1932

Abstract

Genome-wide screening is a potent approach for comprehensively understanding the molecular mechanisms of biological phenomena. However, despite its widespread use in the past decades across various biological targets, its application to biochemical reactions with temporal and reversible biological outputs remains a formidable challenge. To uncover the molecular machinery underlying various biochemical reactions, we have recently developed the revival screening method, which combines flow cytometry–based cell sorting with library reconstruction from collected cells. Our refinements to the traditional genome-wide screening technique have proven successful in revealing the molecular machinery of biochemical reactions of interest. In this article, we elucidate the technical basis of revival screening, focusing on its application to CRISPR-Cas9 single guide RNA (sgRNA) library screening. Finally, we also discuss the future of genome-wide screening while describing recent achievements from in vitro and in vivo screening.

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2024-08-27
2025-02-10
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Literature Cited

  1. 1.
    Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J, et al. 2017.. RNA targeting with CRISPR–Cas13. . Nature 550::28084
    [Crossref] [Google Scholar]
  2. 2.
    Altschuler SJ, Wu LF. 2010.. Cellular heterogeneity: Do differences make a difference?. Cell 141::55963
    [Crossref] [Google Scholar]
  3. 3.
    Bikard D, Jiang W, Samai P, Hochschild A, Zhang F, et al. 2013.. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. . Nucleic Acids Res. 41::742937
    [Crossref] [Google Scholar]
  4. 4.
    Birsoy K, Wang T, Chen WW, Freinkman E, Abu-Remaileh M, Sabatini DM. 2015.. An essential role of the mitochondrial electron transport chain in cell proliferation is to enable aspartate synthesis. . Cell 162::54051
    [Crossref] [Google Scholar]
  5. 5.
    Bock C, Datlinger P, Chardon FM, Coelho MA, Dong MB, et al. 2022.. High-content CRISPR screening. . Nat. Rev. Methods Primers 2::8
    [Crossref] [Google Scholar]
  6. 6.
    Cai EP, Ishikawa Y, Zhang W, Leite NC, Li J, et al. 2020.. Genome scale in vivo CRISPR screen identifies RNLS as a target for beta cell protection in type 1 diabetes. . Nat. Metab. 2::93445
    [Crossref] [Google Scholar]
  7. 7.
    Chang K, Elledge SJ, Hannon GJ. 2006.. Lessons from nature: microRNA-based shRNA libraries. . Nat. Methods 3::70714
    [Crossref] [Google Scholar]
  8. 8.
    Chen S, Sanjana NE, Zheng K, Shalem O, Lee K, et al. 2015.. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. . Cell 160::124660
    [Crossref] [Google Scholar]
  9. 9.
    Chen Z, Arai E, Khan O, Zhang Z, Ngiow SF, et al. 2021.. In vivo CD8+ T cell CRISPR screening reveals control by Fli1 in infection and cancer. . Cell 184::126280.e22
    [Crossref] [Google Scholar]
  10. 10.
    Cho SW, Kim S, Kim Y, Kweon J, Kim HS, et al. 2014.. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. . Genome Res. 24::13241
    [Crossref] [Google Scholar]
  11. 11.
    Chow RD, Guzman CD, Wang G, Schmidt F, Youngblood MW, et al. 2017.. AAV-mediated direct in vivo CRISPR screen identifies functional suppressors in glioblastoma. . Nat. Neurosci. 20::132941
    [Crossref] [Google Scholar]
  12. 12.
    Cong L, Ran FA, Cox DB, Lin S, Barretto R, et al. 2013.. Multiplex genome engineering using CRISPR/Cas systems. . Science 339::81923
    [Crossref] [Google Scholar]
  13. 13.
    Cox DB, Gootenberg JS, Abudayyeh OO, Franklin B, Kellner MJ, et al. 2017.. RNA editing with CRISPR-Cas13. . Science 358::101927
    [Crossref] [Google Scholar]
  14. 14.
