Variations in genome-wide RNAi screens: lessons from influenza research

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• 作者：Yu-Chi Chou (1) (2)
  Michael MC Lai (2) (3) (4) (5)
  Yi-Chen Wu (1)
  Nai-Chi Hsu (1)
  King-Song Jeng (1) (2)
  Wen-Chi Su (3) (4)
  
  1. National RNAi Core Facility Platform ; Academia Sinica ; Taipei ; 11529 ; Taiwan
  2. Institute of Molecular Biology ; Academia Sinica ; Taipei ; 11529 ; Taiwan
  3. Research Center for Emerging Viruses ; China Medical University Hospital ; Room 602 ; 6聽F ; Cancer Center Building ; No. 6 ; Hsueh-Shih Road ; Taichung ; 40402 ; Taiwan
  4. China Medical University ; Room 602 ; 6聽F ; Cancer Center Building ; No. 6 ; Hsueh-Shih Road ; Taichung ; 40402 ; Taiwan
  5. Center of Infectious Disease and Signaling Research ; National Cheng Kung University ; Tainan ; 70101 ; Taiwan
  
• 关键词：RNA interference (RNAi) ; Genome ; wide screen ; Arrayed siRNA screen ; Pooled shRNA screen ; Influenza virus ; Lentivirus
• 刊名：Journal of Clinical Bioinformatics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：5
• 期：1
• 全文大小：772 KB
• 参考文献：1. Bouvier, NM, Palese, P (2008) The biology of influenza viruses. Vaccine 26: pp. D49-53 CrossRef
  2. Hao, L, Sakurai, A, Watanabe, T, Sorensen, E, Nidom, CA, Newton, MA (2008) Drosophila RNAi screen identifies host genes important for influenza virus replication. Nature 454: pp. 890-3 CrossRef
  3. Brass, AL, Huang, IC, Benita, Y, John, SP, Krishnan, MN, Feeley, EM (2009) The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Cell 139: pp. 1243-54 CrossRef
  4. Shapira, SD, Gat-Viks, I, Shum, BO, Dricot, A, De Grace, MM, Wu, L (2009) A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell 139: pp. 1255-67 CrossRef
  5. Konig, R, Stertz, S, Zhou, Y, Inoue, A, Hoffmann, HH, Bhattacharyya, S (2010) Human host factors required for influenza virus replication. Nature 463: pp. 813-7 CrossRef
  6. Karlas, A, Machuy, N, Shin, Y, Pleissner, KP, Artarini, A, Heuer, D (2010) Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication. Nature 463: pp. 818-22 CrossRef
  7. Su, WC, Chen, YC, Tseng, CH, Hsu, PW, Tung, KF, Jeng, KS (2013) Pooled RNAi screen identifies ubiquitin ligase Itch as crucial for influenza A virus release from the endosome during virus entry. Proc Natl Acad Sci U S A 110: pp. 17516-21 CrossRef
  8. Moffat, J, Grueneberg, DA, Yang, X, Kim, SY, Kloepfer, AM, Hinkle, G (2006) A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124: pp. 1283-98 CrossRef
  9. Tran, AT, Rahim, MN, Ranadheera, C, Kroeker, A, Cortens, JP, Opanubi, KJ (2013) Knockdown of specific host factors protects against influenza virus-induced cell death. Cell Death Dis 4: pp. e769 CrossRef
  10. Sieczkarski, SB, Whittaker, GR (2003) Differential requirements of Rab5 and Rab7 for endocytosis of influenza and other enveloped viruses. Traffic 4: pp. 333-43 CrossRef
  11. Sun, E, He, J, Zhuang, X (2013) Dissecting the role of COPI complexes in influenza virus infection. J Virol 87: pp. 2673-85 CrossRef
  12. Guinea, R, Carrasco, L (1995) Requirement for vacuolar proton-ATPase activity during entry of influenza virus into cells. J Virol 69: pp. 2306-12
  13. Chen, J, Huang, S, Chen, Z (2010) Human cellular protein nucleoporin hNup98 interacts with influenza A virus NS2/nuclear export protein and overexpression of its GLFG repeat domain can inhibit virus propagation. J Gen Virol 91: pp. 2474-84 CrossRef
