Multiple mechanisms confining RNA polymerase II ubiquitylation to polymerases undergoing transcriptional arrest

Cell

Volumn 121, Issue 6, 2005, Pages 913-923

  Somesh, Baggavalli P ^a   Reid, James ^a   Liu, Wei Feng ^a,c   Søgaard, T Max M ^a   Erdjument Bromage, Hediye ^b   Tempst, Paul ^b   Svejstrup, Jesper Q ^a  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^b MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^c SHANDONG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DEF1 PROTEIN; ELONGATION FACTOR; PHOSPHATASE; PROTEIN; RNA POLYMERASE II; SERINE; SERINE 5 PHOSPHATASE; UNCLASSIFIED DRUG;

ARTICLE; CARBOXY TERMINAL SEQUENCE; DNA DAMAGE; ENZYME DEGRADATION; GENE MUTATION; PHOSPHORYLATION; PRIORITY JOURNAL; RNA TRANSCRIPTION; UBIQUITINATION;

EID: 20444428382     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2005.04.010     Document Type: Article

References (43)

1. K.M. Arndt, and C.M. Kane Running with RNA polymerase: eukaryotic transcript elongation Trends Genet. 19 2003 543 550
2. D.E. Awrey, R.G. Weilbaecher, S.A. Hemming, S.M. Orlicky, C.M. Kane, and A.M. Edwards Transcription elongation through DNA arrest sites. A multistep process involving both RNA polymerase II subunit RPB9 and TFIIS J. Biol. Chem. 272 1997 14747 14754
3. S.L. Beaudenon, M.R. Huacani, G. Wang, D.P. McDonnell, and J.M. Huibregtse Rsp5 ubiquitin-protein ligase mediates DNA damage-induced degradation of the large subunit of RNA polymerase II in Saccharomyces cerevisiae Mol. Cell. Biol. 19 1999 6972 6979
4. V.A. Bohr, C.A. Smith, D.S. Okumoto, and P.C. Hanawalt DNA repair in an active gene: removal of pyrimidine dimers from the DHFR gene of CHO cells is much more efficient than in the genome overall Cell 40 1985 359 369
5. D.B. Bregman, R. Halaban, A.J. van Gool, K.A. Henning, E.C. Friedberg, and S.L. Warren UV-induced ubiquitination of RNA polymerase II: a novel modification deficient in Cockayne syndrome cells Proc. Natl. Acad. Sci. USA 93 1996 11586 11590
6. E.J. Cho, M.S. Kobor, M. Kim, J. Greenblatt, and S. Buratowski Opposing effects of Ctk1 kinase and Fcp1 phosphatase at Ser 2 of the RNA polymerase II C-terminal domain Genes Dev. 15 2001 3319 3329
7. P. Cramer, D.A. Bushnell, and R.D. Kornberg Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution Science 292 2001 1863 1876
8. A.M. Edwards, S.A. Darst, W.J. Feaver, N.E. Thompson, R.R. Burgess, and R.D. Kornberg Purification and lipid-layer crystallization of yeast RNA polymerase II Proc. Natl. Acad. Sci. USA 87 1990 2122 2126
9. W.J. Feaver, O. Gileadi, Y. Li, and R.D. Kornberg CTD kinase associated with yeast RNA polymerase II initiation factor b Cell 67 1991 1223 1230
10. A. Ferdous, F. Gonzalez, L. Sun, T. Kodadek, and S.A. Johnston The 19S regulatory particle of the proteasome is required for efficient transcription elongation by RNA polymerase II Mol. Cell 7 2001 981 991
11. N.R. Gavva, R. Gavva, K. Ermekova, M. Sudol, and C.J. Shen Interaction of WW domains with hematopoietic transcription factor p45/NF-E2 and RNA polymerase II J. Biol. Chem. 272 1997 24105 24108
12. T.G. Gillette, F. Gonzalez, A. Delahodde, S.A. Johnston, and T. Kodadek Physical and functional association of RNA polymerase II and the proteasome Proc. Natl. Acad. Sci. USA 101 2004 5904 5909
13. A.L. Gnatt, P. Cramer, J. Fu, D.A. Bushnell, and R.D. Kornberg Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution Science 292 2001 1876 1882
14. R. Groisman, J. Polanowska, I. Kuraoka, J. Sawada, M. Saijo, R. Drapkin, A.F. Kisselev, K. Tanaka, and Y. Nakatani The ubiquitin ligase activity in the DDB2 and CSA complexes is differentially regulated by the COP9 signalosome in response to DNA damage Cell 113 2003 357 367
15. J. Hansson, M. Munn, W.D. Rupp, R. Kahn, and R.D. Wood Localization of DNA repair synthesis by human cell extracts to a short region at the site of a lesion J. Biol. Chem. 264 1989 21788 21792
16. K.A. Henning, L. Li, N. Iyer, L.D. McDaniel, M.S. Reagan, R. Legerski, R.A. Schultz, M. Stefanini, A.R. Lehmann, and L.V. Mayne The Cockayne syndrome group A gene encodes a WD repeat protein that interacts with CSB protein and a subunit of RNA polymerase II TFIIH Cell 82 1995 555 564
17. J.M. Huibregtse, J.C. Yang, and S.L. Beaudenon The large subunit of RNA polymerase II is a substrate of the Rsp5 ubiquitin-protein ligase Proc. Natl. Acad. Sci. USA 94 1997 3656 3661
18. J.C. Jones, H.P. Phatnani, T.A. Haystead, J.A. MacDonald, S.M. Alam, and A.L. Greenleaf C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats J. Biol. Chem. 279 2004 24957 24964
