A functional genome-wide RNAi screen identifies TAF1 as a regulator for apoptosis in response to genotoxic stress

Nucleic Acids Research

Volumn 36, Issue 16, 2008, Pages 5250-5259

  Kimura, Junko ^a   Nguyen, Su Tien ^a   Liu, Hanshao ^a   Taira, Naoe ^a   Miki, Yoshio ^a   Yoshida, Kiyotsugu ^a  

^a TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; CYCLIN DEPENDENT KINASE INHIBITOR 1B; SHORT HAIRPIN RNA; TATA BINDING PROTEIN ASSOCIATED FACTOR; TATA BINDING PROTEIN ASSOCIATED FACTOR 1; UNCLASSIFIED DRUG;

APOPTOSIS; ARTICLE; CELL STRAIN HEK293; CELL STRAIN MCF 7; CELL SURVIVAL; CONTROLLED STUDY; EXPRESSION VECTOR; GENE IDENTIFICATION; GENE SILENCING; GENETIC SCREENING; GENETIC TRANSFECTION; GENOME ANALYSIS; GENOTOXICITY; HELA CELL; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; OXIDATIVE STRESS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEPLETION; PROTEIN EXPRESSION; PROTEIN FUNCTION; RNA INTERFERENCE; TRANSCRIPTION REGULATION;

APOPTOSIS; APOPTOSIS REGULATORY PROTEINS; CELL CYCLE PROTEINS; CELL LINE; CYCLIN-DEPENDENT KINASE INHIBITOR P27; ETOPOSIDE; GENE EXPRESSION REGULATION; GENOME, HUMAN; HUMANS; OXIDATIVE STRESS; RNA INTERFERENCE; TATA-BINDING PROTEIN ASSOCIATED FACTORS; TRANSCRIPTION FACTOR TFIID;

EID: 52649118681     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn506     Document Type: Article

References (45)