  14. Schneider, J, Wolff, T (2009) Nuclear functions of the influenza A and B viruses NS1 proteins: do they play a role in viral mRNA export?. Vaccine 27: pp. 6312-6 CrossRef
  15. Tran, AT, Cortens, JP, Du, Q, Wilkins, JA, Coombs, KM (2013) Influenza virus induces apoptosis via BAD-mediated mitochondrial dysregulation. J Virol 87: pp. 1049-60 CrossRef
  16. Takizawa, T, Matsukawa, S, Higuchi, Y, Nakamura, S, Nakanishi, Y, Fukuda, R (1993) Induction of programmed cell death (apoptosis) by influenza virus infection in tissue culture cells. J Gen Virol 74: pp. 2347-55 CrossRef
  17. Fesq, H, Bacher, M, Nain, M, Gemsa, D (1994) Programmed cell death (apoptosis) in human monocytes infected by influenza A virus. Immunobiology 190: pp. 175-82 CrossRef
  18. Strezoska, Z, Licon, A, Haimes, J, Spayd, KJ, Patel, KM, Sullivan, K (2012) Optimized PCR conditions and increased shRNA fold representation improve reproducibility of pooled shRNA screens. PLoS One 7: pp. e42341 CrossRef
  19. Davis, HE, Rosinski, M, Morgan, JR, Yarmush, ML (2004) Charged polymers modulate retrovirus transduction via membrane charge neutralization and virus aggregation. Biophys J 86: pp. 1234-42 CrossRef
  20. Watanabe, T, Watanabe, S, Kawaoka, Y (2010) Cellular networks involved in the influenza virus life cycle. Cell Host Microbe 7: pp. 427-39 CrossRef
  21. Stertz, S, Shaw, ML (2011) Uncovering the global host cell requirements for influenza virus replication via RNAi screening. Microbes Infect 13: pp. 516-25 CrossRef
  22. Brass, AL, Dykxhoorn, DM, Benita, Y, Yan, N, Engelman, A, Xavier, RJ (2008) Identification of host proteins required for HIV infection through a functional genomic screen. Science 319: pp. 921-6 CrossRef
  23. Konig, R, Zhou, Y, Elleder, D, Diamond, TL, Bonamy, GM, Irelan, JT (2008) Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 135: pp. 49-60 CrossRef
  24. Zhou, H, Xu, M, Huang, Q, Gates, AT, Zhang, XD, Castle, JC (2008) Genome-scale RNAi screen for host factors required for HIV replication. Cell Host Microbe 4: pp. 495-504 CrossRef
  25. Yeung, ML, Houzet, L, Yedavalli, VS, Jeang, KT (2009) A genome-wide short hairpin RNA screening of jurkat T-cells for human proteins contributing to productive HIV-1 replication. J Biol Chem 284: pp. 19463-73 CrossRef
  26. Rato, S, Maia, S, Brito, PM, Resende, L, Pereira, CF, Moita, C (2010) Novel HIV-1 knockdown targets identified by an enriched kinases/phosphatases shRNA library using a long-term iterative screen in Jurkat T-cells. PLoS One 5: pp. e9276 CrossRef
  27. Lu, J, Pan, Q, Rong, L, He, W, Liu, SL, Liang, C (2011) The IFITM proteins inhibit HIV-1 infection. J Virol 85: pp. 2126-37 CrossRef
  
• 刊物主题：Bioinformatics; Biomedicine general; Health Informatics;
• 出版者：BioMed Central
• ISSN：2043-9113

文摘

Genome-wide RNA interference (RNAi) screening is an emerging and powerful technique for genetic screens, which can be divided into arrayed RNAi screen and pooled RNAi screen/selection based on different screening strategies. To date, several genome-wide RNAi screens have been successfully performed to identify host factors essential for influenza virus replication. However, the host factors identified by different research groups are not always consistent. Taking influenza virus screens as an example, we found that a number of screening parameters may directly or indirectly influence the primary hits identified by the screens. This review highlights the differences among the published genome-wide screening approaches and offers recommendations for performing a good pooled shRNA screen/selection.