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Archives of Pharmacal Research

, Volume 41, Issue 9, pp 875–884 | Cite as

High-throughput genetic screens using CRISPR–Cas9 system

  • Jiyeon Kweon
  • Yongsub Kim
Review

Abstract

The CRISPR–Cas9 system is a powerful tool for genome engineering, and its programmability and simplicity have enabled various types of gene manipulation such as gene disruption and transcriptional and epigenetic perturbation. Particularly, CRISPR-based pooled libraries facilitate high-throughput screening for functional regulatory elements in the human genome. In this review, we describe recent advances in CRISPR–Cas9 technology and its use in high-throughput genetic screening. We also discuss its potential for drug target discovery and current challenges of this technique in biomedical research.

Keywords

CRISPR–Cas9 system Genome engineering High-throughput screening Pooled CRISPR screens 

Notes

Acknowledgements

This work was supported by the National Research Foundation of Korea (Y.K., NRF-2016R1D1A1A02937096, J.K., NRF-2016R1A6A3A04009014) and a grant of the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (Y.K., HI17C0337).

Compliance with ethical standards

Conflict of interest

The authors declare no competing financial interests.

References

  1. Adamson B, Norman TM, Jost M, Cho MY, Nunez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS (2016) A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response. Cell 167(1867–1882):e21Google Scholar
  2. Bibikova M, Beumer K, Trautman JK, Carroll D (2003) Enhancing gene targeting with designed zinc finger nucleases. Science 300:764CrossRefPubMedGoogle Scholar
  3. Boehm JS, Hahn WC (2011) Towards systematic functional characterization of cancer genomes. Nat Rev Genet 12:487–498CrossRefPubMedGoogle Scholar
  4. 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 GC, Zhang F, Orkin SH, Bauer DE (2015) BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature 527:192–197CrossRefPubMedPubMedCentralGoogle Scholar
  5. Carpenter AE, Sabatini DM (2004) Systematic genome-wide screens of gene function. Nat Rev Genet 5:11–22CrossRefPubMedGoogle Scholar
  6. Chavez A, Scheiman J, Vora S, Pruitt BW, Tuttle M, Iyer EP, Lin S, Kiani S, Guzman CD, Wiegand DJ, Ter-Ovanesyan D, Braff JL, Davidsohn N, Housden BE, Perrimon N, Weiss R, Aach J, Collins JJ, Church GM (2015) Highly efficient Cas9-mediated transcriptional programming. Nat Methods 12:326–328CrossRefPubMedPubMedCentralGoogle Scholar
  7. Cho SW, Kim S, Kim JM, Kim JS (2013) Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol 31:230–232CrossRefPubMedGoogle Scholar
  8. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823CrossRefPubMedPubMedCentralGoogle Scholar
  9. Consortium EP (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74CrossRefGoogle Scholar
  10. Dahlman JE, Abudayyeh OO, Joung J, Gootenberg JS, Zhang F, Konermann S (2015) Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease. Nat Biotechnol 33:1159–1161CrossRefPubMedPubMedCentralGoogle Scholar
  11. Diaz AA, Qin H, Ramalho-Santos M, Song JS (2015) HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis. Nucleic Acids Res 43:e16CrossRefPubMedGoogle Scholar
  12. 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, Regev A (2016) Perturb-Seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell 167(1853–1866):e17Google Scholar
  13. Doench JG (2018) Am I ready for CRISPR? A user’s guide to genetic screens. Nat Rev Genet 19:67–80CrossRefPubMedGoogle Scholar
  14. Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R, Virgin HW, Listgarten J, Root DE (2016) Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR–Cas9. Nat Biotechnol 34:184–191CrossRefPubMedPubMedCentralGoogle Scholar
  15. Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR (2017) Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage. Nature 551:464–471CrossRefPubMedPubMedCentralGoogle Scholar
