High-throughput functional genomics using CRISPR-Cas9

Nature Reviews Genetics

Volumn 16, Issue 5, 2015, Pages 299-311

  Shalem, Ophir ^a,b   Sanjana, Neville E ^a,b   Zhang, Feng ^a,b  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAS9 NUCLEASE; CRISPR ASSOCIATED PROTEIN; GUIDE RNA; NUCLEASE; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CRISPR CAS SYSTEM; DNA REPAIR; FUNCTIONAL GENOMICS; GENE INACTIVATION; GENE TARGETING; HUMAN; LOSS OF FUNCTION MUTATION; PHENOTYPE; PRIORITY JOURNAL; REVIEW; RNA INTERFERENCE; TRANSCRIPTION INITIATION; ANIMAL; BIOLOGICAL MODEL; GENE LIBRARY; GENETIC SCREENING; GENOMICS; HIGH THROUGHPUT SEQUENCING; MOUSE; PROCEDURES;

ANIMALS; CRISPR-CAS SYSTEMS; GENE KNOCKOUT TECHNIQUES; GENE LIBRARY; GENETIC TESTING; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICE; MODELS, GENETIC; RNA INTERFERENCE;

EID: 84928205754     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg3899     Document Type: Review

References (127)

1. Boutros M. & Ahringer J. The art and design of genetic screens: RNA interference. Nature Rev. Genet. 9, 554-566 (2008
2. Kile B. T. & Hilton D. J. The art and design of genetic screens: mouse. Nature Rev. Genet. 6, 557-567 (2005
3. Grimm S. The art and design of genetic screens: mammalian culture cells. Nature Rev. Genet. 5, 179-189 (2004
4. Jorgensen E. M. & Mango S. E. The art and design of genetic screens: Caenorhabditis elegans. Nature Rev. Genet. 3, 356-369 (2002
5. St Johnston D. The art and design of genetic screens: Drosophila melanogaster. Nature Rev. Genet. 3, 176-188 (2002
6. Patton E. E. & Zon L. I. The art and design of genetic screens: zebrafish. Nature Rev. Genet. 2, 956-966 (2001
7. Forsburg S. L. The art and design of genetic screens: yeast. Nature Rev. Genet. 2, 659-668 (2001
8. Page D. R. & Grossniklaus U. The art and design of genetic screens: Arabidopsis thaliana. Nature Rev. Genet. 3, 124-136 (2002
9. Shuman H. A. & Silhavy T. J. The art and design of genetic screens: Escherichia coli. Nature Rev. Genet. 4, 419-431 (2003
10. Sundaram M. V. The love-hate relationship between Ras and Notch. Genes Dev. 19, 1825-1839 (2005
11. Nüsslein-Volhard C., Frohnhöfer H. G. & Lehmann R. Determination of anteroposterior polarity in Drosophila. Science 238, 1675-1681 (1987
12. Nüsslein-Volhard C. & Wieschaus E. Mutations affecting segment number and polarity in Drosophila. Nature 287, 795-801 (1980
13. Driever W., et al. A genetic screen for mutations affecting embryogenesis in zebrafish. Development 123, 37-46 (1996
14. Haffter P., et al. The identification of genes with unique and essential functions in the development of the zebrafish Danio rerio. Development 123, 1-36 (1996
15. Schneeberger K. Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nature Rev. Genet. 15, 662-676 (2014
16. Copeland N. G. & Jenkins N. A. Harnessing transposons for cancer gene discovery. Nature Rev. Cancer 10, 696-706 (2010
17. Dupuy A. J., Akagi K., Largaespada D. A., Copeland N. G. & Jenkins N. A. Mammalian mutagenesis using a highly mobile somatic Sleeping Beauty transposon system. Nature 436, 221-226 (2005
18. Rad R., et al. PiggyBac transposon mutagenesis: a tool for cancer gene discovery in mice. Science 330, 1104-1107 (2010
19. Kotecki M., Reddy P. S. & Cochran B. H. Isolation and characterization of a near-haploid human cell line. Exp. Cell Res. 252, 273-280 (1999
20. Carette J. E., et al. Haploid genetic screens in human cells identify host factors used by pathogens. Science 326, 1231-1235 (2009
21. Guo G., Wang W. & Bradley A. Mismatch repair genes identified using genetic screens in Blm-deficient embryonic stem cells. Nature 429, 891-895 (2004
22. Fire A., et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811 (1998
23. Ketting R. F. The many faces of RNAi. Dev. Cell 20, 148-161 (2011
24. Meister G. & Tuschl T. Mechanisms of gene silencing by double-stranded RNA. Nature 431, 343-349 (2004
25. McManus M. T. & Sharp P. A. Gene silencing in mammals by small interfering RNAs. Nature Rev. Genet. 3, 737-747 (2002
