A Lentiviral RNAi Library for Human and Mouse Genes Applied to an Arrayed Viral High-Content Screen

Cell

Volumn 124, Issue 6, 2006, Pages 1283-1298

  Moffat, Jason ^a,b   Grueneberg, Dorre A ^a   Yang, Xiaoping ^a   Kim, So Young ^a,c,e   Kloepfer, Angela M ^a   Hinkle, Gregory ^a,c   Piqani, Bruno ^a   Eisenhaure, Thomas M ^d   Luo, Biao ^a   Grenier, Jennifer K ^a   Carpenter, Anne E ^a,b   Foo, Shi Yin ^d   Stewart, Sheila A ^f   Stockwell, Brent R ^g   Hacohen, Nir ^a,d,e   Hahn, William C ^a,c,e   Lander, Eric S ^a,b,e   Sabatini, David M ^a,b   Root, David E ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^c DANA FARBER CANCER INSTITUTE   (United States)

^d MASSACHUSETTS GENERAL HOSPITAL   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

^f WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^g Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SHORT HAIRPIN RNA; VIRUS RNA;

ARTICLE; CANCER CELL; CELL PROLIFERATION; CELL TYPE; CONTROLLED STUDY; GENE CONSTRUCT; GENE EXPRESSION; GENE IDENTIFICATION; GENE LIBRARY; GENE SEQUENCE; GENE TARGETING; GENETIC SCREENING; GENOME ANALYSIS; LENTIVIRINAE; MAMMAL; MITOSIS; NONHUMAN; PRIORITY JOURNAL; RNA INTERFERENCE; VALIDATION PROCESS;

MAMMALIA; MURINAE;

EID: 33646033137     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2006.01.040     Document Type: Article

References (42)

