Recognition of RNA polymerase II and transcription bubbles by XPG, CSB, and TFIIH: Insights for transcription-coupled repair and Cockayne syndrome

Molecular Cell

Volumn 20, Issue 2, 2005, Pages 187-198

  Sarker, Altaf H ^a   Tsutakawa, Susan E ^a   Kostek, Seth ^b   Ng, Cliff ^a   Shin, David S ^c   Peris, Marian ^b   Campeau, Eric ^a,d   Tainer, John A ^a,c   Nogales, Eva ^a,b   Cooper, Priscilla K ^a  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

^d UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE II;

ARTICLE; COCKAYNE SYNDROME; GENE INTERACTION; GENE MUTATION; INDUCED MUTATION; MOLECULAR RECOGNITION; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN HYDROLYSIS; PROTEIN PROTEIN INTERACTION; TRANSCRIPTION TERMINATION;

ADENOSINE TRIPHOSPHATASES; COCKAYNE SYNDROME; CRYSTALLOGRAPHY, X-RAY; DNA REPAIR; DNA-BINDING PROTEINS; ENDONUCLEASES; HELA CELLS; HUMANS; MODELS, MOLECULAR; MUTATION; NUCLEAR PROTEINS; RNA POLYMERASE II; TIME FACTORS; TRANSCRIPTION FACTOR TFIIH; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 26944448202     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2005.09.022     Document Type: Article

References (64)

