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Genome engineering using the CRISPR-Cas9 system
Open accessAbstract
Targeted nucleases are powerful tools for mediating genome alteration with high precision. The RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system can be used to facilitate efficient genome engineering in eukaryotic cells by simply specifying a 20-nt targeting sequence within its guide RNA. Here we describe a set of tools for Cas9-mediated genome editing via nonhomologous end joining (NHEJ) or homology-directed repair (HDR) in mammalian cells, as well as generation of modified cell lines for downstream functional studies. To minimize off-target cleavage, we further describe a double-nicking strategy using the Cas9 nickase mutant with paired guide RNAs. This protocol provides experimentally derived guidelines for the selection of target sites, evaluation of cleavage efficiency and analysis of off-target activity. Beginning with target design, gene modifications can be achieved within as little as 1-2 weeks, and modified clonal cell lines can be derived within 2-3 weeks.
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“Moreover, genome editing technology (e.g. the clustered regularly interspaced short palindromic repeats (CRISPR) technology) promises to be the most important translational perspective in the future [419–421].”
From Cardiovascular disease models: A game changing paradigm in drug discovery and screening (2019) · cites this paper as [421]
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“The third option is the plasmid-based CRISPR/Cas9 system [93]. This is an appealing delivery approach owing to the simplicity and low cost of manipulation.”
From Non-viral delivery systems for CRISPR/Cas9-based genome editing: challenges and opportunities (2018) · cites this paper as [93]
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“Meanwhile, different cell types or targeted genes can also affect the efficiency of the CRISPR/Cas9 system [93, 199].”
From Non-viral delivery systems for CRISPR/Cas9-based genome editing: challenges and opportunities (2018) · cites this paper as [93]
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A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116
Multiplex Genome Engineering Using CRISPR/Cas Systems
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339
Self-citationRNA-Guided Human Genome Engineering via Cas9
Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., & Church, G. M. (2013) · Science · doi:10.1126/science.1232033 · Cited by 9,210
CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A., & Horvath, P. (2007) · Science · doi:10.1126/science.1138140 · Cited by 5,947
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.022 · Cited by 5,016
DNA targeting specificity of RNA-guided Cas9 nucleases
Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., Li, Y., Fine, E. J., Wu, X., Shalem, O., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2647 · Cited by 4,741
Self-citationCRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes
Gilbert, L. A., Larson, M. H., Morsut, L., Liu, Z., Brar, G. A., Torres, S. E., Stern-Ginossar, N., Brandman, O., Whitehead, E. H., Doudna, J. A., et al. (2013) · Cell · doi:10.1016/j.cell.2013.06.044 · Cited by 3,696
Wang, H., Yang, H., Shivalila, C. S., Dawlaty, M. M., Cheng, A. W., Zhang, F., & Jaenisch, R. (2013) · Cell · doi:10.1016/j.cell.2013.04.025 · Cited by 3,495
Self-citationDouble nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity
