, PA and Zhang, F (2014) CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell 159, 440455.
Plessis, A, Perrin, A, Haber, JE and Dujon, B (1992) Site-specific recombination determined by I-SceI, a mitochondrial group I intron-encoded endonuclease expressed in the yeast nucleus. Genetics 130, 451460.
Porteus, MH (2015) Towards a new era in medicine: therapeutic genome editing. Genome Biology 16, 286.
Pourcel, C, Salvignol, G and Vergnaud, G (2005) CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology (Reading England) 151(Pt 3), 653663.
Qi, LS, Larson, MH, Gilbert, LA, Doudna, JA, Weissman, JS, Arkin, AP and Lim, WA (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 11731183.
Quiberoni, A, Moineau, S, Rousseau, GM, Reinheimer, J and Ackermann, HW (2010) Streptococcus thermophilus bacteriophages. International Dairy Journal 20, 657664.
Ramanan, V, Shlomai, A, Cox, DBT, Schwartz, RE, Michailidis, E, Bhatta, A, Scott, DA, Zhang, F, Rice, CM and Bhatia, SN (2015) CRISPR/cas9 cleavage of viral DNA efficiently suppresses hepatitis B virus. Scientific Reports 5, 10833.
Ran, FA, Hsu, PD, Lin, C-Y, Gootenberg, JS, Konermann, S, Trevino, AE, Scott, DA, Inoue, A, Matoba, S, Zhang, Y and Zhang, F (2013) Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154, 13801389.
Ran, FA, Cong, L, Yan, WX, Scott, DA, Gootenberg, JS, Kriz, AJ, Zetsche, B, Shalem, O, Wu, X, Makarova, KS, Koonin, EV, Sharp, PA and Zhang, F (2015) In vivo genome editing using Staphylococcus aureus Cas9. Nature 520, 186191.
Rauch, BJ, Silvis, MR, Hultquist, JF, Waters, CS, Mcgregor, MJ, Krogan, NJ and Bondy-Denomy, J (2017) Inhibition of CRISPR-Cas9 with bacteriophage proteins. Cell 168, 150158.
Rees, HA and Liu, DR (2018) Base editing: precision chemistry on the genome and transcriptome of living cells. Nature Publishing Group 19, 770788.
Richardson, CD, Ray, GJ, Dewitt, MA, Curie, GL and Corn, JE (2016) Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nature Biotechnology 34, 339344.
Richardson, CD, Kazane, KR, Feng, SJ, Zelin, E, Bray, NL, Schafer, AJ, Floor, SN and Corn, JE (2018) CRISPR-Cas9 genome editing in human cells occurs via the Fanconi anemia pathway. Nature Genetics 50, 11321139.
Rodriguez, EA, Campbell, RE, Lin, JY, Lin, MZ, Miyawaki, A, Palmer, AE, Shu, X, Zhang, J and Tsien, RY (2017) The growing and glowing toolbox of fluorescent and photoactive proteins. Trends in Biochemical Sciences 42, 111129.
Rose, JC, Stephany, JJ, Valente, WJ, Trevillian, BM, Dang, HV, Bielas, JH, Maly, DJ and Fowler, DM (2017) Rapidly inducible Cas9 and DSB-ddPCR to probe editing kinetics. Nature Methods 14, 891896.
Roth, TL, Puig-Saus, C, Yu, R, Shifrut, E, Carnevale, J, Li, PJ, Hiatt, J, Saco, J, Krystofinski, P, Li, H, Tobin, V, Nguyen, DN, Lee, MR, Putnam, AL, Ferris, AL, Chen, JW, Schickel, JN, Pellerin, L, Carmody, D, Alkorta-Aranburu, G, Del Gaudio, D, Matsumoto, H, Morell, M, Mao, Y, Cho, M, Quadros, RM, Gurumurthy, CB, Smith, B, Haugwitz, M, Hughes, SH, Weissman, JS, Schumann, K, Esensten, JH, May, AP, Ashworth, A, Kupfer, GM, Greeley, SAW, Bacchetta, R, Meffre, E, Roncarolo, MG, Romberg, N, Herold, KC, Ribas, A, Leonetti, MD and Marson, A (2018) Reprogramming human T cell function and specificity with non-viral genome targeting. Nature 559, 405409.