1. Hannon,G.J. (2002) RNA interference. Nature, 418, 244-251.
2. Echeverri,C.J. and Perrimon,N. (2006) High-throughput RNAi screening in cultured cells: A user's guide. Nat. Rev. Genet., 7, 373-384.
3. Bjorklund,M., Taipale,M., Varjosalo,M., Saharinen,J., Lahdenpera,J. and Taipale,J. (2006) Identification of pathways regulating cell size and cell-cycle progression by RNAi. Nature, 439, 1009-1013.
4. Eggert,U.S., Kiger,A.A., Richter,C., Perlman,Z.E., Perrimon,N., Mitchison,T.J. and Field,C.M. (2004) Parallel chemical genetic and genome-wide RNAi screens identify cytokinesis inhibitors and targets. PLoS Biol., 2, e379.
5. 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. (2004) Genome-wide survey of protein kinases required for cell cycle progression. Nature, 432, 980-987.
6. 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. (2005) A genetic screen for candidate tumor suppressors identifies REST. Cell, 121, 837-848.
7. Kolfschoten,I.G., van Leeuwen,B., Berns,K., Mullenders,J., Beijersbergen,R.L., Bernards,R., Voorhoeve,P.M. and Agami,R. (2005) A genetic screen identifies PITX1 as a suppressor of RAS activity and tumorigenicity. Cell, 121, 849-858.
8. Nicke,B., Bastien,J., Khanna,S.J., Warne,P.H., Cowling,V., Cook,S.J., Peters,G., Delpuech,O., Schulze,A., Berns,K. et al. (2005) Involvement of MINK, a Ste20 family kinase, in Ras oncogene-induced growth arrest in human ovarian surface epithelial cells. Mol. Cell 20, 673-685.
9. Ngo,V.N., Davis,R.E., Lamy,L., Yu,X., Zhao,H., Lenz,G., Lam,L.T., Dave,S., Yang,L., Powell,J. et al. (2006) A loss-of-function RNA interference screen for molecular targets in cancer. Nature, 441, 106-110.
10. Wu,W., Hodges,E. and Hoog,C. (2006) Thorough validation of siRNA-induced cell death phenotypes defines new anti-apoptotic protein. Nucleic Acids Res., 34, e13.
11. Kastan,M.B. and Bartek,J. (2004) Cell-cycle checkpoints and cancer. Nature, 432, 316-323.
12. Massague,J. (2004) G1 cell-cycle control and cancer. Nature, 432, 298-306.
13. Rajagopalan,H. and Lengauer,C. (2004) Aneuploidy and cancer. Nature 432, 338-341.
14. Fukano,H., Hayatsu,N., Goto,R. and Suzuki,Y. (2006) A technique to enzymatically construct libraries which express short hairpin RNA of arbitrary stem length. Biochem. Biophys. Res. Commun., 347, 543-550.
15. Taira,N., Nihira,K., Yamaguchi,T., Miki,Y. and Yoshida,K. (2007) DYRK2 is targeted to the nucleus and controls p53 via Ser46 phosphorylation in the apoptotic response to DNA damage. Mol. Cell, 25, 725-738.
16. Yoshida,K., Yamaguchi,T., Natsume,T., Kufe,D. and Miki,Y. (2005) JNK phosphorylation of 14-3-3 proteins regulates nuclear targeting of c-Abl in the apoptotic response to DNA damage. Nat. Cell Biol., 7, 278-285.
17. Yoshida,K., Kharbanda,S. and Kufe,D. (1999) Functional interaction between SHPTP1 and the Lyn tyrosine kinase in the apoptotic response to DNA damage. J. Biol. Chem., 274, 34663-34668.
18. Yoshida,K. and Kufe,D. (2001) Negative regulation of the SHPTP1 protein tyrosine phosphatase by protein kinase C delta in response to DNA damage. Mol. Pharmacol., 60, 1431-1438.
19. Yoshida,K., Wang,H.G., Miki,Y. and Kufe,D. (2003) Protein kinase Cdelta is responsible for constitutive and DNA damage-induced phosphorylation of Rad9. EMBO J., 22, 1431-1441.
20. Nguyen,S.T., Hasegawa,S., Tsuda,H., Tomioka,H., Ushijima,M. Noda,M., Omura,K. and Miki,Y. (2007) Identification of a predictive gene expression signature of cervical lymph node metastasis in oral squamous cell carcinoma. Cancer Sci., 98, 740-746.
21. Deng,X., Gao,F. and May,W.S. Jr (2003) Bc12 retards G1/S cell cycle transition by regulating intracellular ROS. Blood, 102, 3179-3185.
22. Hengst,L. and Reed,S.I. (1996) Translational control of p27Kip1 accumulation during the cell cycle. Science, 271, 1861-1864.
23. Pagano,M., Tam,S.W., Theodoras,A.M., Beer-Romero,P., Del Sal,G., Chau,V., Yew,P.R., Draetta,G.F. and Rolfe,M. (1995) Role of the ubiquitin-proteasome pathway in regulating abundance of the cyclin-dependent kinase inhibitor p27. Science, 269, 682-685.