    Cusanovich DA, Hill AJ, Aghamirzaie D, Daza RM, Pliner HA, et al. 2018.. A single-cell atlas of in vivo mammalian chromatin accessibility. . Cell 174::130924.e18
    [Crossref] [Google Scholar]
  15. 15.
    Dai M, Yan G, Wang N, Daliah G, Edick AM, et al. 2021.. In vivo genome-wide CRISPR screen reveals breast cancer vulnerabilities and synergistic mTOR/Hippo targeted combination therapy. . Nat. Commun. 12::3055
    [Crossref] [Google Scholar]
  16. 16.
    Daniloski Z, Jordan TX, Wessels H, Hoagland DA, Kasela S, et al. 2020.. Identification of required host factors for SARS-CoV-2 infection in human cells. . Cell 184::92105.e16
    [Crossref] [Google Scholar]
  17. 17.
    deJesus R, Moretti F, McAllister G, Wang Z, Bergman P, et al. 2016.. Functional CRISPR screening identifies the ufmylation pathway as a regulator of SQSTM1/p62. . eLife 5::e17290
    [Crossref] [Google Scholar]
  18. 18.
    Dong MB, Wang G, Chow RD, Ye L, Zhu L, et al. 2019.. Systematic immunotherapy target discovery using genome-scale in vivo CRISPR screens in CD8 T cells. . Cell 178::1189204.e23
    [Crossref] [Google Scholar]
  19. 19.
    Dubrot J, Lane-Reticker SK, Kessler EA, Ayer A, Mishra G, et al. 2021.. In vivo screens using a selective CRISPR antigen removal lentiviral vector system reveal immune dependencies in renal cell carcinoma. . Immunity 54::57185.e6
    [Crossref] [Google Scholar]
  20. 20.
    Enari M, Sakahira H, Yokoyama H, Okawa K et al. 1998.. A caspase-activated DNase that degrades DNA during apoptosis, and its inhibitor ICAD. . Nature 391::4350
    [Crossref] [Google Scholar]
  21. 21.
    Frecha C, Costa C, Nègre D, Gauthier E, Russell SJ, et al. 2008.. Stable transduction of quiescent T cells without induction of cycle progression by a novel lentiviral vector pseudotyped with measles virus glycoproteins. . Blood 112::484352
    [Crossref] [Google Scholar]
  22. 22.
    Frecha C, Lévy C, Costa C, Nègre D, Amirache F, et al. 2011.. Measles virus glycoprotein-pseudotyped lentiviral vector-mediated gene transfer into quiescent lymphocytes requires binding to both SLAM and CD46 entry receptors. . J. Virol. 85::597585
    [Crossref] [Google Scholar]
  23. 23.
    Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, et al. 2010.. Creation of a bacterial cell controlled by a chemically synthesized genome. . Science 329::5256
    [Crossref] [Google Scholar]
  24. 24.
    Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, et al. 2014.. Genome-scale CRISPR-mediated control of gene repression and activation. . Cell 159::64761
    [Crossref] [Google Scholar]
  25. 25.
    Goodwin JM, Dowdle WE, deJesus R, Wang Z, Bergman P, et al. 2017.. Autophagy-independent lysosomal targeting regulated by ULK1/2-FIP200 and ATG9. . Cell Rep. 20::234156
    [Crossref] [Google Scholar]
  26. 26.
    Haapaniemi EM, Botla SK, Persson J, Schmierer B, Taipale J. 2018.. CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response. . Nat. Med. 24::92730
    [Crossref] [Google Scholar]
  27. 27.
    Hart T, Moffat J. 2015.. BAGEL: a computational framework for identifying essential genes from pooled library screens. . BMC Bioinform. 17::164
    [Crossref] [Google Scholar]
  28. 28.
    Horlbeck MA, Gilbert LA, Villalta JE, Adamson B, Pak RA, et al. 2016.. Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. . eLife 5::e19760
    [Crossref] [Google Scholar]
  29. 29.