Rouet, P, Smih, F and Jasin, M (1994) Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Molecular and Cellular Biology 14, 80968106.
Rudin, N, Sugarman, E and Haber, JE (1989) Genetic and physical analysis of double-strand break repair and recombination in Saccharomyces cerevisiae. Genetics 122, 519534.
Sanchez-Rivera, FJ, Papagiannakopoulos, T, Romero, R, Tammela, T, Bauer, MR, Bhutkar, A, Joshi, NS, Subbaraj, L, Bronson, RT, Xue, W and Jacks, T (2014) Rapid modelling of cooperating genetic events in cancer through somatic genome editing. Nature 516, 428431.
Sanjana, NE, Wright, J, Zheng, K, Shalem, O, Fontanillas, P, Joung, J, Cheng, C, Regev, A and Zhang, F (2016) High-resolution interrogation of functional elements in the noncoding genome. Science 353, 15451549.
Sanson, KR, Hanna, RE, Hegde, M, Donovan, KF, Strand, C, Sullender, ME, Vaimberg, EW, Goodale, A, Root, DE, Piccioni, F and Doench, JG (2018) Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities. Nature Communications 9, 5416.
Sapranauskas, R, Gasiunas, G, Fremaux, C, Barrangou, R, Horvath, P and Siksnys, V (2011) The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Research 39, gkr606gk9282.
Schindele, P, Wolter, F and Puchta, H (2018) Transforming plant biology and breeding with CRISPR/Cas9, Cas12 and Cas13. FEBS letters 592, 19541967.
Schmid-Burgk, JL, Schmidt, T, Gaidt, MM, Pelka, K, Latz, E, Ebert, TS and Hornung, V (2014) Outknocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines. Genome Research 24, 17191723.
Schmid-Burgk, JL, Honing, K, Ebert, TS and Hornung, V (2016) CRISPaint allows modular base-specific gene tagging using a ligase-4-dependent mechanism. Nature Communications 7, 12338.
Schmidt, F, Cherepkova, MY and Platt, RJ (2018) Transcriptional recording by CRISPR spacer acquisition from RNA. Nature 562, 380385.
Schunder, E, Rydzewski, K, Grunow, R and Heuner, K (2013) First indication for a functional CRISPR/Cas system in Francisella tularensis. International Journal of Medical Microbiology 303, 5160.
Schwank, G, Koo, BK, Sasselli, V, Dekkers, JF, Heo, I, Demircan, T, Sasaki, N, Boymans, S, Cuppen, E, Van Der Ent, CK, Nieuwenhuis, EE, Beekman, JM and Clevers, H (2013) Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. Cell Stem Cell 13, 653658.
Scott, DA and Zhang, F (2017) Implications of human genetic variation in CRISPR-based therapeutic genome editing. Nature Medicine 23, 10951101.
Shalem, O, Sanjana, NE, Hartenian, E, Shi, X, Scott, DA, Mikkelsen, TS, Heckl, D, Ebert, BL, Root, DE, Doench, JG and Zhang, F (2014) Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 8487.
Shalem, O, Sanjana, NE and Zhang, F (2015) High-throughput functional genomics using CRISPR-Cas9. Nature Reviews Genetics 16, 299311.
Shan, Q, Wang, Y, Li, J, Zhang, Y, Chen, K, Liang, Z, Zhang, K, Liu, J, Xi, JJ, Qiu, J-L and Gao, C (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nature Biotechnology 31, 686688.
Shapiro, RS, Chavez, A and Collins, JJ (2018) CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms. Nature Reviews Microbiology 16, 333339.
Shimatani, Z, Kashojiya, S, Takayama, M, Terada, R, Arazoe, T, Ishii, H, Teramura, H, Yamamoto, T, Komatsu, H, Miura, K, Ezura, H, Nishida, K, Ariizumi, T and Kondo, A (2017) Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion. Nature Biotechnology 35, 441443.