26. Root D. E., Hacohen N., Hahn W. C., Lander E. S. & Sabatini D. M. Genome-scale loss of function screening with a lentiviral RNAi library. Nature Methods 3, 715-719 (2006
27. Silva J. M., et al. Second-generation shRNA libraries covering the mouse and human genomes. Nature Genet. 37, 1281-1288 (2005
28. Chang K., Elledge S. J. & Hannon G. J. Lessons from nature: microRNA-based shRNA libraries. Nature Methods 3, 707-714 (2006
29. Paddison P. J., et al. A resource for large-scale RNA-interference-based screens in mammals. Nature 428, 427-431 (2004
30. Moffat J. & Sabatini D. M. Building mammalian signalling pathways with RNAi screens. Nature Rev. Mol. Cell Biol. 7, 177-187 (2006
31. Berns K., et al. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428, 431-437 (2004
32. Boutros M., et al. Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 303, 832-835 (2004
33. Jackson A. L. & Linsley P. S. Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application. Nature Rev. Drug Discov. 9, 57-67 (2010
34. Birmingham A., et al. 3′ UTR seed matches but not overall identity are associated with RNAi off-targets. Nature Methods 3, 199-204 (2006
35. Jackson A. L., et al. Expression profiling reveals off-target gene regulation by RNAi. Nature Biotech. 21, 635-637 (2003
36. Bolotin A., Quinquis B., Sorokin A. & Ehrlich S. D. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151, 2551-2561 (2005
37. Garneau J. E., et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67-71 (2010
38. Deltcheva E., et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471, 602-607 (2011
39. Sapranauskas R., et al. The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res. 39, 9275-9282 (2011
40. Gasiunas G., Barrangou R., Horvath P. & Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl Acad. Sci. USA 109, E2579-E2586 (2012
41. Jinek M., et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012
42. Cong L., et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823 (2013
43. Mali P., et al. RNA-guided human genome engineering via Cas9. Science 339, 823-826 (2013
44. Shalem O., et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84-87 (2014
45. Wang T., Wei J. J., Sabatini D. M. & Lander E. S. Genetic screens in human cells using the CRISPR-Cas9 system. Science 343, 80-84 (2014
46. Koike-Yusa H., Li Y., Tan E. P., Velasco-Herrera M. D. C. & Yusa K. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nature Biotech. 32, 267-273 (2014
47. Zhou Y., et al. High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature 509, 487-491 (2014
48. Gilbert L. A., et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159, 647-661 (2014
49. Konermann S., et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517, 583-588 (2015
50. Kim H. & Kim J. S. A guide to genome engineering with programmable nucleases. Nature Rev. Genet. 15, 321-334 (2014
51. Hsu P. D., Lander E. S. & Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157, 1262-1278 (2014
52. Rouet P., Smih F. & Jasin M. Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol. Cell. Biol. 14, 8096-8106 (1994
53. Doench J. G., et al. Rational design of highly active sgRNAs for CRISPR-Cas9 mediated gene inactivation. Nature Biotech. 32, 1262-1267 (2014
54. Echeverri C. J. & Perrimon N. High-throughput RNAi screening in cultured cells: a user"s guide. Nature Rev. Genet. 7, 373-384 (2006
55. Mohr S. E., Smith J. A., Shamu C. E., Neumüller R. A. & Perrimon N. RNAi screening comes of age: improved techniques and complementary approaches. Nature Rev. Mol. Cell Biol. 15, 591-600 (2014
56. Schramek D., et al. Direct in vivo RNAi screen unveils myosin IIa as a tumor suppressor of squamous cell carcinomas. Science 343, 309-313 (2014
57. Beronja S., et al. RNAi screens in mice identify physiological regulators of oncogenic growth. Nature 501, 185-190 (2013
58. Zhou P., et al. In vivo discovery of immunotherapy targets in the tumour microenvironment. Nature 506, 52-57 (2014
59. He L. & Hannon G. J. MicroRNAs: small RNAs with a big role in gene regulation. Nature Rev. Genet. 5, 522-531 (2004
60. Maillard P. V., et al. Antiviral RNA interference in mammalian cells. Science 342, 235-238 (2013