  16. 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, Qi LS (2013) CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154:442–451CrossRefPubMedPubMedCentralGoogle Scholar
  17. Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC, Qi LS, Kampmann M, Weissman JS (2014) Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159:647–661CrossRefPubMedPubMedCentralGoogle Scholar
  18. Han K, Jeng EE, Hess GT, Morgens DW, Li A, Bassik MC (2017) Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions. Nat Biotechnol 35:463–474CrossRefPubMedPubMedCentralGoogle Scholar
  19. Hannon GJ (2002) RNA interference. Nature 418:244–251CrossRefPubMedGoogle Scholar
  20. Hart T, Moffat J (2016) BAGEL: a computational framework for identifying essential genes from pooled library screens. BMC Bioinform 17:164CrossRefGoogle Scholar
  21. 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, Moffat J (2015) High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell 163:1515–1526CrossRefPubMedGoogle Scholar
  22. 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, Moffat J (2017) Evaluation and design of genome-wide CRISPR/SpCas9 knockout screens. G3 (Bethesda) 7:2719–2727CrossRefGoogle Scholar
  23. Heigwer F, Zhan T, Breinig M, Winter J, Brugemann D, Leible S, Boutros M (2016) CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries. Genome Biol 17:55CrossRefPubMedPubMedCentralGoogle Scholar
  24. Hess GT, Fresard L, Han K, Lee CH, Li A, Cimprich KA, Montgomery SB, Bassik MC (2016) Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells. Nat Methods 13:1036–1042CrossRefPubMedPubMedCentralGoogle Scholar
  25. Hilton IB, Dippolito AM, Vockley CM, Thakore PI, Crawford GE, Reddy TE, Gersbach CA (2015) Epigenome editing by a CRISPR–Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol 33:510–517CrossRefPubMedPubMedCentralGoogle Scholar
  26. Horlbeck MA, Gilbert LA, Villalta JE, Adamson B, Pak RA, Chen Y, Fields AP, Park CY, Corn JE, Kampmann M, Weissman JS (2016) Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. Elife.  https://doi.org/10.7554/eLife.19760 Google Scholar
  27. Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, Joung JK (2013) Efficient genome editing in zebrafish using a CRISPR–Cas system. Nat Biotechnol 31:227–229CrossRefPubMedPubMedCentralGoogle Scholar
  28. Jaitin DA, Weiner A, Yofe I, Lara-Astiaso D, Keren-Shaul H, David E, Salame TM, Tanay A, Van Oudenaarden A, Amit I (2016) Dissecting immune circuits by linking CRISPR-pooled screens with single-cell RNA-Seq. Cell 167(1883–1896):e15Google Scholar
  29. Jeong HH, Kim SY, Rousseaux MWC, Zoghbi HY, Liu Z (2017) CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution. Bioinformatics 33:2963–2965CrossRefPubMedGoogle Scholar
  30. Joung J, Engreitz JM, Konermann S, Abudayyeh OO, Verdine VK, Aguet F, Gootenberg JS, Sanjana NE, Wright JB, Fulco CP, Tseng YY, Yoon CH, Boehm JS, Lander ES, Zhang F (2017a) Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood. Nature 548:343–346CrossRefPubMedPubMedCentralGoogle Scholar
  31. Joung J, Konermann S, Gootenberg JS, Abudayyeh OO, Platt RJ, Brigham MD, Sanjana NE, Zhang F (2017b) Genome-scale CRISPR–Cas9 knockout and transcriptional activation screening. Nat Protoc 12:828–863CrossRefPubMedPubMedCentralGoogle Scholar
  32. Kaelin WG Jr (2012) Molecular biology. Use and abuse of RNAi to study mammalian gene function. Science 337:421–422CrossRefPubMedPubMedCentralGoogle Scholar
  33. Kearns NA, Pham H, Tabak B, Genga RM, Silverstein NJ, Garber M, Maehr R (2015) Functional annotation of native enhancers with a Cas9-histone demethylase fusion. Nat Methods 12:401–403CrossRefPubMedPubMedCentralGoogle Scholar
  34. Kim Y, Kweon J, Kim A, Chon JK, Yoo JY, Kim HJ, Kim S, Lee C, Jeong E, Chung E, Kim D, Lee MS, Go EM, Song HJ, Kim H, Cho N, Bang D, Kim S, Kim JS (2013a) A library of TAL effector nucleases spanning the human genome. Nat Biotechnol 31:251–258CrossRefPubMedGoogle Scholar