Shipman, SL, Nivala, J, Macklis, JD and Church, GM (2016) Molecular recordings by directed CRISPR spacer acquisition. Science 353, aaf1175.
Shipman, SL, Nivala, J, Macklis, JD and Church, GM (2017) CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria. Nature 547, 345349.
Shi, J, Wang, E, Milazzo, JP, Wang, Z, Kinney, JB and Vakoc, CR (2015) Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nature Biotechnology 33, 661667.
Shmakov, S, Abudayyeh, OO, Makarova, KS, Wolf, YI, Gootenberg, JS, Semenova, E, Minakhin, L, Joung, J, Konermann, S, Severinov, K, Zhang, F and Koonin, EV (2015) Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Molecular Cell 60, 385397.
Shmakov, S, Smargon, A, Scott, D, Cox, D, Pyzocha, N, Yan, W, Abudayyeh, OO, Gootenberg, JS, Makarova, KS, Wolf, YI, Severinov, K, Zhang, F and Koonin, EV (2017) Diversity and evolution of class 2 CRISPR-Cas systems. Nature Reviews Microbiology 15, 169182.
Shmakov, SA, Makarova, KS, Wolf, YI, Severinov, KV and Koonin, EV (2018) Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis. Proceedings of the National Academy of Sciences of the United States of America 115, E5307E5316.
Sidik, SM, Huet, D, Ganesan, SM, Huynh, M-H, Wang, T, Nasamu, AS, Thiru, P, Saeij, JPJ, Carruthers, VB, Niles, JC and Lourido, S (2016) A genome-wide CRISPR screen in toxoplasma identifies essential Apicomplexan genes. Cell 166, 14231435.
Silas, S, Mohr, G, Sidote, DJ, Markham, LM, Sanchez-Amat, A, Bhaya, D, Lambowitz, AM and Fire, AZ (2016) Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Cas1 fusion protein. Science 351, aad4234.
Slaymaker, IM, Gao, L, Zetsche, B, Scott, DA, Yan, WX and Zhang, F (2015) Rationally engineered Cas9 nucleases with improved specificity. Science 351, 8488.
Slaymaker, IM, Mesa, P, Kellner, MJ, Kannan, S, Brignole, E, Koob, J, Feliciano, PR, Stella, S, Abudayyeh, OO, Gootenberg, JS, Strecker, J, Montoya, G and Zhang, F (2019) High-resolution structure of Cas13b and biochemical characterization of RNA targeting and cleavage. Cell Reports 26, 111.
Smargon, AA, Cox, DBT, Pyzocha, NK, Zheng, K, Slaymaker, IM, Gootenberg, JS, Abudayyeh, OA, Essletzbichler, P, Shmakov, S, Makarova, KS, Koonin, EV and Zhang, F (2017) Cas13b Is a type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx28. Molecular Cell 65, 618630.
Smith, JJ, Timoshevskaya, N, Ye, C, Holt, C, Keinath, MC, Parker, HJ, Cook, ME, Hess, JE, Narum, SR, Lamanna, F, Kaessmann, H, Timoshevskiy, VA, Waterbury, CKM, Saraceno, C, Wiedemann, LM, Robb, SMC, Baker, C, Eichler, EE, Hockman, D, Sauka-Spengler, T, Yandell, M, Krumlauf, R, Elgar, G and Amemiya, CT (2018) The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nature Genetics 50, 270277.
Sollelis, L, Ghorbal, M, Macpherson, CR, Martins, RM, Kuk, N, Crobu, L, Bastien, P, Scherf, A, Lopez-Rubio, J-J and Sterkers, Y (2015) First efficient CRISPR-Cas9-mediated genome editing in Leishmania parasites. Cellular Microbiology 17, 14051412.
Sontheimer, EJ and Barrangou, R (2015) The bacterial origins of the CRISPR genome-editing revolution. Human Gene Therapy 26, 413424.
Sorek, R, Kunin, V and Hugenholtz, P (2008) CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea. Nature Reviews Microbiology 6, 181186.