Ran, F. A., Hsu, P. D., Lin, C.-Y., Gootenberg, J. S., Konermann, S., Trevino, A. E., Scott, D. A., Inoue, A., Matoba, S., Zhang, Y., et al. (2013) · Cell · doi:10.1016/j.cell.2013.08.021 · Cited by 3,299
Self-citationHigh-Frequency off-Target Mutagenesis Induced by CRISPR-Cas Nucleases in Human Cells
Fu, Y., Foden, J. A., Khayter, C., Maeder, M. L., Reyon, D., Joung, J. K., & Sander, J. D. (2013) · Nature Biotechnology · doi:10.1038/nbt.2623 · Cited by 3,292
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Gerin, I., Ury, B., Breloy, I., Bouchet-Séraphin, C., Bolsée, J., Halbout, M., Graff, J., Vertommen, D., Muccioli, G. G., Séta, N., et al. (2016) · Nature Communications · doi:10.1038/ncomms11534 · Cited by 145
RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics
Salzer, E., Cağdaş, D. N., Hons, M., Mace, E. M., Garncarz, W., Petronczki, Ö. Y., Platzer, R., Pfajfer, L., Bilić, I., Ban, S. A., et al. (2016) · Nature Immunology · doi:10.1038/ni.3575 · Cited by 145
Morphogen gradient reconstitution reveals Hedgehog pathway design principles
Li, P., Markson, J. S., Wang, S., Chen, S., Vachharajani, V. T., & Elowitz, M. B. (2018) · Science · doi:10.1126/science.aao0645 · Cited by 141
Dynein–Dynactin–NuMA clusters generate cortical spindle-pulling forces as a multi-arm ensemble
Okumura, M., Natsume, T., Kanemaki, M. T., & Kiyomitsu, T. (2018) · eLife · doi:10.7554/elife.36559 · Cited by 146
Skúlason, S., Parsons, K. J., Svanbäck, R., Räsänen, K., Ferguson, M. M., Adams, C. E., Amundsen, P., Bartels, P., Bean, C. W., BOUGHMAN, J. W., et al. (2019) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12534 · Cited by 145
Lipid-gated monovalent ion fluxes regulate endocytic traffic and support immune surveillance
Freeman, S. A., Uderhardt, S., Sarić, A., Collins, R. F., Buckley, C. M. F., Mylvaganam, S., Boroumand, P., Plumb, J. D., Germain, R. N., Ren, D., et al. (2019) · Science · doi:10.1126/science.aaw9544 · Cited by 141
CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteinsPreprint
Savic, D., Partridge, E. C., Newberry, K. M., Smith, S. B., Meadows, S. K., Roberts, B. S., Mackiewicz, M., Mendenhall, E. M., & Myers, R. (2015) · Genome Research · doi:10.1101/gr.193540.115 · Cited by 141
Diaferia, G. R., Balestrieri, C., Prosperini, E., Nicoli, P., Spaggiari, P., Zerbi, A., & Natoli, G. (2016) · The EMBO Journal · doi:10.15252/embj.201592404 · Cited by 149
Bone morphogenetic protein and retinoic acid synergistically specify female germ‐cell fate in mice
Miyauchi, H., Ohta, H., Nagaoka, S. I., Nakaki, F., Sasaki, K., Hayashi, K., Yabuta, Y., Nakamura, T., Yamamoto, T., & Saitou, M. (2017) · The EMBO Journal · doi:10.15252/embj.201796875 · Cited by 144
Valdez, C., Wong, Y. C., Schwake, M., Bu, G., Wszołek, Z. K., & Krainc, D. (2017) · Human Molecular Genetics · doi:10.1093/hmg/ddx364 · Cited by 148
Delivery of CRISPR/Cas9 for therapeutic genome editing
Xu, X., Wan, T., Xin, H., Li, D., Pan, H., Wu, J., & Ping, Y. (2019) · The Journal of Gene Medicine · doi:10.1002/jgm.3107 · Cited by 134
The endoplasmic reticulum P5A-ATPase is a transmembrane helix dislocase
McKenna, M. J., Sim, S. I., Ordureau, A., Wei, L., Harper, J. W., Shao, S., & Park, E. (2020) · Science · doi:10.1126/science.abc5809 · Cited by 138
Zhang, W., Ma, L., Yang, M., Shao, Q., Xu, J., Lu, Z., Zhao, Z., Chen, R., Chai, Y., & Chen, J. (2020) · Genes & Development · doi:10.1101/gad.332494.119 · Cited by 143
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Sarraf, S. A., Shah, H. V., Kanfer, G., Pickrell, A. M., Holtzclaw, L. A., Ward, M. E., & Youle, R. J. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.10.041 · Cited by 143