61. Li Y., Lu, J., Han Y., Fan X. & Ding S. W. RNA interference functions as an antiviral immunity mechanism in mammals. Science 342, 231-234 (2013
62. Burgess D. J. Small RNAs: antiviral RNAi in mammals. Nature Rev. Genet. 14, 821 (2013
63. Pan Q., van der Laan L. J. W., Janssen H. L. A. & Peppelenbosch M. P. A dynamic perspective of RNAi library development. Trends Biotechnol. 30, 206-215 (2012
64. Qi, L. S., et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173-1183 (2013
65. Larson M. H., et al. CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nature Protoc. 8, 2180-2196 (2013
66. Gilbert L. A., et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154, 442-451 (2013
67. Bikard D., et al. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 41, 7429-7437 (2013
68. Konermann S., et al. Optical control of mammalian endogenous transcription and epigenetic states. Nature 500, 472-476 (2013
69. Yang X., et al. A public genome-scale lentiviral expression library of human ORFs. Nature Methods 8, 659-661 (2011
70. Maeder M. L., et al. CRISPR RNA-guided activation of endogenous human genes. Nature Methods 10, 977-979 (2013
71. Perez-Pinera P., et al. RNA-guided gene activation by CRISPR-Cas9 based transcription factors. Nature Methods 10, 973-976 (2013
72. Cheng A. W., et al. Multiplexed activation of endogenous genes by CRISPR on, an RNA-guided transcriptional activator system. Cell Res. 23, 1163-1171 (2013
73. Mali P., et al. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nature Biotech. 31, 833-838 (2013
74. Tanenbaum M. E., Gilbert L. A., Qi, L. S., Weissman J. S. & Vale R. D. A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159, 635-646 (2014
75. Nishimasu H., et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156, 935-949 (2014
76. Zalatan J. G., et al. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160, 339-350 (2015
77. Bregman A., et al. Promoter elements regulate cytoplasmic mRNA decay. Cell 147, 1473-1483 (2011
78. Trcek T., Larson D. R., Moldón A., Query C. C. & Singer R. H. Single-molecule mRNA decay measurements reveal promoter-regulated mRNA stability in yeast. Cell 147, 1484-1497 (2011
79. Hasson S. A., et al. High-content genome-wide RNAi screens identify regulators of parkin upstream of mitophagy. Nature 504, 291-295 (2013
80. Moffat J., et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124, 1283-1298 (2006
81. Neumann B., et al. High-throughput RNAi screening by time-lapse imaging of live human cells. Nature Methods 3, 385-390 (2006
82. LeProust E. M., et al. Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process. Nucleic Acids Res. 38, 2522-2540 (2010
83. Cleary M. A., et al. Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis. Nature Methods 1, 241-248 (2004
84. Malina A., et al. Repurposing CRISPR/Cas9 for in situ functional assays. Genes Dev. 27, 2602-2614 (2013
85. Zender L., et al. An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer. Cell 135, 852-864 (2008
86. Rudalska R., et al. In vivo RNAi screening identifies a mechanism of sorafenib resistance in liver cancer. Nature Med. 20, 1138-1146 (2014
87. Cheung H. W., et al. Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer. Proc. Natl Acad. Sci. USA 108, 12372-12377 (2011
88. Whitehurst A. W., et al. Synthetic lethal screen identification of chemosensitizer loci in cancer cells. Nature 446, 815-819 (2007
89. Hsu P. D., et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nature Biotech. 31, 827-832 (2013
90. Bassik M. C., et al. Rapid creation and quantitative monitoring of high coverage shRNA libraries. Nature Methods 6, 443-445 (2009
91. Whittaker S. R., et al. A genome-scale RNA interference screen implicates NF1 loss in resistance to RAF inhibition. Cancer Discov. 3, 350-362 (2013
92. Birmingham A., et al. Statistical methods for analysis of high-throughput RNA interference screens. Nature Methods 6, 569-575 (2009
93. Hoffman G. R., et al. Functional epigenetics approach identifies BRM/SMARCA2 as a critical synthetic lethal target in BRG1 deficient cancers. Proc. Natl Acad. Sci. USA 111, 3128-3133 (2014