Soyk, S, Lemmon, ZH, Oved, M, Fisher, J, Liberatore, KL, Park, SJ, Goren, A, Jiang, K, Ramos, A, Van Der Knaap, E, Van Eck, J, Zamir, D, Eshed, Y and Lippman, ZB (2017) Bypassing negative epistasis on yield in tomato imposed by a domestication gene. Cell 169, 11421155 e1112.
Stella, S, Alcón, P and Montoya, G (2017) Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage. Nature 546, 559563.
Sternberg, SH, Redding, S, Jinek, M, Greene, EC and Doudna, JA (2014) DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 6267.
Strecker, J, Jones, S, Koopal, B, Schmid-Burgk, J, Zetsche, B, Gao, L, Makarova, KS, Koonin, EV and Zhang, F (2019) Engineering of CRISPR-Cas12b for human genome editing. Nature Communications 10, 866.
Strohkendl, I, Saifuddin, FA, Rybarski, JR, Finkelstein, IJ and Russell, R (2018) Kinetic basis for DNA target specificity of CRISPR-Cas12a. Molecular Cell 71, 816824.
Suzuki, K, Tsunekawa, Y, Hernandez-Benitez, R, Wu, J, Zhu, J, Kim, EJ, Hatanaka, F, Yamamoto, M, Araoka, T, Li, Z, Kurita, M, Hishida, T, Li, M, Aizawa, E, Guo, S, Chen, S, Goebl, A, Soligalla, RD, Qu, J, Jiang, T, Fu, X, Jafari, M, Esteban, CR, Berggren, WT, Lajara, J, Nunez-Delicado, E, Guillen, P, Campistol, JM, Matsuzaki, F, Liu, GH, Magistretti, P, Zhang, K, Callaway, EM, Zhang, K and Belmonte, JC (2016) In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. Nature 540, 144149.
Swarts, DC, Van Der Oost, J and Jinek, M (2017) Structural basis for guide RNA processing and seed-dependent DNA targeting by CRISPR-Cas12a. Molecular Cell 66, 221233.
Tabebordbar, M, Zhu, K, Cheng, JKW, Chew, WL, Widrick, JJ, Yan, WX, Maesner, C, Wu, EY, Xiao, R, Ran, FA, Cong, L, Zhang, F, Vandenberghe, LH, Church, GM and Wagers, AJ (2016) In vivo gene editing in dystrophic mouse muscle and muscle stem cells. Science 351, 407411.
Tak, YE, Kleinstiver, BP, Nuñez, JK, Hsu, JY, Horng, JE, Gong, J, Weissman, JS and Joung, JK (2017) Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors. Nature Methods 14, 11631166.
Tambe, A, East-Seletsky, A, Knott, GJ, Doudna, JA and O'connell, MR (2018) RNA binding and HEPN-nuclease activation Are decoupled in CRISPR-Cas13a. Cell Reports 24, 10251036.
Tanenbaum, ME, Gilbert, LA, Qi, LS, Weissman, JS and Vale, RD (2014) A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159, 635646.
Tang, W and Liu, DR (2018) Rewritable multi-event analog recording in bacterial and mammalian cells. Science 360, eaap8992.
Telenti, A (2009) Safety concerns about CCR5 as an antiviral target. Curr Opin HIV AIDS 4, 131135.
Teng, F, Cui, T, Feng, G, Guo, L, Xu, K, Gao, Q, Li, T, Li, J, Zhou, Q and Li, W (2018) Repurposing CRISPR-Cas12b for mammalian genome engineering. Cell Discovery 4, 63.
Thakore, PI, D'ippolito, AM, Song, L, Safi, A, Shivakumar, NK, Kabadi, AM, Reddy, TE, Crawford, GE and Gersbach, CA (2015) Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nature Methods 12, 11431149.
Thomas, KR and Capecchi, MR (1987) Site-directed mutagenesis by gene targeting in mouse embryo-derived stem cells. Cell 51, 503512.