Wyvekens, N., Topkar, V. V., Khayter, C., Joung, J. K., & Tsai, S. Q. (2015) · Human Gene Therapy · doi:10.1089/hum.2015.084 · Cited by 147
RYBP stimulates PRC1 to shape chromatin-based communication between Polycomb repressive complexes
Rose, N. R., King, H. W., Blackledge, N. P., Fursova, N. A., Ember, K. J., Fischer, R., Kessler, B. M., & Klose, R. J. (2016) · eLife · doi:10.7554/elife.18591 · Cited by 156
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Kage, F., Winterhoff, M., Dimchev, V., Mueller, J. O., Thalheim, T., Freise, A., Brühmann, S., Kollasser, J., Block, J., Dimchev, G. A., et al. (2017) · Nature Communications · doi:10.1038/ncomms14832 · Cited by 143
Pcdhαc2 is required for axonal tiling and assembly of serotonergic circuitries in mice
Chen, W. V., Nwakeze, C. L., Denny, C. A., O’Keeffe, S., Rieger, M. A., Mountoufaris, G., Kirner, A., Dougherty, J. D., Hen, R., Wu, Q., et al. (2017) · Science · doi:10.1126/science.aal3231 · Cited by 143
Burnight, E. R., Gupta, M., Wiley, L. A., Anfinson, K. R., Tran, A. A., Triboulet, R., Hoffmann, J. M., Klaahsen, D., Andorf, J. L., Jiao, C., et al. (2017) · Molecular Therapy · doi:10.1016/j.ymthe.2017.05.015 · Cited by 153
Guo, T., Feng, Y.-L., Xiao, J., Liu, Q., Sun, X., Xiang, J.-F., Kong, N., Liu, S., Chen, G., Wang, Y., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1518-x · Cited by 151
The hexosamine biosynthesis pathway is a targetable liability in KRAS/LKB1 mutant lung cancer
Kim, J., Lee, H. M., Cai, F., Ko, B., Yang, C., Lieu, E. L., Muhammad, N., Rhyne, S., Li, K., Haloul, M., et al. (2020) · Nature Metabolism · doi:10.1038/s42255-020-00316-0 · Cited by 143
Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions
Martins, R., Maier, J., Gorki, A.-D., Huber, K. V. M., Sharif, O., Starkl, P., Saluzzo, S., Quattrone, F., Gawish, R., Lakovits, K., et al. (2016) · Nature Immunology · doi:10.1038/ni.3590 · Cited by 142
LINE-1 protein localization and functional dynamics during the cell cycle
Mita, P., Wudzinska, A., Sun, X., Andrade, J., Nayak, S., Kahler, D. J., Badri, S., LaCava, J., Ueberheide, B., Yun, C. Y., et al. (2018) · eLife · doi:10.7554/elife.30058 · Cited by 142
Adeno-to-squamous transition drives resistance to KRAS inhibition in LKB1 mutant lung cancer
Tong, X., Patel, A. S., Kim, E., Li, H., Chen, Y., Li, S., Liu, S., Dilly, J., Kapner, K. S., Zhang, N., et al. (2024) · Cancer Cell · doi:10.1016/j.ccell.2024.01.012 · Cited by 142
Distinct Stimulatory Mechanisms Regulate the Catalytic Activity of Polycomb Repressive Complex 2
Lee, C., Holder, M., Grau, D., Saldaña-Meyer, R., Yu, J.-R., Ganai, R. A., Zhang, J., Wang, M., LeRoy, G., Dobenecker, M., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.03.019 · Cited by 150
CRISPR/Cas9 technology as a potent molecular tool for gene therapy
Karimian, A., Azizian, K., Parsian, H., Rafieyan, S., Shafiei‐Irannejad, V., Kheyrollah, M., Yousefi, M., Majidinia, M., & Yousefi, B. (2019) · Journal of Cellular Physiology · doi:10.1002/jcp.27972 · Cited by 148
SIRT7-mediated ATM deacetylation is essential for its deactivation and DNA damage repair
Tang, M., Li, Z., Zhang, C., Lu, X., Tu, B., Cao, Z., Li, Y., Chen, Y., Jiang, L., Wang, H., et al. (2019) · Science Advances · doi:10.1126/sciadv.aav1118 · Cited by 144
Bhattacharya, K., Weidenauer, L., Luengo, T. M., Pieters, E. C., Echeverría, P. C., Bernasconi, L., Wider, D., Sadian, Y., Koopman, M. B., Villemin, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19783-w · Cited by 142