24. 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. (2004) A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature, 428, 431-437.
25. Brummelkamp,T.R., Berns,K., Hijmans,E.M., Mullenders,J., Fabius,A., Heimerikx,M., Velds,A., Kerkhoven,R.M., Madiredjo,M., Bernards,R. et al. (2004) Functional identification of cancer-relevant genes through large-scale RNA interference screens in mammalian cells. Cold Spring Harb. Symp. Quant. Biol., 69, 439-445.
26. 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. (2004) A resource for large-scale RNA-interference-based screens in mammals. Nature, 428, 427-431.
27. Burley,S.K. and Roeder,R.G. (1996) Biochemistry and structural biology of transcription factor IID (TFIID). Annu. Rev. Biochem., 65 769-799.
28. Tora,L. (2002) A unified nomenclature for TATA box binding protein (TBP)-associated factors (TAFs) involved in RNA polymerase II transcription. Genes Dev., 16, 673-675.
29. Albright,S.R. and Tjian,R. (2000) TAFs revisited: More data reveal new twists and confirm old ideas. Gene, 242, 1-13.
30. Green,M.R. (2000) TBP-associated factors (TAFIIs): Multiple, selective transcriptional mediators in common complexes. Trends Biochem. Sci. 25, 59-63.
31. Thomas,M.C. and Chiang,C.M. (2006) The general transcription machinery and general cofactors. Crit. Rev. Biochem. Mol. Biol., 41, 105-178.
32. Sekiguchi,T., Nohiro,Y., Nakamura,Y., Hisamoto,N. and Nishimoto,T. (1991) The human CCG1 gene, essential for progression of the G1 phase, encodes a 210-kilodalton nuclear DNA-binding protein. Mol. Cell Biol. 11, 3317-3325.
33. Ruppert,S., Wang,E.H. and Tjian,R. (1993) Cloning and expression of human TAFII250: A TBP-associated factor implicated in cell-cycle regulation. Nature, 362, 175-179.
34. Wang,E.H. and Tjian,R. (1994) Promoter-selective transcriptional defect in cell cycle mutant ts13 rescued by hTAFII250. Science, 263 811-814.
35. Dikstein,R., Ruppert,S. and Tjian,R. (1996) TAFII250 is a bipartite protein kinase that phosphorylates the base transcription factor RAP74. Cell, 84, 781-790.
36. Mizzen,C.A., Yang,X.J., Kokubo,T., Brownell,J.E., Bannister,A.J., Owen-Hughes,T., Workman,J., Wang,L., Berger,S.L., Kouzarides,T. et al. (1996) The TAF(II)250 subunit of TFIID has histone acetyltransferase activity. Cell, 87, 1261-1270.
37. Pham,A.D. and Sauer,F. (2000) Ubiquitin-activating/conjugating activity of TAFII250, a mediator of activation of gene expression in Drosophila. Science, 289, 2357-2360.
38. O'Brien,T. and Tjian,R. (1998) Functional analysis of the human TAFII250 N-terminal kinase domain. Mol. Cell, 1, 905-911.
39. Siegert,J.L. and Robbins,P.D. (1999) Rb inhibits the intrinsic kinase activity of TATA-binding protein-associated factor TAFII250. Mol. Cell. Biol., 19, 846-854.
40. Sherr,C.J. and Roberts,J.M. (1999) CDK inhibitors: Positive and negative regulators of G1-phase progression. Genes Der., 13, 1501-1512.
41. Slingerland,J. and Pagano,M. (2000) Regulation of the cdk inhibitor p27 and its deregulation in cancer. J. Cell Physiol., 183, 10-17.
42. Pellegata,N.S., Quintanilla-Martinez,L., Siggelkow,H., Samson,E., Bink,K., Hofler,H., Fend,F., Graw,J. and Atkinson,M.J. (2006) Germ-line mutations in p27Kip1 cause a multiple endocrine neoplasia syndrome in rats and humans. Proc. Natl Acad. Sci. USA, 103, 15558-15563.
43. Fero,M.L., Rivkin,M., Tasch,M., Porter,P., Carow,C.E., Firpo,E., Polyak,K., Tsai,L.H., Broudy,V., Perlmutter,R.M. et al. (1996) A syndrome of multiorgan hyperplasia with features of gigantism, tumorigenesis, and female sterility in p27(Kipl)-deficient mice. Cell 85, 733-744.
44. Kiyokawa,H., Kineman,R.D., Manova-Todorova,K.O., Soares,V.C., Hoffman,E.S., Ono,M., Khanam,D., Hayday,A.C., Frohman,L.A. and Koff,A. (1996) Enhanced growth of mice lacking the cyclin-dependent kinase inhibitor function of p27(Kip1). Cell, 85, 721-732.
45. Nakayama,K., Ishida,N., Shirane,M., Inomata,A., Inoue,T., Shishido,N., Horii,I., Loh,D.Y. and Nakayama,K. (1996) Mice lacking p27(Kip1) display increased body size, multiple organ hyperplasia, retinal dysplasia, and pituitary tumors. Cell, 85, 707-720.