Toledo, CM, Ding, Y, Hoellerbauer, P, Davis, RJ, Basom, R, Girard, EJ, Lee, E, Corrin, P, Hart, T, Bolouri, H, Davison, J, Zhang, Q, Hardcastle, J, Aronow, BJ, Plaisier, CL, Baliga, NS, Moffat, J, Lin, Q, Li, XN, Nam, DH, Lee, J, Pollard, SM, Zhu, J, Delrow, JJ, Clurman, BE, Olson, JM and Paddison, PJ (2015) Genome-wide CRISPR-Cas9 screens reveal loss of redundancy between PKMYT1 and WEE1 in Glioblastoma stem-like cells. Cell Reports 13, 24252439.
Truong, D-JJ, Kühner, K, Kühn, R, Werfel, S, Engelhardt, S, Wurst, W and Ortiz, O (2015) Development of an intein-mediated split-Cas9 system for gene therapy. Nucleic Acids Research 43, 64506458.
Tsai, SQ and Joung, JK (2016) Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases. Nature Reviews Genetics 17, 300312.
Tsai, SQ, Wyvekens, N, Khayter, C, Foden, JA, Thapar, V, Reyon, D, Goodwin, MJ, Aryee, MJ and Joung, JK (2014) Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nature Biotechnology 32, 569576.
Tsai, SQ, Zheng, Z, Nguyen, NT, Liebers, M, Topkar, VV, Thapar, V, Wyvekens, N, Khayter, C, Iafrate, AJ, Le, LP, Aryee, MJ and Joung, JK (2015) GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nature Biotechnology 33, 187197.
Tsai, SQ, Nguyen, NT, Malagon-Lopez, J, Topkar, VV, Aryee, MJ and Joung, JK (2017) CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets. Nature Methods 14, 607614.
Tso, CF, Simon, T, Greenlaw, AC, Puri, T, Mieda, M and Herzog, ED (2017) Astrocytes regulate daily rhythms in the Suprachiasmatic nucleus and behavior. Current Biology 27, 10551061.
Tycko, J, Barrera, LA, Huston, NC, Friedland, AE, Wu, X, Gootenberg, JS, Abudayyeh, OO, Myer, VE, Wilson, CJ and Hsu, PD (2018) Pairwise library screen systematically interrogates Staphylococcus aureus Cas9 specificity in human cells. Nature Communications 9, 2962.
Urnov, FD, Rebar, EJ, Holmes, MC, Zhang, HS and Gregory, PD (2010) Genome editing with engineered zinc finger nucleases. Nature Reviews Genetics 11, 636646.
Vakulskas, CA, Dever, DP, Rettig, GR, Turk, R, Jacobi, AM, Collingwood, MA, Bode, NM, Mcneill, MS, Yan, S, Camarena, J, Lee, CM, Park, SH, Wiebking, V, Bak, RO, Gomez-Ospina, N, Pavel-Dinu, M, Sun, W, Bao, G, Porteus, MH and Behlke, MA (2018) A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells. Nature Medicine 24, 12161224.
Van Der Oost, J, Westra, ER, Jackson, RN and Wiedenheft, B (2014) Unravelling the structural and mechanistic basis of CRISPR-Cas systems. Nature Reviews Microbiology 12, 479492.
VERTEX (2018a) A Safety and Efficacy Study Evaluating CTX001 in Subjects With Severe Sickle Cell Disease. Identifier: NCT03745287, (
VERTEX (2018b) A Safety and Efficacy Study Evaluating CTX001 in Subjects With Transfusion-Dependent β-Thalassemia. Identifier: NCT03655678 (
Vestergaard, G, Garrett, RA and Shah, SA (2014) CRISPR adaptive immune systems of Archaea. RNA Biology 11, 156167.
Villiger, L, Grisch-Chan, HM, Lindsay, H, Ringnalda, F, Pogliano, CB, Allegri, G, Fingerhut, R, Haberle, J, Matos, J, Robinson, MD, Thony, B and Schwank, G (2018) Treatment of a metabolic liver disease by in vivo genome base editing in adult mice. Nature Medicine 24, 15191525.
Vinayak, S, Pawlowic, MC, Sateriale, A and Brooks, CF (2015) Genetic modification of the diarrhoeal pathogen cryptosporidium parvum. Nature 523, 477480.