Mianné, J., Chessum, L., Kumar, S., Aguilar, C., Codner, G. F., Hutchison, M., Parker, A. J., Mallon, A., Wells, S. E., Simon, M. M., et al. (2016) · Genome Medicine · doi:10.1186/s13073-016-0273-4 · Cited by 138
Neuronal apolipoprotein E4 increases cell death and phosphorylated tau release in alzheimer disease
Wadhwani, A. R., Affaneh, A., Van Gulden, S., & Kessler, J. A. (2019) · Annals of Neurology · doi:10.1002/ana.25455 · Cited by 142
Banh, R. S., Iorio, C., Marcotte, R., Xu, Y., Cojocari, D., Rahman, A. M. A., Pawling, J., Zhang, W., Sinha, A., Rose, C. M., et al. (2016) · Nature Cell Biology · doi:10.1038/ncb3376 · Cited by 136
An anti-CRISPR protein disables type V Cas12a by acetylation
Dong, L., Guan, X., Li, N., Zhang, F., Zhu, Y., Ren, K., Yu, L., Zhou, F., Han, Z., Gao, N., et al. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0206-1 · Cited by 141
Self-citationTodd, C. D., Deniz, Ö., Taylor, D., & Branco, M. R. (2019) · eLife · doi:10.7554/elife.44344 · Cited by 148
Zhu, P., Wang, Y., Du, Y., He, L., Huang, G., Zhang, G., Yan, X., & Fan, Z. (2015) · Nature Communications · doi:10.1038/ncomms8122 · Cited by 141
Velde, R. V., Yoon, N., Marusyk, V., Durmaz, A., Dhawan, A., Miroshnychenko, D., Lozano‐Peral, D., Desai, B., Balynska, O. V., Poleszczuk, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16212-w · Cited by 141
Park, S.-J., Zhang, D., Qi, Y., Li, Y., Lee, K. Y., Bezzerides, V. J., Yang, P., Xia, S., Kim, S. L., Liu, X., et al. (2019) · Circulation · doi:10.1161/circulationaha.119.039711 · Cited by 140
Heijink, A. M., Talens, F., Jae, L. T., van Gijn, S. E., Fehrmann, R. S. N., Brummelkamp, T. R., & van Vugt, M. A. T. M. (2019) · Nature Communications · doi:10.1038/s41467-018-07927-y · Cited by 140
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Gregersen, L. H., Mitter, R., Ugalde, A. P., Nojima, T., Proudfoot, N. J., Agami, R., Stewart, A., & Svejstrup, J. Q. (2019) · Cell · doi:10.1016/j.cell.2019.04.038 · Cited by 140
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Tanasa, M. P., Imarisio, S., Menzies, F. M., Jiménez-Sánchez, M., Siddiqi, F. H., Wu, X., Renna, M., O’Kane, C. J., Crowther, D. C., & Rubinsztein, D. C. (2016) · Nature Communications · doi:10.1038/ncomms13821 · Cited by 141
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Yao, Z., Darowski, K. D., St‐Denis, N., Wong, V., Offensperger, F., Villedieu, A., Amin, S., Malty, R. H., Aoki, H., Guo, H., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2016.12.004 · Cited by 140
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Schroeder, L. K., Barentine, A. E. S., Merta, H., Schweighofer, S., Zhang, Y., Baddeley, D., Bewersdorf, J., & Bahmanyar, S. (2018) · The Journal of Cell Biology · doi:10.1083/jcb.201809107 · Cited by 140
Hiepen, C., Jatzlau, J., Hildebrandt, S., Kampfrath, B., Goktas, M., Murgai, A., Cuellar‐Camacho, J. L., Haag, R., Ruppert, C., Sengle, G., et al. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000557 · Cited by 148
Kregel, S., Wang, C., Han, X., Xiao, L., Fernández‐Salas, E., Bawa, P., McCollum, B. L., Wilder-Romans, K., Apel, I. J., Cao, X., et al. (2020) · Neoplasia · doi:10.1016/j.neo.2019.12.003 · Cited by 144
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Fugger, K., Bajrami, I., dos Santos, M. S., Young, S. J., Kunzelmann, S., Kelly, G. P., Hewitt, G., Patel, H., Goldstone, R. J., Carell, T., et al. (2021) · Science · doi:10.1126/science.abb4542 · Cited by 141