  35. Kim Y, Kweon J, Kim JS (2013b) TALENs and ZFNs are associated with different mutation signatures. Nat Methods 10:185CrossRefPubMedGoogle Scholar
  36. Kim K, Ryu SM, Kim ST, Baek G, Kim D, Lim K, Chung E, Kim S, Kim JS (2017) Highly efficient RNA-guided base editing in mouse embryos. Nat Biotechnol 35:435–437CrossRefPubMedGoogle Scholar
  37. Klann TS, Black JB, Chellappan M, Safi A, Song L, Hilton IB, Crawford GE, Reddy TE, Gersbach CA (2017) CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome. Nat Biotechnol 35:561–568CrossRefPubMedPubMedCentralGoogle Scholar
  38. Koike-Yusa H, Li Y, Tan EP, Velasco-Herrera Mdel C, Yusa K (2014) Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nat Biotechnol 32:267–273CrossRefPubMedGoogle Scholar
  39. Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR (2016) Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533:420–424CrossRefPubMedPubMedCentralGoogle Scholar
  40. Konermann S, Brigham MD, Trevino AE, Joung J, Abudayyeh OO, Barcena C, Hsu PD, Habib N, Gootenberg JS, Nishimasu H, Nureki O, Zhang F (2015) Genome-scale transcriptional activation by an engineered CRISPR–Cas9 complex. Nature 517:583–588CrossRefPubMedGoogle Scholar
  41. Korkmaz G, Lopes R, Ugalde AP, Nevedomskaya E, Han R, Myacheva K, Zwart W, Elkon R, Agami R (2016) Functional genetic screens for enhancer elements in the human genome using CRISPR–Cas9. Nat Biotechnol 34:192–198CrossRefPubMedGoogle Scholar
  42. Kweon J, Jang AH, Kim DE, Yang JW, Yoon M, Rim Shin H, Kim JS, Kim Y (2017) Fusion guide RNAs for orthogonal gene manipulation with Cas9 and Cpf1. Nat Commun 8:1723CrossRefPubMedPubMedCentralGoogle Scholar
  43. Kwon DY, Zhao YT, Lamonica JM, Zhou Z (2017) Locus-specific histone deacetylation using a synthetic CRISPR–Cas9-based HDAC. Nat Commun 8:15315CrossRefPubMedPubMedCentralGoogle Scholar
  44. Lei Y, Zhang X, Su J, Jeong M, Gundry MC, Huang YH, Zhou Y, Li W, Goodell MA (2017) Targeted DNA methylation in vivo using an engineered dCas9–MQ1 fusion protein. Nat Commun 8:16026CrossRefPubMedPubMedCentralGoogle Scholar
  45. Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu XS (2014) MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol 15:554CrossRefPubMedPubMedCentralGoogle Scholar
  46. Li W, Koster J, Xu H, Chen CH, Xiao T, Liu JS, Brown M, Liu XS (2015) Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR. Genome Biol 16:281CrossRefPubMedPubMedCentralGoogle Scholar
  47. List M, Schmidt S, Christiansen H, Rehmsmeier M, Tan Q, Mollenhauer J, Baumbach J (2016) Comprehensive analysis of high-throughput screens with HiTSeekR. Nucleic Acids Res 44:6639–6648CrossRefPubMedPubMedCentralGoogle Scholar
  48. Liu XS, Wu H, Ji X, Stelzer Y, Wu X, Czauderna S, Shu J, Dadon D, Young RA, Jaenisch R (2016) Editing DNA methylation in the mammalian genome. Cell 167(233–247):e17Google Scholar
  49. 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, Lim DA (2017) CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science 355:7111CrossRefGoogle Scholar
  50. Long L, Guo H, Yao D, Xiong K, Li Y, Liu P, Zhu Z, Liu D (2015) Regulation of transcriptionally active genes via the catalytically inactive Cas9 in C. elegans and D. rerio. Cell Res 25:638–641CrossRefPubMedPubMedCentralGoogle Scholar
  51. Ma H, Dang Y, Wu Y, Jia G, Anaya E, Zhang J, Abraham S, Choi JG, Shi G, Qi L, Manjunath N, Wu H (2015) A CRISPR-based screen identifies genes essential for West-Nile-Virus-induced cell death. Cell Rep 12:673–683CrossRefPubMedPubMedCentralGoogle Scholar
  52. Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T (2016a) Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol 34:528–530CrossRefPubMedPubMedCentralGoogle Scholar
  53. Ma Y, Zhang J, Yin W, Zhang Z, Song Y, Chang X (2016b) Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells. Nat Methods 13:1029–1035CrossRefPubMedGoogle Scholar