Vojta, A, Dobrinić, P, Tadić, V, Bočkor, L, Korać, P, Julg, B, Klasić, M and Zoldoš, V (2016) Repurposing the CRISPR-Cas9 system for targeted DNA methylation. Nucleic Acids Research 44, 56155628.
Voytas, DF and Gao, C (2014) Precision genome engineering and agriculture: opportunities and regulatory challenges. PLoS Biology 12, e1001877.
Wang, H, Yang, H, Shivalila, CS, Dawlaty, MM, Cheng, AW, Zhang, F and Jaenisch, R (2013) One-Step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153, 910918.
Wang, T, Wei, JJ, Sabatini, DM and Lander, ES (2014) Genetic screens in human cells using the CRISPR-Cas9 system. Science 343, 8084.
Wang, T, Birsoy, K, Hughes, NW, Krupczak, KM, Post, Y, Wei, JJ, Lander, ES and Sabatini, DM (2015) Identification and characterization of essential genes in the human genome. Science 350, 10961101.
Wang, H, Xu, X, Nguyen, CM, Liu, Y, Gao, Y, Lin, X, Daley, T, Kipniss, NH, La Russa, M and Qi, LS (2018) CRISPR-mediated programmable 3D genome positioning and nuclear organization. Cell 175, 14051417.
Wang, B, Wang, M, Zhang, W, Xiao, T, Chen, CH, Wu, A, Wu, F, Traugh, N, Wang, X, Li, Z, Mei, S, Cui, Y, Shi, S, Lipp, JJ, Hinterndorfer, M, Zuber, J, Brown, M, Li, W and Liu, XS (2019) Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute. Nat Protoc 14, 756780.
Wan, H, Feng, C, Teng, F, Yang, S, Hu, B, Niu, Y, Xiang, AP, Fang, W, Ji, W, Li, W, Zhao, X and Zhou, Q (2015) One-step generation of p53 gene biallelic mutant Cynomolgus monkey via the CRISPR/Cas system. Cell Research 25, 258261.
Watters, KE, Fellmann, C, Bai, HB, Ren, SM and Doudna, JA (2018) Systematic discovery of natural CRISPR-Cas12a inhibitors. Science 362, 236239.
Winter, J, Breinig, M, Heigwer, F, Brugemann, D, Leible, S, Pelz, O, Zhan, T and Boutros, M (2016) Carpools: an R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens. Bioinformatics 32, 632634.
Wong, AS, Choi, GC, Cui, CH, Pregernig, G, Milani, P, Adam, M, Perli, SD, Kazer, SW, Gaillard, A, Hermann, M, Shalek, AK, Fraenkel, E and Lu, TK (2016) Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM. Proceedings of the National Academy of Sciences of the United States of America 113, 25442549.
Woo, JW, Kim, J, Kwon, SI, Corvalan, C, Cho, SW, Kim, H, Kim, SG, Kim, ST, Choe, S and Kim, JS (2015) DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nature Biotechnology 33, 11621164.
Wright, AV, Sternberg, SH, Taylor, DW, Staahl, BT, Bardales, JA, Kornfeld, JE and Doudna, JA (2015) Rational design of a split-Cas9 enzyme complex. Proceedings of the National Academy of Sciences of the United States of America 112, 29842989.
Wu, Y, Liang, D, Wang, Y, Bai, M, Tang, W, Bao, S, Yan, Z, Li, D and Li, J (2013) Correction of a genetic disease in mouse via use of CRISPR-Cas9. Cell Stem Cell 13, 659662.
Wu, D, Guan, X, Zhu, Y, Ren, K and Huang, Z (2017) Structural basis of stringent PAM recognition by CRISPR-C2c1 in complex with sgRNA. Cell Research 27, 705708.
Xiong, X, Chen, M, Lim, WA, Zhao, D and Qi, LS (2016) CRISPR/cas9 for human genome engineering and disease research. Annual Review of Genomics and Human Genetics 17, 131154.
Xu, R, Li, H, Qin, R, Wang, L, Li, L, Wei, P and Yang, J (2014) Gene targeting using the Agrobacterium tumefaciens-mediated CRISPR-Cas system in rice. Rice (N Y) 7, 5.