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Regner, M. J., Wiśniewska, K., García‐Recio, S., Thennavan, A., Méndez-Giráldez, R., Malladi, V. S., Hawkins, G. M., Parker, J. S., Perou, C. M., Bae-Jump, V. L., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.10.013 · Cited by 144
Busch, B., Bley, N., Müller, S., Glaß, M., Misiak, D., Lederer, M., Vetter, M., Strauß, H., Thomssen, C., & Hüttelmaier, S. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw099 · Cited by 139
Vaites, L. P., Paulo, J. A., Huttlin, E. L., & Harper, J. W. (2018) · Molecular and Cellular Biology · doi:10.1128/mcb.00392-17 · Cited by 120
Zheng, P., Chen, Q., Tian, X., Qian, N., Chai, P., Liu, B., Hu, J., Blackstone, C. D., Zhu, D., Teng, J., et al. (2018) · Cell Research · doi:10.1038/s41422-018-0065-z · Cited by 144
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Jang, M., Park, R., Kim, H.-J., Namkoong, S., Jo, D., Huh, Y. H., Jang, I., Lee, J. I., & Park, J. (2018) · Scientific Reports · doi:10.1038/s41598-018-30977-7 · Cited by 143
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Williamson, I., Kane, L., Devenney, P. S., Flyamer, I. M., Anderson, E., Kilanowski, F. M., Hill, R. E., Bickmore, W. A., & Lettice, L. A. (2019) · Development · doi:10.1242/dev.179523 · Cited by 148
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Zhang, X., Chen, L., Zhu, B., Wang, L., Chen, C., Hong, M., Huang, Y., Li, H., Han, H., Cai, B., et al. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-0518-8 · Cited by 141
Leary, N., Walser, S., He, Y., Cousin, N., Pereira, P., Gallo, A., Collado‐Díaz, V., Halin, C., Garcı́a-Silva, S., Peinado, H., et al. (2022) · Journal of Extracellular Vesicles · doi:10.1002/jev2.12197 · Cited by 142
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Xie, Y., Chai, P., Till, N. A., Hemberger, H., Lebedenko, C. G., Porat, J., Watkins, C. P., Caldwell, R. M., George, B. M., Perr, J., et al. (2024) · Cell · doi:10.1016/j.cell.2024.07.044 · Cited by 139
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Kiesgen, S., Messinger, J. C., Chintala, N. K., Tano, Z., & Adusumilli, P. S. (2021) · Nature Protocols · doi:10.1038/s41596-020-00467-0 · Cited by 138
Neggers, J. E., Vercruysse, T., Jacquemyn, M., Vanstreels, E., Baloglu, E., Shacham, S., Crochiere, M. L., Landesman, Y., & Daelemans, D. (2015) · Chemistry & Biology · doi:10.1016/j.chembiol.2014.11.015 · Cited by 139
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Ding, X., Chaudhuri, A. R., Callén, E., Pang, Y., Biswas, K., Klarmann, K. D., Martin, B. K., Burkett, S. S., Cleveland, L., Stauffer, S., et al. (2016) · Nature Communications · doi:10.1038/ncomms12425 · Cited by 140
Zhao, X., Liu, L., Lang, J., Cheng, K., Wang, Y., Li, X., Shi, J. Y., Wang, Y., & Nie, G. (2018) · Cancer Letters · doi:10.1016/j.canlet.2018.05.042 · Cited by 139
Li, L., Tian, E., Chen, X., Chao, J., Klein, J. A., Qu, Q., Sun, G., Sun, G., Huang, Y., Warden, C., et al. (2018) · Cell stem cell · doi:10.1016/j.stem.2018.07.009 · Cited by 139
Determining cellular CTCF and cohesin abundances to constrain 3D genome models
Cattoglio, C., Pustova, I., Walther, N., Ho, J. J., Hantsche-Grininger, M., Inouye, C. J., Hossain, M. J., Dailey, G. M., Ellenberg, J., Darzacq, X., et al. (2019) · eLife · doi:10.7554/elife.40164 · Cited by 133
TTC5 mediates autoregulation of tubulin via mRNA degradation
Lin, Z., Gasic, I., Chandrasekaran, V., Peters, N., Shao, S., Mitchison, T. J., & Hegde, R. S. (2019) · Science · doi:10.1126/science.aaz4352 · Cited by 138