    Hsieh AC, Bo R, Manola JB, Vazquez F, Baré O, et al. 2004.. A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens. . Nucleic Acids Res. 32::893901
    [Crossref] [Google Scholar]
  30. 30.
    Hsu PD, Lander ES, Zhang F. 2014.. Development and applications of CRISPR-Cas9 for genome engineering. . Cell 157::126278
    [Crossref] [Google Scholar]
  31. 31.
    Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, et al. 2013.. DNA targeting specificity of RNA-guided Cas9 nucleases. . Nat. Biotechnol. 31::82732
    [Crossref] [Google Scholar]
  32. 32.
    Huang DW, Sherman BT, Lempicki RA. 2009.. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. . Nat. Protoc. 4::4457
    [Crossref] [Google Scholar]
  33. 33.
    Hutchison CA, Chuang RY, Noskov VN, Assad-Garcia N, Deerinck TJ, et al. 2016.. Design and synthesis of a minimal bacterial genome. . Science 351::eaad6253
    [Crossref] [Google Scholar]
  34. 34.
    Ikawa M, Tergaonkar V, Ogura A, Ogonuki N, Inoue K, Verma IM. 2002.. Restoration of spermatogenesis by lentiviral gene transfer: offspring from infertile mice. . PNAS 99::752429
    [Crossref] [Google Scholar]
  35. 35.
    Jia Y, Li L, Lin Y, Gopal P, Shen S, et al. 2022.. In vivo CRISPR screening identifies BAZ2 chromatin remodelers as druggable regulators of mammalian liver regeneration. . Cell Stem Cell 29::37285.e8
    [Crossref] [Google Scholar]
  36. 36.
    Jinek M, Chylinski K, Fonfara I, Hauer MH, Doudna JA, et al. 2012.. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. . Science 337::81621
    [Crossref] [Google Scholar]
  37. 37.
    Joglekar AV, Sandoval S. 2017.. Pseudotyped lentiviral vectors: one vector, many guises. . Hum. Gene Ther. Methods 28::291301
    [Crossref] [Google Scholar]
  38. 38.
    Kaizuka T, Morishita H, Hama Y, Tsukamoto S, Matsui T, et al. 2016.. An autophagic flux probe that releases an internal control. . Mol. Cell 64::83549
    [Crossref] [Google Scholar]
  39. 39.
    Kamimoto K, Hoffmann CZ, Morris SA. 2020.. Dissecting cell identity via network inference and in silico gene perturbation. . Nature 614::74251
    [Crossref] [Google Scholar]
  40. 40.
    Kanatsu-Shinohara M, Toyokuni S, Shinohara T. 2004.. Transgenic mice produced by retroviral transduction of male germ line stem cells in vivo. . Biol. Reprod. 98::1309095
    [Google Scholar]
  41. 41.
    Kang Y, Stein CS, Heth J, Sinn PL, Penisten AK, et al. 2002.. In vivo gene transfer using a nonprimate lentiviral vector pseudotyped with Ross River virus glycoproteins. . J. Virol. 76::937888
    [Crossref] [Google Scholar]
  42. 42.
    Keys HR, Knouse KA. 2022.. Genome-scale CRISPR screening in a single mouse liver. . Cell Genom. 2::100217
    [Crossref] [Google Scholar]
  43. 43.
    Konermann S, Brigham MD, Trevino AE, Joung J, Abudayyeh OO, et al. 2014.. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. . Nature 517::58388
    [Crossref] [Google Scholar]
  44. 44.
    Kory N, Wyant GA, Prakash G, Uit de Bos J, Bottanelli F, et al. 2018.. SFXN1 is a mitochondrial serine transporter required for one-carbon metabolism. . Science 362::eaat9528
    [Crossref] [Google Scholar]
  45. 45.
    Kramer NJ, Haney MS, Morgens DW, Jovičić A, Couthouis J, et al. 2018.. CRISPR–Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide repeat protein toxicity. . Nat. Genet. 50::60312
    [Crossref] [Google Scholar]
  46. 46.