  54. Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, Joung JK (2013) CRISPR RNA-guided activation of endogenous human genes. Nat Methods 10:977–979CrossRefPubMedPubMedCentralGoogle Scholar
  55. Mali P, Yang L, Esvelt KM, Aach J, Guell M, Dicarlo JE, Norville JE, Church GM (2013) RNA-guided human genome engineering via Cas9. Science 339:823–826CrossRefPubMedPubMedCentralGoogle Scholar
  56. 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, Haining WN (2017) In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target. Nature 547:413–418CrossRefPubMedPubMedCentralGoogle Scholar
  57. Meier JA, Zhang F, Sanjana NE (2017) GUIDES: sgRNA design for loss-of-function screens. Nat Methods 14:831–832CrossRefPubMedPubMedCentralGoogle Scholar
  58. Miller JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ, Dulay GP, Hua KL, Ankoudinova I, Cost GJ, Urnov FD, Zhang HS, Holmes MC, Zhang L, Gregory PD, Rebar EJ (2011) A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29:143–148CrossRefPubMedGoogle Scholar
  59. Mohr SE, Smith JA, Shamu CE, Neumuller RA, Perrimon N (2014) RNAi screening comes of age: improved techniques and complementary approaches. Nat Rev Mol Cell Biol 15:591–600CrossRefPubMedPubMedCentralGoogle Scholar
  60. Najm FJ, Strand C, Donovan KF, Hegde M, Sanson KR, Vaimberg EW, Sullender ME, Hartenian E, Kalani Z, Fusi N, Listgarten J, Younger ST, Bernstein BE, Root DE, Doench JG (2017) Orthologous CRISPR–Cas9 enzymes for combinatorial genetic screens. Nat Biotechnol 36:179CrossRefPubMedPubMedCentralGoogle Scholar
  61. Pan D, Kobayashi A, Jiang P, Ferrari De Andrade L, Tay RE, Luoma A, Tsoucas D, Qiu X, Lim K, Rao P, Long HW, Yuan GC, Doench J, Brown M, Liu S, Wucherpfennig KW (2018) A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science.  https://doi.org/10.1126/science.aao1710 PubMedCentralGoogle Scholar
  62. Park DS, Yoon M, Kweon J, Jang AH, Kim Y, Choi SC (2017a) Targeted base editing via RNA-guided cytidine deaminases in Xenopus laevis embryos. Mol Cells 40:823–827PubMedPubMedCentralGoogle Scholar
  63. 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, Walker BD (2017b) A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors. Nat Genet 49:193–203CrossRefPubMedGoogle Scholar
  64. 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, Restifo NP (2017) Identification of essential genes for cancer immunotherapy. Nature 548:537–542CrossRefPubMedPubMedCentralGoogle Scholar
  65. Perez AR, Pritykin Y, Vidigal JA, Chhangawala S, Zamparo L, Leslie CS, Ventura A (2017) GuideScan software for improved single and paired CRISPR guide RNA design. Nat Biotechnol 35:347–349CrossRefPubMedPubMedCentralGoogle Scholar
  66. 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, Gersbach CA (2013) RNA-guided gene activation by CRISPR–Cas9-based transcription factors. Nat Methods 10:973–976CrossRefPubMedPubMedCentralGoogle Scholar
  67. Porteus MH, Baltimore D (2003) Chimeric nucleases stimulate gene targeting in human cells. Science 300:763CrossRefPubMedGoogle Scholar
  68. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152:1173–1183CrossRefPubMedPubMedCentralGoogle Scholar
  69. Sanjana NE, Shalem O, Zhang F (2014) Improved vectors and genome-wide libraries for CRISPR screening. Nat Methods 11:783–784CrossRefPubMedPubMedCentralGoogle Scholar
  70. Sanjana NE, Wright J, Zheng K, Shalem O, Fontanillas P, Joung J, Cheng C, Regev A, Zhang F (2016) High-resolution interrogation of functional elements in the noncoding genome. Science 353:1545–1549CrossRefPubMedPubMedCentralGoogle Scholar
  71. Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelson T, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F (2014) Genome-scale CRISPR–Cas9 knockout screening in human cells. Science 343:84–87CrossRefPubMedGoogle Scholar
  72. 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, Kondo A (2017) Targeted base editing in rice and tomato using a CRISPR–Cas9 cytidine deaminase fusion. Nat Biotechnol 35:441–443CrossRefPubMedGoogle Scholar