Mejhert, N., Kuruvilla, L., Gabriel, K. R., Elliott, S. D., Guie, M.-A., Wang, H., Lai, Z. W., Lane, E. A., Christiano, R., Danial, N. N., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.01.014 · Cited by 121
AMPylation matches BiP activity to client protein load in the endoplasmic reticulum
Preißler, S., Rato, C., Chen, R., Antrobus, R., Ding, S., Fearnley, I. M., & Ron, D. (2015) · eLife · doi:10.7554/elife.12621 · Cited by 134
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Fernando, T. R., Contreras, J. R., Zampini, M., Rodriguez-Malave, N. I., Alberti, M. O., Anguiano, J., Tran, T. M., Palanichamy, J. K., Gajeton, J., Ung, N. M., et al. (2017) · Molecular Cancer · doi:10.1186/s12943-017-0692-x · Cited by 141
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Hung, K. L., Meitlis, I., Hale, M. R., Chen, C., Singh, S., Jackson, S. W., Miao, C. H., Khan, I., Rawlings, D. J., & James, R. G. (2017) · Molecular Therapy · doi:10.1016/j.ymthe.2017.11.012 · Cited by 140
Violante, S. N., Achetib, N., van Roermund, C. W. T., Hagen, J., Dodatko, T., Vaz, F. M., Waterham, H. R., Chen, H., Baes, M. I., Yu, C., et al. (2018) · The FASEB Journal · doi:10.1096/fj.201801498r · Cited by 139
Genetics, Mechanisms, and Therapeutic Progress in Polyglutamine Spinocerebellar Ataxias
Buijsen, R. A. M., Toonen, L. J. A., Gardiner, S. L., & van Roon‐Mom, W. (2019) · Neurotherapeutics · doi:10.1007/s13311-018-00696-y · Cited by 143
Microhomologies are prevalent at Cas9-induced larger deletions
Owens, D. D. G., Caulder, A., Frontera, V., Harman, J. R., Allan, A. J., Bucakci, A., Greder, L., Codner, G. F., Hublitz, P., McHugh, P. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz459 · Cited by 136
Kuechler, A., Zink, A. M., Wieland, T., Lüdecke, H.-J., Cremer, K., Salviati, L., Magini, P., Najafi, K., Zweier, C., Czeschik, J. C., et al. (2014) · European Journal of Human Genetics · doi:10.1038/ejhg.2014.165 · Cited by 140
DND1 maintains germline stem cells via recruitment of the CCR4–NOT complex to target mRNAs
Yamaji, M., Jishage, M., Meyer, C., Suryawanshi, H., Der, E. B., Yamaji, M., Garzia, A., Morozov, P. S., Manickavel, S., McFarland, H. L., et al. (2017) · Nature · doi:10.1038/nature21690 · Cited by 136
Fan, Y., & Lin, X. (2018) · Genetics · doi:10.1534/genetics.117.300656 · Cited by 136
Mitigating off-target effects in CRISPR/Cas9-mediated in vivo gene editing
Han, H. A., Pang, J. K. S., & Soh, B.-S. (2020) · Journal of Molecular Medicine · doi:10.1007/s00109-020-01893-z · Cited by 134
Allosteric Activation Dictates PRC2 Activity Independent of Its Recruitment to Chromatin
Lee, C., Yu, J.-R., Kumar, S., Jin, Y., LeRoy, G., Bhanu, N. V., Kaneko, S., Garcia, B. A., Hamilton, A. D., & Reinberg, D. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.03.020 · Cited by 140
Wu, H., Yang, H., Rhee, J., Zhang, J. Z., Lam, C. K., Sallam, K., Chang, A. C. Y., Ma, N., Lee, J., Zhang, H., et al. (2019) · European Heart Journal · doi:10.1093/eurheartj/ehz326 · Cited by 135
Lou, F., Sun, Y., Xu, Z., Niu, L., Wang, Z., Deng, S., Liu, Z., Zhou, H., Bai, J., Yin, Q., et al. (2020) · Immunity · doi:10.1016/j.immuni.2020.06.004 · Cited by 135
Systematic quantitative analysis of ribosome inventory during nutrient stress
An, H., Ordureau, A., Körner, M., Paulo, J. A., & Harper, J. W. (2020) · Nature · doi:10.1038/s41586-020-2446-y · Cited by 136
Programmable RNA sensing for cell monitoring and manipulation
Qian, Y., Li, J., Zhao, S., Matthews, E. A., Adoff, M., Zhong, W., An, X., Yeo, M., Park, C., Yang, X., et al. (2022) · Nature · doi:10.1038/s41586-022-05280-1 · Cited by 137