Xu, X, Tao, Y, Gao, X, Zhang, L, Li, X, Zou, W, Ruan, K, Wang, F, Xu, G-L and Hu, R (2016) A CRISPR-based approach for targeted DNA demethylation. Cell Discovery 2, 16009.
Yamada, M, Watanabe, Y, Gootenberg, JS, Hirano, H, Ran, FA, Nakane, T, Ishitani, R, Zhang, F, Nishimasu, H and Nureki, O (2017) Crystal structure of the minimal Cas9 from Campylobacter jejuni reveals the molecular diversity in the CRISPR-Cas9 systems. Molecular Cell 65, 11091121.
Yamano, T, Nishimasu, H, Zetsche, B, Hirano, H, Slaymaker, IM, Li, Y, Fedorova, I, Nakane, T, Makarova, KS, Koonin, EV, Ishitani, R, Zhang, F and Nureki, O (2016) Crystal structure of Cpf1 in complex with guide RNA and target DNA. Cell 165, 949962.
Yamasaki, T, Hoyos-Ramirez, E, Martenson, JS, Morimoto-Tomita, M and Tomita, S (2017) GARLH family proteins stabilize GABAA receptors at synapses. Neuron 93, 11381152.
Yang, H, Wang, H, Shivalila, CS, Cheng, AW, Shi, L and Jaenisch, R (2013) One-Step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell 154, 13701379.
Yang, L, Guell, M, Niu, D, George, H, Lesha, E, Grishin, D, Aach, J, Shrock, E, Xu, W, Poci, J, Cortazio, R, Wilkinson, RA, Fishman, JA and Church, G (2015) Genome-wide inactivation of porcine endogenous retroviruses (PERVs). Science 350, 11011104.
Yang, H, Gao, P, Rajashankar, KR and Patel, DJ (2016) PAM-dependent target DNA recognition and cleavage by C2c1 CRISPR-Cas endonuclease. Cell 167, 18141828.
Yan, WX, Mirzazadeh, R, Garnerone, S, Scott, D, Schneider, MW, Kallas, T, Custodio, J, Wernersson, E, Li, Y, Gao, L, Federova, Y, Zetsche, B, Zhang, F, Bienko, M and Crosetto, N (2017) BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks. Nature Communications 8, 15058.
Yan, S, Tu, Z, Liu, Z, Fan, N, Yang, H, Yang, S, Yang, W, Zhao, Y, Ouyang, Z, Lai, C, Yang, H, Li, L, Liu, Q, Shi, H, Xu, G, Zhao, H, Wei, H, Pei, Z, Li, S, Lai, L and Li, XJ (2018 a) A Huntingtin Knockin Pig model recapitulates features of selective neurodegeneration in Huntington's disease. Cell 173, 9891002.
Yan, WX, Chong, S, Zhang, H, Makarova, KS, Koonin, EV, Cheng, DR and Scott, DA (2018 b) Cas13d Is a compact RNA-targeting type VI CRISPR effector positively modulated by a WYL-domain-containing accessory protein. Molecular Cell 70, 327339.
Yan, WX, Hunnewell, P, Alfonse, LE, Carte, JM, Keston-Smith, E, Sothiselvam, S, Garrity, AJ, Chong, S, Makarova, KS, Koonin, EV, Cheng, DR and Scott, DA (2019) Functionally diverse type V CRISPR-Cas systems. Science 363, 8891.
Zaidi, SS-E-A, Mahfouz, MM and Mansoor, S (2017) CRISPR-Cpf1: a new tool for plant genome editing. Trends in Plant Science 22, 550553.
Zalatan, JG, Lee, ME, Almeida, R, Gilbert, LA, Whitehead, EH, La Russa, M, Tsai, JC, Weissman, JS, Dueber, JE, Qi, LS and Lim, WA (2015) Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160, 339350.
Zetsche, B, Gootenberg, JS, Abudayyeh, OO, Slaymaker, IM, Makarova, KS, Essletzbichler, P, Volz, SE, Joung, J, Van Der Oost, J, Regev, A, Koonin, EV and Zhang, F (2015a) Cpf1 Is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163, 759771.