  73. Tanenbaum ME, Gilbert LA, Qi LS, Weissman JS, Vale RD (2014) A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159:635–646CrossRefPubMedPubMedCentralGoogle Scholar
  74. Trumbach D, Pfeiffer S, Poppe M, Scherb H, Doll S, Wurst W, Schick JA (2017) ENCoRE: an efficient software for CRISPR screens identifies new players in extrinsic apoptosis. BMC Genomics 18:905CrossRefPubMedPubMedCentralGoogle Scholar
  75. Tzelepis K, Koike-Yusa H, De Braekeleer E, Li Y, Metzakopian E, Dovey OM, Mupo A, Grinkevich V, Li M, Mazan M, Gozdecka M, Ohnishi S, Cooper J, Patel M, Mckerrell T, Chen B, Domingues AF, Gallipoli P, Teichmann S, Ponstingl H, Mcdermott U, Saez-Rodriguez J, Huntly BJP, Iorio F, Pina C, Vassiliou GS, Yusa K (2016) A CRISPR dropout screen identifies genetic vulnerabilities and therapeutic targets in acute myeloid leukemia. Cell Rep 17:1193–1205CrossRefPubMedPubMedCentralGoogle Scholar
  76. Virreira Winter S, Zychlinsky A, Bardoel BW (2016) Genome-wide CRISPR screen reveals novel host factors required for Staphylococcus aureus alpha-hemolysin-mediated toxicity. Sci Rep 6:24242CrossRefPubMedPubMedCentralGoogle Scholar
  77. Vojta A, Dobrinic P, Tadic V, Bockor L, Korac P, Julg B, Klasic M, Zoldos V (2016) Repurposing the CRISPR–Cas9 system for targeted DNA methylation. Nucleic Acids Res 44:5615–5628CrossRefPubMedPubMedCentralGoogle Scholar
  78. Wang KC, Chang HY (2011) Molecular mechanisms of long noncoding RNAs. Mol Cell 43:904–914CrossRefPubMedPubMedCentralGoogle Scholar
  79. Wang T, Wei JJ, Sabatini DM, Lander ES (2014) Genetic screens in human cells using the CRISPR–Cas9 system. Science 343:80–84CrossRefPubMedGoogle Scholar
  80. Wang T, Birsoy K, Hughes NW, Krupczak KM, Post Y, Wei JJ, Lander ES, Sabatini DM (2015) Identification and characterization of essential genes in the human genome. Science 350:1096–1101CrossRefPubMedPubMedCentralGoogle Scholar
  81. Wang T, Yu H, Hughes NW, Liu B, Kendirli A, Klein K, Chen WW, Lander ES, Sabatini DM (2017) Gene essentiality profiling reveals gene networks and synthetic lethal interactions with oncogenic Ras. Cell 168(890–903):e15Google Scholar
  82. Winter J, Breinig M, Heigwer F, Brugemann D, Leible S, Pelz O, Zhan T, Boutros M (2016) caRpools: an R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens. Bioinformatics 32:632–634CrossRefPubMedGoogle Scholar
  83. Winter J, Schwering M, Pelz O, Rauscher B, Zhan T, Heigwer F, Boutros M (2017) CRISPRAnalyzeR: interactive analysis, annotation and documentation of pooled CRISPR screensGoogle Scholar
  84. Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH, La Russa M, Tsai JC, Weissman JS, Dueber JE, Qi LS, Lim WA (2015) Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160:339–350CrossRefPubMedGoogle Scholar
  85. 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, Diamond MS (2016) A CRISPR screen defines a signal peptide processing pathway required by flaviviruses. Nature 535:164–168CrossRefPubMedPubMedCentralGoogle Scholar
  86. Zhou Y, Zhu S, Cai C, Yuan P, Li C, Huang Y, Wei W (2014) High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature 509:487–491CrossRefPubMedGoogle Scholar
  87. Zhu S, Li W, Liu J, Chen CH, Liao Q, Xu P, Xu H, Xiao T, Cao Z, Peng J, Yuan P, Brown M, Liu XS, Wei W (2016) Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR–Cas9 library. Nat Biotechnol 34:1279–1286CrossRefPubMedPubMedCentralGoogle Scholar
  88. Zong Y, Wang Y, Li C, Zhang R, Chen K, Ran Y, Qiu JL, Wang D, Gao C (2017) Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nat Biotechnol 35:438–440CrossRefPubMedGoogle Scholar

Copyright information

© The Pharmaceutical Society of Korea 2018

Authors and Affiliations

  1. 1.Department of Biomedical SciencesUniversity of Ulsan College of Medicine, Asan Medical CenterSeoulRepublic of Korea

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