Generation and validation of homozygous fluorescent knock-in cells using CRISPR-Cas9 genome editing
Koch, B., Nijmeijer, B., Kueblbeck, M., Cai, Y., Walther, N., & Ellenberg, J. (2018) · Nature Protocols · doi:10.1038/nprot.2018.042 · Cited by 134
TPC2 controls pigmentation by regulating melanosome pH and size
Ambrosio, A. L., Boyle, J. A., Aradi, A., Christian, K. A., & Pietro, S. M. D. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1600108113 · Cited by 141
Kang, Y., Stroud, D. A., Baker, M. J., Souza, D. P. D., Frazier, A. E., Liem, M. K., Tull, D., Mathivanan, S., McConville, M. J., Thorburn, D. R., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.06.014 · Cited by 132
Cryo-EM structure of a mitochondrial calcium uniporter
Yoo, J., Wu, M., Yin, Y., Herzik, M. A., Lander, G. C., & Lee, S. (2018) · Science · doi:10.1126/science.aar4056 · Cited by 134
RIG-I activation is critical for responsiveness to checkpoint blockade
Heidegger, S. M., Wintges, A., Stritzke, F., Bek, S., Steiger, K., Koenig, P.-A., Göttert, S., Engleitner, T., Öllinger, R., Nedelko, T., et al. (2019) · Science Immunology · doi:10.1126/sciimmunol.aau8943 · Cited by 136
Mowat, C., Mosley, S. R., Namdar, A., Schiller, D., & Baker, K. (2021) · The Journal of Experimental Medicine · doi:10.1084/jem.20210108 · Cited by 129
Miura, H., Gurumurthy, C. B., Sato, T., Sato, M., & Ohtsuka, M. (2015) · Scientific Reports · doi:10.1038/srep12799 · Cited by 133
Nanomedicine-mediated cancer stem cell therapy
Shen, S., Xia, J., & Wang, J. (2015) · Biomaterials · doi:10.1016/j.biomaterials.2015.09.037 · Cited by 132
GARLH Family Proteins Stabilize GABAA Receptors at Synapses
Yamasaki, T., Hoyos, E., Martenson, J. S., Morimoto‐Tomita, M., & Tomita, S. (2017) · Neuron · doi:10.1016/j.neuron.2017.02.023 · Cited by 135
Shi, T., Gao, J., Wang, W., Wang, K., Xu, G., Huang, H., & Ji, X. (2019) · ACS Synthetic Biology · doi:10.1021/acssynbio.8b00478 · Cited by 133
Bi-allelic Mutations in TTC21A Induce Asthenoteratospermia in Humans and Mice
Liu, W., He, X., Yang, S., Zouari, R., Wang, J., Wu, H., Kherraf, Z., Liu, C., Coutton, C., Zhao, R., et al. (2019) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2019.02.020 · Cited by 133
Self-citationTanaka, Y., Shimanaka, Y., Caddeo, A. M., Kubo, T., Mao, Y., Kubota, T., Kubota, N., Yamauchi, T., Mancina, R. M., Baselli, G., et al. (2020) · Gut · doi:10.1136/gutjnl-2020-320646 · Cited by 134
Kalbasi, A. K., Tariveranmoshabad, M., Hakimi, K. N., Kremer, S. V., Campbell, K. M., Funes, J. M., Vega-Crespo, A., Parisi, G., Champhekar, A. S., Nguyen, C., et al. (2020) · Science Translational Medicine · doi:10.1126/scitranslmed.abb0152 · Cited by 136
Massively parallel functional testing of MSH2 missense variants conferring Lynch syndrome risk
Jia, X., Burugula, B. B., Chen, V., Lemons, R. M., Jayakody, S., Maksutova, M., & Kitzman, J. O. (2020) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2020.12.003 · Cited by 141
A RhoA–YAP–c-Myc signaling axis promotes the development of polycystic kidney diseasePreprint
Cai, J., Song, X., Wang, W., Watnick, T. J., Pei, Y., Qian, F., & Pan, D. (2018) · Genes & Development · doi:10.1101/gad.315127.118 · Cited by 127
Choi, S., Jeong, H.-J., Kim, H., Choi, D., Cho, S.-C., Seong, J. K., Koo, S.-H., & Kang, J.-S. (2019) · Autophagy · doi:10.1080/15548627.2019.1569931 · Cited by 132
Differentiation of hypothalamic-like neurons from human pluripotent stem cells