Zetsche, B, Volz, SE and Zhang, F (2015b) A split-Cas9 architecture for inducible genome editing and transcription modulation. Nature Biotechnology 33, 139142.
Zetsche, B, Heidenreich, M, Mohanraju, P, Fedorova, I, Kneppers, J, Degennaro, EM, Winblad, N, Choudhury, SR, Abudayyeh, OO, Gootenberg, JS, Wu, WY, Scott, DA, Severinov, K, Van Der Oost, J and Zhang, F (2016) Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array. Nature Biotechnology 35, 3134.
Zetsche, B, Strecker, J, Abudayyeh, OO, Gootenberg, JS, Scott, DA and Zhang, F (2017) A survey of genome editing activity for 16 Cpf1 orthologs. bioRxiv.
Zhang, F, Wang, LP, Brauner, M, Liewald, JF, Kay, K, Watzke, N, Wood, PG, Bamberg, E, Nagel, G, Gottschalk, A and Deisseroth, K (2007) Multimodal fast optical interrogation of neural circuitry. Nature 446, 633639.
Zhang, F, Cong, L, Lodato, S, Kosuri, S, Church, GM and Arlotta, P (2011) Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nature Biotechnology 29, 149153.
Zhang, Y, Heidrich, N, Ampattu, BJ, Gunderson, CW, Seifert, HS, Schoen, C, Vogel, J and Sontheimer, EJ (2013) Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Molecular Cell 50, 488503.
Zhang, H, Zhang, J, Wei, P, Zhang, B, Gou, F, Feng, Z, Mao, Y, Yang, L, Zhang, H, Xu, N and Zhu, JK (2014) The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnology Journal 12, 797807.
Zhang, R, Miner, JJ, Gorman, MJ, Rausch, K, Ramage, H, White, JP, Zuiani, A, Zhang, P, Fernandez, E, Zhang, Q, Dowd, KA, Pierson, TC, Cherry, S and Diamond, MS (2016) A CRISPR screen defines a signal peptide processing pathway required by flaviviruses. Nature 535, 164172.
Zhang, S, Takaku, M, Zou, L, Gu, AD, Chou, WC, Zhang, G, Wu, B, Kong, Q, Thomas, SY, Serody, JS, Chen, X, Xu, X, Wade, PA, Cook, DN, Ting, JPY and Wan, YY (2017) Reversing SKI-SMAD4-mediated suppression is essential for TH17 cell differentiation. Nature 551, 105109.
Zhang, B, Ye, W, Ye, Y, Zhou, H, Saeed, AFUH, Chen, J, Lin, J, Perčulija, V, Chen, Q, Chen, C-J, Chang, M-X, Choudhary, MI and Ouyang, S (2018 a) Structural insights into Cas13b-guided CRISPR RNA maturation and recognition. Cell Research 28, 11981201.
Zhang, C, Konermann, S, Brideau, NJ, Lotfy, P, Wu, X, Novick, SJ, Strutzenberg, T, Griffin, PR, Hsu, PD and Lyumkis, D (2018 b) Structural basis for the RNA-guided ribonuclease activity of CRISPR-Cas13d. Cell 175, 212223.
Zhou, Y, Zhu, S, Cai, C, Yuan, P, Li, C, Huang, Y and Wei, W (2014) High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature 509, 487491.
Zhu, S, Li, W, Liu, J, Chen, C-H, Liao, Q, Xu, P, Xu, H, Xiao, T, Cao, Z, Peng, J, Yuan, P, Brown, M, Liu, XS and Wei, W (2016) Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library. Nature Biotechnology 34, 12791286.
Zong, Y, Wang, Y, Li, C, Zhang, R, Chen, K, Ran, Y, Qiu, JL, Wang, D and Gao, C (2017) Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nature Biotechnology 35, 438440.
Zuo, E, Sun, Y, Wei, W, Yuan, T, Ying, W, Sun, H, Yuan, L, Steinmetz, LM, Li, Y and Yang, H (2019) Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science 364, 289292.