94. Wu, X., et al. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nature Biotech. 32, 670-676 (2014
95. Bae S., Kweon J., Kim H. S. & Kim J. S. Microhomology-based choice of Cas9 nuclease target sites. Nature Methods 11, 705-706 (2014
96. Hendel A., et al. Quantifying genome-editing outcomes at endogenous loci with SMRT sequencing. Cell Rep. 7, 293-305 (2014
97. Pattanayak V., et al. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nature Biotech. 31, 839-843 (2013
98. Fu, Y., et al. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nature Biotech. 31, 822-826 (2013
99. Lin Y., et al. CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Res. 42, 7473-7485 (2014
100. Sanjana N. E., Shalem O. & Zhang F. Improved vectors and genome-wide libraries for CRISPR screening. Nature Methods 11, 783-784 (2014
101. Veres A., et al. Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. Cell Stem Cell 15, 27-30 (2014
102. Smith C., et al. Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs. Cell Stem Cell 15, 12-13 (2014
103. Frock R. L., et al. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nature Biotech. 33, 179-186 (2015
104. Tsai S. Q., et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nature Biotech. 33, 187-197 (2015
105. Kuscu C., Arslan S., Singh R., Thorpe J. & Adli M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nature Biotech. 32, 677-683 (2014
106. Sternberg S. H., Redding S., Jinek M., Greene E. C. & Doudna J. A. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62-67 (2014
107. Chen B., et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155, 1479-1491 (2013
108. Fu, Y., Sander J. D., Reyon D., Cascio V. M. & Joung J. K. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nature Biotech. 32, 279-284 (2014
109. Ran F. A., et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154, 1380-1389 (2013
110. Jinek M., et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343, 1247997 (2014
111. Ran F. A., et al. In vivo genome editing with Staphylococcus aureus Cas9. Nature (in the press
112. Esvelt K. M., et al. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nature Methods 10, 1116-1121 (2013
113. Qiu S., Adema C. M. & Lane T. A computational study of off-target effects of RNA interference. Nucleic Acids Res. 33, 1834-1847 (2005
114. Buehler E., et al. siRNA off-target effects in genome-wide screens identify signaling pathway members. Sci. Rep. 2, 428 (2012
115. Franceschini A., et al. Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens. Proc. Natl Acad. Sci. USA 111, 4548-4553 (2014
116. Zhong R., et al. Computational detection and suppression of sequence-specific off-target phenotypes from whole genome RNAi screens. Nucleic Acids Res. 42, 8214-8222 (2014
117. Gu S., et al. The loop position of shRNAs and pre-miRNAs is critical for the accuracy of dicer processing in vivo. Cell 151, 900-911 (2012
118. Frank F., Sonenberg N. & Nagar B. Structural basis for 5′ nucleotide base-specific recognition of guide RNA by human AGO2. Nature 465, 818-822 (2010
119. Platt R. J., et al. CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell 159, 440-455 (2014
120. Swiech L., et al. In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9. Nature Biotech. 33, 102-106 (2015
121. Dorsett Y. & Tuschl T. siRNAs: applications in functional genomics and potential as therapeutics. Nature Rev. Drug Discov. 3, 318-329 (2004
122. Bartel D. P. MicroRNAs: genomics biogenesis mechanism and function. Cell 116, 281-297 (2004
123. Wang H., et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153, 910-918 (2013
124. Bassik M. C., et al. A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility. Cell 152, 909-922 (2013
125. Findlay G. M., Boyle E. A., Hause R. J., Klein J. C. & Shendure J. Saturation editing of genomic regions by multiplex homology-directed repair. Nature 513, 120-123 (2014
126. Kellis M., et al. Defining functional DNA elements in the human genome. Proc. Natl Acad. Sci. USA 111, 6131-6138 (2014
127. ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) project. Science 306, 636-640 (2004