    Langfelder P, Horvath S. 2008.. WGCNA: an R package for weighted correlation network analysis. . BMC Bioinform. 9::559
    [Crossref] [Google Scholar]
  47. 47.
    Li J, Zhu D, Hu S, Nie Y. 2022.. CRISPR-CasRx knock-in mice for RNA degradation. . Sci. China Life Sci. 65::224856
    [Crossref] [Google Scholar]
  48. 48.
    Li S, Li X, Xue W, Zhang L, Yang L, et al. 2020.. Screening for functional circular RNAs using the CRISPR–Cas13 system. . Nat. Methods 18::5159
    [Crossref] [Google Scholar]
  49. 49.
    Li Y, Muffat J, Omer Javed A, Keys HR, Lungjangwa T, et al. 2019.. Genome-wide CRISPR screen for Zika virus resistance in human neural cells. . PNAS 116::952732
    [Crossref] [Google Scholar]
  50. 50.
    Li YE, Preissl S, Hou X, Zhang Z, Zhang K, et al. 2020.. An atlas of gene regulatory elements in adult mouse cerebrum. . Nature 598::12936
    [Crossref] [Google Scholar]
  51. 51.
    Liang J, Lingeman E, Luong TT, Ahmed S, Muhar M, et al. 2020.. A genome-wide ER-phagy screen highlights key roles of mitochondrial metabolism and ER-resident UFMylation. . Cell 180::116077.e20
    [Crossref] [Google Scholar]
  52. 52.
    Lindtner S, Catta-Preta R, Tian H, Su-Feher L, Price JD, et al. 2019.. Genomic resolution of DLX-orchestrated transcriptional circuits driving development of forebrain GABAergic neurons. . Cell Rep. 28::204863.e8
    [Crossref] [Google Scholar]
  53. 53.
    Loeb J. 1915.. On the nature of the conditions which determine or prevent the entrance of the spermatozoon into the egg. . Am. Nat. 49::25785
    [Crossref] [Google Scholar]
  54. 54.
    Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, et al. 2013.. CRISPR RNA-guided activation of endogenous human genes. . Nat. Methods 10::97779
    [Crossref] [Google Scholar]
  55. 55.
    Mali P, Yang L, Esvelt KM, Aach J, Guell M, et al. 2013.. RNA-guided human genome engineering via Cas9. . Science 339::82326
    [Crossref] [Google Scholar]
  56. 56.
    Manguso RT, Pope HW, Zimmer MD, Brown FD, Yates KB, et al. 2017.. In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target. . Nature 547::41318
    [Crossref] [Google Scholar]
  57. 57.
    Marceau CD, Puschnik AS, Majzoub K, Ooi YS, Brewer SM, et al. 2016.. Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens. . Nature 6::15963
    [Crossref] [Google Scholar]
  58. 58.
    Maruoka M, Zhang P, Mori H, Imanishi E, Packwood DM, et al. 2021.. Caspase cleavage releases a nuclear protein fragment that stimulates phospholipid scrambling at the plasma membrane. . Mol. Cell 81::1397410.e9
    [Crossref] [Google Scholar]
  59. 59.
    Morgens DW, Wainberg M, Boyle EA, Ursu O, Araya CL, et al. 2017.. Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens. . Nat. Commun. 8::15178
    [Crossref] [Google Scholar]
  60. 60.
    Morita K, Hama Y, Izume T, Tamura N, Ueno T, et al. 2018.. Genome-wide CRISPR screen identifies TMEM41B as a gene required for autophagosome formation. . J. Cell Biol. 217::381728
    [Crossref] [Google Scholar]
  61. 61.
    Muñoz DM, Cassiani PJ, Li L, Billy E, Korn JM, et al. 2016.. CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions. . Cancer Discov. 6::90013
    [Crossref] [Google Scholar]
  62. 62.