1. Abbas-Terki T., Blanco-Bose W., Deglon N., Pralong W., and Aebischer P. Lentiviral-mediated RNA interference. Hum. Gene Ther. 13 (2002) 2197-2201
2. Aza-Blanc P., Cooper C.L., Wagner K., Batalov S., Deveraux Q.L., and Cooke M.P. Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol. Cell 12 (2003) 627-637
3. Berns K., Hijmans E.M., Mullenders J., Brummelkamp T.R., Velds A., Heimerikx M., Kerkhoven R.M., Madiredjo M., Nijkamp W., Weigelt B., et al. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428 (2004) 431-437
4. Bettencourt-Dias M., Giet R., Sinka R., Mazumdar A., Lock W.G., Balloux F., Zafiropoulos P.J., Yamaguchi S., Winter S., Carthew R.W., et al. Genome-wide survey of protein kinases required for cell cycle progression. Nature 432 (2004) 980-987
5. Boutros M., Kiger A.A., Armknecht S., Kerr K., Hild M., Koch B., Haas S.A., Consortium H.F., Paro R., and Perrimon N. Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 303 (2004) 832-835
6. Brummelkamp T.R., Bernards R., and Agami R. A system for stable expression of short interfering RNAs in mammalian cells. Science 296 (2002) 550-553
7. Dickins R.A., Hemann M.T., Zilfou J.T., Simpson D.R., Ibarra I., Hannon G.J., and Lowe S.W. Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nat. Genet. 37 (2005) 1289-1295
8. Elbashir S.M., Harborth J., Lendeckel W., Yalcin A., Weber K., and Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411 (2001) 494-498
9. Federico M. Lentivirus Gene Engineering Protocols Volume 229 (2003), Humana Press, Totowa, NJ
10. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., and Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391 (1998) 806-811
11. Fraser A.G., Kamath R.S., Zipperlen P., Martinez-Campos M., Sohrmann M., and Ahringer J. Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408 (2000) 325-330
12. Gasparri F., Mariani M., Sola F., and Galvani A. Quantification of the proliferation index of human dermal fibroblast cultures with the ArrayScan high-content screening reader. J. Biomol. Screen. 9 (2004) 232-243
13. Golsteyn R.M. Cdk1 and Cdk2 complexes (cyclin dependent kinases) in apoptosis: a role beyond the cell cycle. Cancer Lett. 217 (2005) 129-138
14. Gumireddy K., Reddy M.V., Cosenza S.C., Boominathan R., Baker S.J., Papathi N., Jiang J., Holland J., and Reddy E.P. ON01910, a non-ATP-competitive small molecule inhibitor of Plk1, is a potent anticancer agent. Cancer Cell 7 (2005) 275-286
15. Hahn W.C., Counter C.M., Lundberg A.S., Beijersbergen R.L., Brooks M.W., and Weinberg R.A. Creation of human tumour cells with defined genetic elements. Nature 400 (1999) 464-468
16. Harborth J., Elbashir S.M., Bechert K., Tuschl T., and Weber K. Identification of essential genes in cultured mammalian cells using small interfering RNAs. J. Cell Sci. 114 (2001) 4557-4565
17. Hendzel M.J., Wei Y., Mancini M.A., Van Hooser A., Ranalli T., Brinkley B.R., Bazett-Jones D.P., and Allis C.D. Mitosis-specific phosphorylation of histone H3 initiates primarily within pericentromeric heterochromatin during G2 and spreads in an ordered fashion coincident with mitotic chromosome condensation. Chromosoma 106 (1997) 348-360
18. Jackson A.L., and Linsley P.S. Noise amidst the silence: off-target effects of siRNAs?. Trends Genet. 20 (2004) 521-524
19. Kamath R.S., Fraser A.G., Dong Y., Poulin G., Durbin R., Gotta M., Kanapin A., Le Bot N., Moreno S., Sohrmann M., et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421 (2003) 231-237
20. Keen N., and Taylor S. Aurora-kinase inhibitors as anticancer agents. Nat. Rev. Cancer 4 (2004) 927-936
21. Kennerdell J.R., and Carthew R.W. Use of dsRNA-mediated genetic interference to demonstrate that frizzled and frizzled 2 act in the wingless pathway. Cell 95 (1998) 1017-1026
22. Khvorova A., Reynolds A., and Jayasena S.D. Functional siRNAs and miRNAs exhibit strand bias. Cell 115 (2003) 209-216
23. Kiger A.A., Baum B., Jones S., Jones M.R., Coulson A., Echeverri C., and Perrimon N. A functional genomic analysis of cell morphology using RNA interference. J. Biol. 2 (2003) 27
24. Kittler R., Putz G., Pelletier L., Poser I., Heninger A.K., Drechsel D., Fischer S., Konstantinova I., Habermann B., Grabner H., et al. An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Nature 432 (2004) 1036-1040
25. Kolfschoten I.G., van Leeuwen B., Berns K., Mullenders J., Beijersbergen R.L., Bernards R., Voorhoeve P.M., and Agami R. A genetic screen identifies PITX1 as a suppressor of RAS activity and tumorigenicity. Cell 121 (2005) 849-858
26. Lum L., Yao S., Mozer B., Rovescalli A., Von Kessler D., Nirenberg M., and Beachy P.A. Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells. Science 299 (2003) 2039-2045
27. Mackeigan J.P., Murphy L.O., and Blenis J. Sensitized RNAi screen of human kinases and phosphatases identifies new regulators of apoptosis and chemoresistance. Nat. Cell Biol. 7 (2005) 591-600
28. Manning G., Whyte D.B., Martinez R., Hunter T., and Sudarsanam S. The protein kinase complement of the human genome. Science 298 (2002) 1912-1934
29. Marron M.B., Hughes D.P., Edge M.D., Forder C.L., and Brindle N.P. Evidence for heterotypic interaction between the receptor tyrosine kinases TIE-1 and TIE-2. J. Biol. Chem. 275 (2000) 39741-39746
30. Naldini L., Blomer U., Gallay P., Ory D., Mulligan R., Gage F.H., Verma I.M., and Trono D. In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector. Science 272 (1996) 263-267
31. Paddison P.J., Caudy A.A., Bernstein E., Hannon G.J., and Conklin D.S. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 16 (2002) 948-958
32. Paddison P.J., Silva J.M., Conklin D.S., Schlabach M., Li M., Aruleba S., Balija V., O'Shaughnessy A., Gnoj L., Scobie K., et al. A resource for large-scale RNA-interference-based screens in mammals. Nature 428 (2004) 427-431
33. Pelkmans L., Fava E., Grabner H., Hannus M., Habermann B., Krausz E., and Zerial M. Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis. Nature 436 (2005) 78-86
34. Sandy P., Ventura A., and Jacks T. Mammalian RNAi: a practical guide. Biotechniques 39 (2005) 215-224
35. Schwarz D.S., Hutvagner G., Du T., Xu Z., Aronin N., and Zamore P.D. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115 (2003) 199-208
36. Silva J.M., Li M.Z., Chang K., Ge W., Golding M.C., Rickles R.J., Siolas D., Hu G., Paddison P.J., Schlabach M.R., et al. Second-generation shRNA libraries covering the mouse and human genomes. Nat. Genet. 37 (2005) 1281-1288
37. Stewart S.A., Dykxhoorn D.M., Palliser D., Mizuno H., Yu E.Y., An D.S., Sabatini D.M., Chen I.S., Hahn W.C., Sharp P.A., et al. Lentivirus-delivered stable gene silencing by RNAi in primary cells. RNA 9 (2003) 493-501
38. Tsiamis A.C., Morris P.N., Marron M.B., and Brindle N.P. Vascular endothelial growth factor modulates the Tie-2:Tie-1 receptor complex. Microvasc. Res. 63 (2002) 149-158
39. Westbrook T.F., Martin E.S., Schlabach M.R., Leng Y., Liang A.C., Feng B., Zhao J.J., Roberts T.M., Mandel G., Hannon G.J., et al. A genetic screen for candidate tumor suppressors identifies REST. Cell 121 (2005) 837-848
40. Winzeler E.A., Shoemaker D.D., Astromoff A., Liang H., Anderson K., Andre B., Bangham R., Benito R., Boeke J.D., Bussey H., et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285 (1999) 901-906
41. Zamore P.D., and Haley B. Ribo-gnome: the big world of small RNAs. Science 309 (2005) 1519-1524
42. Zufferey R., Nagy D., Mandel R.J., Naldini L., and Trono D. Multiply attenuated lentiviral vector achieves efficient gene delivery in vivo. Nat. Biotechnol. 15 (1997) 871-875