Toolkit for evaluating genes required for proliferation and survival using tetracycline-regulated RNAi

Nature Biotechnology

Volumn 29, Issue 1, 2011, Pages 79-85

  Zuber, Johannes ^a   McJunkin, Katherine ^a,b   Fellmann, Christof ^a,d   Dow, Lukas E ^a   Taylor, Meredith J ^a   Hannon, Gregory J ^a,b,c   Lowe, Scott W ^a,b,c  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^b WATSON SCHOOL OF BIOLOGICAL SCIENCES   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^d UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ESSENTIAL GENE; FLUORESCENT REPORTER; IDENTIFICATION AND EVALUATION; IN-VITRO; IN-VIVO; RNA INTERFERENCE; SHORT HAIRPIN RNA; THERAPEUTIC TARGETS; TRANSACTIVATORS; VERSATILE TOOLS;

GENE THERAPY; RNA;

GENE EXPRESSION;

DOXYCYCLINE; MICRORNA; MICRORNA 31; SHORT HAIRPIN RNA; TETRACYCLINE; TRANSACTIVATOR PROTEIN; UNCLASSIFIED DRUG;

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CELL ISOLATION; CELL PROLIFERATION; CELL SURVIVAL; CONTROLLED STUDY; GENE EXPRESSION; GENE REPRESSION; GENE SILENCING; GENETIC SCREENING; HUMAN; HUMAN CELL; LYMPHOMA; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA INTERFERENCE;

ANIMALS; BIOTECHNOLOGY; CELL LINE, TUMOR; CELL PROLIFERATION; CELL SURVIVAL; DISEASE MODELS, ANIMAL; FEMALE; FLUORESCENT DYES; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, REPORTER; HUMANS; LEUKEMIA, MONOCYTIC, ACUTE; MICE; MICE, INBRED C57BL; MICE, TRANSGENIC; RNA INTERFERENCE; RNA, SMALL INTERFERING; TETRACYCLINE; TRANS-ACTIVATORS;

MUS;

EID: 78651312134     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.1720     Document Type: Article

References (31)

1. Martin, S.E. & Caplen, N.J. Applications of RNA interference in mammalian systems. Annu. Rev. Genomics Hum. Genet. 8, 81-108 (2007)
2. Hannon, G.J. RNA interference. Nature 418, 244-251 (2002)
3. Brummelkamp, T.R., Bernards, R. & Agami, R. A system for stable expression of short interfering RNAs in mammalian cells. Science 296, 550-553 (2002)
4. Paddison, P.J., Caudy, A.A., Bernstein, E., Hannon, G.J. & Conklin, D.S. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 16, 948-958 (2002)
5. Hemann, M.T. et al. An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivo. Nat. Genet. 33, 396-400 (2003)
6. Dickins, R.A. et al. Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nat. Genet. 37, 1289-1295 (2005)
7. Barbie, D.A. et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature 462, 108-112 (2009)
8. Luo, J. et al. A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. Cell 137, 835-848 (2009)
9. Ngo, V.N. et al. A loss-of-function RNA interference screen for molecular targets in cancer. Nature 441, 106-110 (2006)
10. Scholl, C. et al. Synthetic lethal interaction between oncogenic KRAS dependency and STK33 suppression in human cancer cells. Cell 137, 821-834 (2009)
11. Stegmeier, F., Hu, G., Rickles, R.J., Hannon, G.J. & Elledge, S.J. A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells. Proc. Natl. Acad. Sci. USA 102, 13212-13217 (2005)
12. Gossen, M. et al. Transcriptional activation by tetracyclines in mammalian cells. Science 268, 1766-1769 (1995)
13. Lund, A.H., Duch, M. & Pedersen, F.S. Transcriptional silencing of retroviral vectors. J. Biomed. Sci. 3, 365-378 (1996)
14. Ellis, J., Hotta, A. & Rastegar, M. Retrovirus silencing by an epigenetic TRIM. Cell 131, 13-14 (2007)
15. Markstein, M., Pitsouli, C., Villalta, C., Celniker, S.E. & Perrimon, N. Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes. Nat. Genet. 40, 476-483 (2008)
16. Pikaart, M.J., Recillas-Targa, F. & Felsenfeld, G. Loss of transcriptional activity of a transgene is accompanied by DNA methylation and histone deacetylation and is prevented by insulators. Genes Dev. 12, 2852-2862 (1998)
17. Agha-Mohammadi, S. et al. Second-generation tetracycline-regulatable promoter: repositioned tet operator elements optimize transactivator synergy while shorter minimal promoter offers tight basal leakiness. J. Gene Med. 6, 817-828 (2004)
18. Wold, M.S. Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu. Rev. Biochem. 66, 61-92 (1997)
19. Hochedlinger, K., Yamada, Y., Beard, C. & Jaenisch, R. Ectopic expression of Oct-4 blocks progenitor-cell differentiation and causes dysplasia in epithelial tissues. Cell 121, 465-477 (2005)
20. Weinstein, I.B. Cancer. Addiction to oncogenes-the Achilles heal of cancer. Science 297, 63-64 (2002)
21. Das, A.T. et al. Viral evolution as a tool to improve the tetracycline-regulated gene expression system. J. Biol. Chem. 279, 18776-18782 (2004)
22. Meacham, C.E., Ho, E.E., Dubrovsky, E., Gertler, F.B. & Hemann, M.T. In vivo RNAi screening identifies regulators of actin dynamics as key determinants of lymphoma progression. Nat. Genet. 41, 1133-1137 (2009)
23. Silva, J.M. et al. Profiling essential genes in human mammary cells by multiplex RNAi screening. Science 319, 617-620 (2008)
24. Schlabach, M.R. et al. Cancer proliferation gene discovery through functional genomics. Science 319, 620-624 (2008)
25. Bassik, M.C. et al. Rapid creation and quantitative monitoring of high coverage shRNA libraries. Nat. Methods 6, 443-445 (2009).
26. Shin, K.J. et al. A single lentiviral vector platform for microRNA-based conditional RNA interference and coordinated transgene expression. Proc. Natl. Acad. Sci. USA 103, 13759-13764 (2006)
27. Zuber, J. et al. Mouse models of human AML accurately predict chemotherapy response. Genes Dev. 23, 877-889 (2009)
28. Huesken, D. et al. Design of a genome-wide siRNA library using an artificial neural network. Nat. Biotechnol. 23, 995-1001 (2005)
29. McCurrach, M.E. & Lowe, S.W. Methods for studying pro- and antiapoptotic genes in nonimmortal cells. Methods Cell Biol. 66, 197-227 (2001)
30. Schmitt, C.A. et al. Dissecting p53 tumor suppressor functions in vivo. Cancer Cell 1, 289-298 (2002)
31. Taylor, J., Schenck, I., Blankenberg, D. & Nekrutenko, A. Using Galaxy to perform large-scale interactive data analyses. Curr. Protoc. Bioinformatics 10, 10.15 (2007).