19. M.L. Kireeva, N. Komissarova, D.S. Waugh, and M. Kashlev The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex J. Biol. Chem. 275 2000 6530 6536
20. M.S. Kobor, J. Archambault, W. Lester, F.C. Holstege, O. Gileadi, D.B. Jansma, E.G. Jennings, F. Kouyoumdjian, A.R. Davidson, R.A. Young, and J. Greenblatt An unusual eukaryotic protein phosphatase required for transcription by RNA polymerase II and CTD dephosphorylation in S. cerevisiae Mol. Cell 4 1999 55 62
21. P. Komarnitsky, E.J. Cho, and S. Buratowski Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription Genes Dev. 14 2000 2452 2460
22. S. Krishnamurthy, X. He, M. Reyes-Reyes, C. Moore, and M. Hampsey Ssu72 Is an RNA polymerase II CTD phosphatase Mol. Cell 14 2004 387 394
23. K.B. Lee, D. Wang, S.J. Lippard, and P.A. Sharp Transcription-coupled and DNA damage-dependent ubiquitination of RNA polymerase II in vitro Proc. Natl. Acad. Sci. USA 99 2002 4239 4244
24. Y. Li, and R.D. Kornberg Interplay of positive and negative effectors in function of the C-terminal repeat domain of RNA polymerase II Proc. Natl. Acad. Sci. USA 91 1994 2362 2366
25. Z. Luo, J. Zheng, Y. Lu, and D.B. Bregman Ultraviolet radiation alters the phosphorylation of RNA polymerase II large subunit and accelerates its proteasome-dependent degradation Mutat. Res. 486 2001 259 274
26. A. Mitsui, and P.A. Sharp Ubiquitination of RNA polymerase II large subunit signaled by phosphorylation of carboxyl-terminal domain Proc. Natl. Acad. Sci. USA 96 1999 6054 6059
27. J. Peng, D. Schwartz, J.E. Elias, C.C. Thoreen, D. Cheng, G. Marsischky, J. Roelofs, D. Finley, and S.P. Gygi A proteomics approach to understanding protein ubiquitination Nat. Biotechnol. 21 2003 921 926
28. C.M. Pickart Ubiquitin in chains Trends Biochem. Sci. 25 2000 544 548
29. C.M. Pickart Mechanisms underlying ubiquitination Annu. Rev. Biochem. 70 2001 503 533
30. J.N. Ratner, B. Balasubramanian, J. Corden, S.L. Warren, and D.B. Bregman Ultraviolet radiation-induced ubiquitination and proteasomal degradation of the large subunit of RNA polymerase II. Implications for transcription-coupled DNA repair J. Biol. Chem. 273 1998 5184 5189
31. J. Reid, and J.Q. Svejstrup DNA damage-induced Def1-RNA polymerase II interaction and Def1 requirement for polymerase ubiquitylation in vitro J. Biol. Chem. 279 2004 29875 29878
32. G. Rigaut, A. Shevchenko, B. Rutz, M. Wilm, M. Mann, and B. Seraphin A generic protein purification method for protein complex characterization and proteome exploration Nat. Biotechnol. 17 1999 1030 1032
33. W. Seufert, and S. Jentsch Ubiquitin-conjugating enzymes UBC4 and UBC5 mediate selective degradation of short-lived and abnormal proteins EMBO J. 9 1990 543 550
34. F. Sherman Getting started with yeast C. Guthrie G.R. Fink Guide to Yeast Genetics and Molecular Biology 1991 Academic Press, Inc. San Diego, CA 3 20
35. J. Spence, R.R. Gali, G. Dittmar, F. Sherman, M. Karin, and D. Finley Cell cycle-regulated modification of the ribosome by a variant multiubiquitin chain Cell 102 2000 67 76
36. J.Q. Svejstrup Mechanisms of transcription-coupled DNA repair Nat. Rev. Mol. Cell Biol. 3 2002 21 29
37. J.Q. Svejstrup Rescue of arrested RNA polymerase II complexes J. Cell Sci. 116 2003 447 451
38. J.Q. Svejstrup The RNA polymerase II transcription cycle: cycling through chromatin Biochim. Biophys. Acta 1677 2004 64 73
39. S. Trigon, H. Serizawa, J.W. Conaway, R.C. Conaway, S.P. Jackson, and M. Morange Characterization of the residues phosphorylated in vitro by different C-terminal domain kinases J. Biol. Chem. 273 1998 6769 6775
40. C. Troelstra, A. van Gool, J. de Wit, W. Vermeulen, D. Bootsma, and J.H. Hoeijmakers ERCC6, a member of a subfamily of putative helicases, is involved in Cockayne's syndrome and preferential repair of active genes Cell 71 1992 939 953
41. A.J. van Gool, R. Verhage, S.M. Swagemakers, P. van de Putte, J. Brouwer, C. Troelstra, D. Bootsma, and J.H. Hoeijmakers RAD26, the functional S. cerevisiae homolog of the Cockayne syndrome B gene ERCC6 EMBO J. 13 1994 5361 5369
42. S.G. Winkler, L. Lacomis, J. Philip, H. Erdjument-Bromage, J.Q. Svejstrup, and P. Tempst Isolation and mass spectrometry of transcription factor complexes Methods 26 2002 260 269
43. E.C. Woudstra, C. Gilbert, J. Fellows, L. Jansen, J. Brouwer, H. Erdjument-Bromage, P. Tempst, and J.Q. Svejstrup A Rad26-Def1 complex coordinates repair and RNA pol II proteolysis in response to DNA damage Nature 415 2002 929 933