    Nishimura H, L'Hernault SW. 2017.. Spermatogenesis. . Curr. Biol. 27::98894
    [Crossref] [Google Scholar]
  63. 63.
    Noguchi Y, Onodera Y, Miyamoyo T, Maruoka M, Kosako H, Suzuki J. 2024.. In vivo CRISPR screening directly targeting testicular cells. . Cell Genom. 4::100510
    [Crossref] [Google Scholar]
  64. 64.
    Ochiai H, Hayashi T, Umeda M, Yoshimura M, Harada A, et al. 2020.. Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells. . Sci. Adv. 6::eaaz6699
    [Crossref] [Google Scholar]
  65. 65.
    Oksuz O, Henninger JE, Warneford-Thomson R, Zheng MM, Erb H, et al. 2023.. Transcription factors interact with RNA to regulate genes. . Mol. Cell 83::244963.e13
    [Crossref] [Google Scholar]
  66. 66.
    Park RJ, Wang T, Koundakjian D, Hultquist JF, Lamothe-Molina PA, et al. 2016.. A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors. . Nat. Genet. 49::193203
    [Crossref] [Google Scholar]
  67. 67.
    Parnas O, Jovanović M, Eisenhaure TM, Herbst RH, Dixit A, et al. 2015.. A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks. . Cell 162::67586
    [Crossref] [Google Scholar]
  68. 68.
    Pelletier JF, Sun L, Wise KS, Assad-Garcia N, Karas BJ, et al. 2020.. Genetic requirements for cell division in a genomically minimal cell. . Cell 184::243040.e16
    [Crossref] [Google Scholar]
  69. 69.
    Pérez-Piñera P, Kocak DD, Vockley CM, Adler AF, Kabadi AM, et al. 2013.. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. . Nat. Methods 10::97376
    [Crossref] [Google Scholar]
  70. 70.
    Picher AJ, Budeus B, Wafzig O, Krüger C, García-Gómez S, et al. 2016.. TruePrime is a novel method for whole genome amplification from single cells based on TthPrimPol. . Nat. Commun. 7::13296
    [Crossref] [Google Scholar]
  71. 71.
    Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, et al. 2013.. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. . Cell 152::117383
    [Crossref] [Google Scholar]
  72. 72.
    Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, et al. 2013.. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. . Cell 154::138089
    [Crossref] [Google Scholar]
  73. 73.
    Ruetz TJ, Kashiwagi CM, Morton B, Yeo RW, Leeman DS, et al. 2021.. In vitro and in vivo CRISPR-Cas9 screens reveal drivers of aging in neural stem cells of the brain. . bioRxiv 2021.11.23.469762. https://doi.org/10.1101/2021.11.23.469762
  74. 74.
    Sanchez CG, Teixeira FK, Czech B, Preall J, Zamparini AL, et al. 2016.. Regulation of ribosome biogenesis and protein synthesis controls germline stem cell differentiation. . Cell Stem Cell 18::27690
    [Crossref] [Google Scholar]
  75. 75.
    Sanjana NE, Shalem O, Zhang F. 2014.. Improved vectors and genome-wide libraries for CRISPR screening. . Nat. Methods 11::78384
    [Crossref] [Google Scholar]
  76. 76.
    Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, et al. 2014.. Genome-scale CRISPR-Cas9 knockout screening in human cells. . Science 343::8487
    [Crossref] [Google Scholar]
  77. 77.
    Shinohara T, Kanatsu-Shinohara M. 2020.. Transgenesis and genome editing of mouse spermatogonial stem cells by lentivirus pseudotyped with Sendai virus F protein. . Stem Cell Rep. 14::44761
    [Crossref] [Google Scholar]
  78. 78.
    Sidik SM, Huet D, Ganesan SM, Huynh M, Wang T, et al. 2016.. A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes. . Cell 166::142335.e12
    [Crossref] [Google Scholar]
  79. 79.
    Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F. 2016.. Rationally engineered Cas9 nucleases with improved specificity. . Science 351::8488
    [Crossref] [Google Scholar]
  80. 80.
    Snel B, Lehmann G, Bork P, Huynen MA. 2000.. STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. . Nucleic Acids Res. 15::344244
    [Crossref] [Google Scholar]
  81. 81.
    Suarez SS. 2008.. Control of hyperactivation in sperm. . Hum. Reprod. Update 14::64757
    [Crossref] [Google Scholar]
  82. 82.
    Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. 2005.. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. . PNAS 102::1554550
    [Crossref] [Google Scholar]
  83. 83.
    Suzuki J, Denning DP, Imanishi E, Horvitz HR, Nagata S. 2013.. Xk-related protein 8 and CED-8 promote phosphatidylserine exposure in apoptotic cells. . Science 341::4036
    [Crossref] [Google Scholar]
  84. 84.
    Suzuki J, Umeda M, Sims PJ, Nagata S. 2010.. Calcium-dependent phospholipid scrambling by TMEM16F. . Nature 468::83438
    [Crossref] [Google Scholar]
  85. 85.
    Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, et al. 2023.. The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest. . Nucleic Acids Res. 6::63846
    [Crossref] [Google Scholar]
  86. 86.
    Tsuchiya M, Tachibana N, Nagao K, Tamura T, Hamachi I. 2023.. Organelle-selective click labeling coupled with flow cytometry allows pooled CRISPR screening of genes involved in phosphatidylcholine metabolism. . Cell Metab. 35::107283.e9
    [Crossref] [Google Scholar]
  87. 87.
    Tsukada M, Ohsumi Y. 1993.. Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. . FEBS Lett. 333::16974
    [Crossref] [Google Scholar]
  88. 88.
    Tzelepis K, Koike-Yusa H, De Braekeleer E, Li Y, Metzakopian E, et al. 2016.. A CRISPR dropout screen identifies genetic vulnerabilities and therapeutic targets in acute myeloid leukemia. . Cell Rep. 17::1193205
    [Crossref] [Google Scholar]
  89. 89.
    Uhlig KM, Schülke S, Scheuplein VA, Malczyk AH, Reusch J, et al. 2015.. Lentiviral protein transfer vectors are an efficient vaccine platform and induce a strong antigen-specific cytotoxic T cell response. . J. Virol. 89::904460
    [Crossref] [Google Scholar]
  90. 90.
    VanDusen NJ, Lee JY, Gu W, Butler CE, Sethi I, et al. 2021.. Massively parallel in vivo CRISPR screening identifies RNF20/40 as epigenetic regulators of cardiomyocyte maturation. . Nat. Commun. 12::4442
    [Crossref] [Google Scholar]
  91. 91.
    Visconti PE, Galantino-Homer H, Moore GD, Bailey JL, Nig X, et al. 1998.. The molecular basis of sperm capacitation. . J. Androl. 19::24248
    [Crossref] [Google Scholar]
  92. 92.
    Wang B, Wang M, Zhang W, Xiao T, Chen CH, et al. 2019.. Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute. . Nat. Protoc. 14::75680
    [Crossref] [Google Scholar]
  93. 93.
    Wang T, Wei JJ, Sabatini DM, Lander ES. 2013.. Genetic screens in human cells using the CRISPR-Cas9 system. . Science 343::8084
    [Crossref] [Google Scholar]
  94. 94.
    Wang X, Tokheim CJ, Wang B, Gu SS, Wang B, et al. 2020.. In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target. . Cell 184::535774.e22
    [Crossref] [Google Scholar]
  95. 95.
    Wang Y, Menon AK, Maki Y, Liu Y, Iwasaki Y, et al. 2022.. Genome-wide CRISPR screen reveals CLPTM1L as a lipid scramblase required for efficient glycosylphosphatidylinositol biosynthesis. . PNAS 119::e2115083119
    [Crossref] [Google Scholar]
  96. 96.