Wang, L., Meece, K., Williams, D. J., Lo, K. A., Zimmer, M., Heinrich, G., Carli, J. F. M., LeDuc, C. A., Sun, L., Zeltser, L. M., et al. (2015) · Journal of Clinical Investigation · doi:10.1172/jci79220 · Cited by 131
Sluch, V. M., Chamling, X., Liu, M. M., Berlinicke, C. A., Cheng, J., Mitchell, K. L., Welsbie, D. S., & Zack, D. J. (2017) · Stem Cells Translational Medicine · doi:10.1002/sctm.17-0059 · Cited by 130
Helsley, R. N., Varadharajan, V., Brown, A. L., Gromovsky, A. D., Schugar, R. C., Ramachandiran, I., Fung, K., Kabbany, M. N., Banerjee, R., Neumann, C. K. A., et al. (2019) · eLife · doi:10.7554/elife.49882 · Cited by 129
Haltenhof, T., Kotte, A., Bortoli, F. D., Schiefer, S., Meinke, S., Emmerichs, A., Petermann, K. K., Timmermann, B., Imhof, P., Franz, A., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.01.028 · Cited by 132
Unconventional initiation of PINK1/Parkin mitophagy by Optineurin
Nguyen, T. N., Sawa-Makarska, J. Z., Khuu, G., Lam, W. K., Adriaenssens, E., Fracchiolla, D., Shoebridge, S., Bernklau, D., Padman, B. S., Skulsuppaisarn, M., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.04.021 · Cited by 138
A cell-intrinsic role for TLR2–MYD88 in intestinal and breast epithelia and oncogenesis
Scheeren, F. A., Kuo, A. H., van Weele, L. J., Cai, S., Glykofridis, I. E., Sikandar, S. S., Zabala, M., Qian, D., Lam, J. S., Johnston, D. M., et al. (2014) · Nature Cell Biology · doi:10.1038/ncb3058 · Cited by 132
Removal of Integrated Hepatitis B Virus DNA Using CRISPR-Cas9
Li, H., Sheng, C., Wang, S., Yang, L., Liang, Y., Huang, Y., Liu, H., Li, P., Yang, C., Yang, X., et al. (2017) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2017.00091 · Cited by 131
Metadata
- Authors
- Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., & Zhang, F.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Zhang, Feng
- Venue
- Nature Protocols
- Published
- 2013-10-24
- Volume
- 8
- Issue
- 11
- Pages
- 2281-2308
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- PMC
- PMC3969860
- OpenAlex
- W1977709885
- Cited by
- 11,133
- References
- 76
- Citations by year
- 2026: 586 · 2025: 971 · 2024: 1018 · 2023: 1029 · 2022: 1148 · 2021: 1242 · 2020: 1232 · 2019: 1130 · 2018: 974 · 2017: 804 · 2016: 566 · 2015: 289 · 2014: 137 · 2013: 1
- FWCI
- 148.15
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Protocols (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Science Foundation (T32GM007753)
- Damon Runyon Cancer Research Foundation
- Fund for Astrophysical Research
- McKnight Foundation
- National Institutes of Health (R01‐grant)
- National Institute of Mental Health (DP1MH100706)
- National Institute of General Medical Sciences (T32GM008313, T32GM007753)
- National Institute of Diabetes and Digestive and Kidney Diseases (F32DK096822, R01DK097768, 1R01-DK097768)
- National Center for Chronic Disease Prevention and Health Promotion (1DP1-MH100706)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
- Keywords
- CRISPR/Cas9, genome editing, guide RNA design, Cas9 nickase, off-target cleavage, non-homologous end joining, homology-directed repair, target site selection, cleavage efficiency, mammalian cells
- MeSH terms
- Base Sequence, Cell Line, Deoxyribonucleases, DNA Mutational Analysis, DNA Repair, Genetic Engineering, Humans, Molecular Sequence Data, Transfection, Mutagenesis, Genome, Cell Culture Techniques, HEK293 Cells, DNA End-Joining Repair, Genotyping Techniques, Clustered Regularly Interspaced Short Palindromic Repeats
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