    Wangensteen KJ, Wang YJ, Dou Z, Wang AW, Mosleh-Shirazi E, et al. 2018.. Combinatorial genetics in liver repopulation and carcinogenesis with a in vivo CRISPR activation platform. . Hepatology 68::66376
    [Crossref] [Google Scholar]
  97. 97.
    Watanabe S, Kanatsu-Shinohara M, Shinohara T. 2019.. Sendai virus-mediated transduction of mammalian spermatogonial stem cells. . Biol. Reprod. 100::52334
    [Crossref] [Google Scholar]
  98. 98.
    Wei J, Alfajaro MM, DeWeirdt PC, Hanna RE, Lu-Culligan WJ, et al. 2020.. Genome-wide CRISPR screens reveal host factors critical for SARS-CoV-2 infection. . Cell 184::7691.e13
    [Crossref] [Google Scholar]
  99. 99.
    Wei L, Lee D, Law C, Zhang MS, Shen J, et al. 2019.. Genome-wide CRISPR/Cas9 library screening identified PHGDH as a critical driver for Sorafenib resistance in HCC. . Nat. Commun. 10::4681
    [Crossref] [Google Scholar]
  100. 100.
    Wertz MH, Mitchem MR, Pineda SS, Hachigian LJ, Lee H, et al. 2020.. Genome-wide in vivo CNS screening identifies genes that modify CNS neuronal survival and mHTT toxicity. . Neuron 106::7689.e8
    [Crossref] [Google Scholar]
  101. 101.
    Wilhelm SM, Carter CA, Tang L, Wilkie DP, McNabola A, et al. 2004.. BAY 43-9006 exhibits broad spectrum oral antitumor activity and targets the RAF/MEK/ERK pathway and receptor tyrosine kinases involved in tumor progression and angiogenesis. . Cancer Res. 64::7099109
    [Crossref] [Google Scholar]
  102. 102.
    Wu H, de Gannes M, Luchetti G, Pilsner JR. 2015.. Rapid method for the isolation of mammalian sperm DNA. . BioTechniques 58::293300
    [Crossref] [Google Scholar]
  103. 103.
    Xia J, Ren D. 2009.. The BSA-induced Ca(2+) influx during sperm capacitation is CATSPER channel-dependent. . Reprod. Biol. Endocrinol. 7::119
    [Crossref] [Google Scholar]
  104. 104.
    Xu D, Cai Y, Tang L, Han X, Gao F, et al. 2020.. A CRISPR/Cas13-based approach demonstrates biological relevance of vlinc class of long non-coding RNAs in anticancer drug response. . Sci. Rep. 10::1794
    [Crossref] [Google Scholar]
  105. 105.
    Yoneshiro T, Wang Q, Tajima K, Matsushita M, Maki H, et al. 2019.. BCAA catabolism in brown fat controls energy homeostasis through SLC25A44. . Nature 572::61419
    [Crossref] [Google Scholar]
  106. 106.
    Zhang X, Tee LY, Wang X, Huang Q, Yang S. 2015.. Off-target effects in CRISPR/Cas9-mediated genome engineering. . Mol. Ther. Nucleic Acids 4::e264
    [Crossref] [Google Scholar]
  107. 107.
    Zhou Q, Schneider IC, Gallet M, Kneissl S, Buchholz CJ. 2011.. Resting lymphocyte transduction with measles virus glycoprotein pseudotyped lentiviral vectors relies on CD46 and SLAM. . Virology 413::14952
    [Crossref] [Google Scholar]
  108. 108.
    Zhou Y, Zhu S, Cai C, Yuan P, Li C, et al. 2014.. High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. . Nature 509::48791
    [Crossref] [Google Scholar]
  109. 109.
    Zhu Q, Zhao X, Zhang Y, Li Y, Liu S, et al. 2023.. Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines. . Nat. Commun. 14::8170
    [Crossref] [Google Scholar]
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