1. J.O. Andressoo, and J.H. Hoeijmakers Transcription-coupled repair and premature ageing Mutat. Res. 577 2005 179 194
2. S.J. Araujo, E.A. Nigg, and R.D. Wood Strong functional interactions of TFIIH with XPC and XPG in human DNA nucleotide excision repair, without a preassembled repairosome Mol. Cell. Biol. 21 2001 2281 2291
3. M. Berneburg, and A.R. Lehmann Xeroderma pigmentosum and related disorders: defects in DNA repair and transcription Adv. Genet. 43 2001 71 102
4. J. Bradsher, J. Auriol, L. Proietti de Santis, S. Iben, J.L. Vonesch, I. Grummt, and J.M. Egly CSB is a component of RNA pol I transcription Mol. Cell 10 2002 819 829
5. D. Bregeon, Z.A. Doddridge, H.J. You, B. Weiss, and P.W. Doetsch Transcriptional mutagenesis induced by uracil and 8-oxoguanine in Escherichia coli Mol. Cell 12 2003 959 970
6. M. Christiansen, T. Stevnsner, C. Modin, P.M. Martensen, R.M. Brosh Jr., and V.A. Bohr Functional consequences of mutations in the conserved SF2 motifs and post-translational phosphorylation of the CSB protein Nucleic Acids Res. 31 2003 963 973
7. E. Citterio, S. Rademakers, G.T. van der Horst, A.J. van Gool, J.H. Hoeijmakers, and W. Vermeulen Biochemical and biological characterization of wild-type and ATPase-deficient Cockayne syndrome B repair protein J. Biol. Chem. 273 1998 11844 11851
8. E. Citterio, V. Van Den Boom, G. Schnitzler, R. Kanaar, E. Bonte, R.E. Kingston, J.H. Hoeijmakers, and W. Vermeulen ATP-dependent chromatin remodeling by the Cockayne syndrome B DNA repair-transcription-coupling factor Mol. Cell. Biol. 20 2000 7643 7653
9. F. Coin, and J.M. Egly Ten years of TFIIH Cold Spring Harb. Symp. Quant. Biol. 63 1998 105 110
10. A. Constantinou, D. Gunz, E. Evans, P. Lalle, P.A. Bates, R.D. Wood, and S.G. Clarkson Conserved residues of human XPG protein important for nuclease activity and function in nucleotide excision repair J. Biol. Chem. 274 1999 5637 5648
11. B.A. Donahue, S. Yin, J.S. Taylor, D. Reines, and P.C. Hanawalt Transcript cleavage by RNA polymerase II arrested by a cyclobutane pyrimidine dimer in the DNA template Proc. Natl. Acad. Sci. USA 91 1994 8502 8506
12. I. Dunand-Sauthier, M. Hohl, F. Thorel, P. Jaquier-Gubler, S.G. Clarkson, and O.D. Scharer The spacer region of XPG mediates recruitment to nucleotide excision repair complexes and determines substrate specificity J. Biol. Chem. 280 2005 7030 7037
13. S. Emmert, H. Slor, D.B. Busch, S. Batko, R.B. Albert, D. Coleman, S.G. Khan, B. Abu-Libdeh, J.J. DiGiovanna, and B.B. Cunningham Relationship of neurologic degeneration to genotype in three xeroderma pigmentosum group G patients J. Invest. Dermatol. 118 2002 972 982
14. E. Evans, J. Fellows, A. Coffer, and R.D. Wood Open complex formation around a lesion during nucleotide excision repair provides a structure for cleavage by human XPG protein EMBO J. 16 1997 625 638
15. E. Evans, J.G. Moggs, J.R. Hwang, J.M. Egly, and R.D. Wood Mechanism of open complex and dual incision formation by human nucleotide excision repair factors EMBO J. 16 1997 6559 6573
16. U. Fiedler, and H.T. Timmers Analysis of the open region of RNA polymerase II transcription complexes in the early phase of elongation Nucleic Acids Res. 29 2001 2706 2714
17. 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
18. Y.N. Harada, N. Shiomi, M. Koike, M. Ikawa, M. Okabe, S. Hirota, Y. Kitamura, M. Kitagawa, T. Matsunaga, O. Nikaido, and T. Shiomi Postnatal growth failure, short life span, and early onset of cellular senescence and subsequent immortalization in mice lacking the xeroderma pigmentosum group G gene Mol. Cell. Biol. 19 1999 2366 2372
19. J.J. Harrington, and M.R. Lieber Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: implications for nucleotide excision repair Genes Dev. 8 1994 1344 1355
20. J.H. Hoeijmakers Genome maintenance mechanisms for preventing cancer Nature 411 2001 366 374
21. M. Hohl, F. Thorel, S.G. Clarkson, and O.D. Scharer Structural determinants for substrate binding and catalysis by the structure-specific endonuclease XPG J. Biol. Chem. 278 2003 19500 19508
22. D.J. Hosfield, C.D. Mol, B. Shen, and J.A. Tainer Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity Cell 95 1998 135 146
23. N. Iyer, M.S. Reagan, K.J. Wu, B. Canagarajah, and E.C. Friedberg Interactions involving the human RNA polymerase II transcription/nucleotide excision repair complex TFIIH, the nucleotide excision repair protein XPG, and Cockayne syndrome group B (CSB) protein Biochemistry 35 1996 2157 2167
24. S. Kamiuchi, M. Saijo, E. Citterio, M. de Jager, J.H. Hoeijmakers, and K. Tanaka Translocation of Cockayne syndrome group A protein to the nuclear matrix: possible relevance to transcription-coupled DNA repair Proc. Natl. Acad. Sci. USA 99 2002 201 206
25. M.L. Kireeva, N. Komissarova, and M. Kashlev Overextended RNA:DNA hybrid as a negative regulator of RNA polymerase II processivity J. Mol. Biol. 299 2000 325 335
26. P. Lalle, T. Nouspikel, A. Constantinou, F. Thorel, and S.G. Clarkson The founding members of xeroderma pigmentosum group G produce XPG protein with severely impaired endonuclease activity J. Invest. Dermatol. 118 2002 344 351
27. P.J. Laybourn, and M.E. Dahmus Phosphorylation of RNA polymerase IIA occurs subsequent to interaction with the promoter and before the initiation of transcription J. Biol. Chem. 265 1990 13165 13173
28. S.K. Lee, S.L. Yu, L. Prakash, and S. Prakash Requirement for yeast RAD26, a homolog of the human CSB gene, in elongation by RNA polymerase II Mol. Cell. Biol. 21 2001 8651 8656
29. S.K. Lee, S.L. Yu, L. Prakash, and S. Prakash Requirement of yeast RAD2, a homolog of human XPG gene, for efficient RNA polymerase II transcription. implications for Cockayne syndrome Cell 109 2002 823 834
30. A.R. Lehmann The xeroderma pigmentosum group D (XPD) gene: one gene, two functions, three diseases Genes Dev. 15 2001 15 23
31. A.R. Lehmann DNA repair-deficient diseases, xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy Biochimie 85 2003 1101 1111
32. G. LeRoy, R. Drapkin, L. Weis, and D. Reinberg Immunoaffinity purification of the human multisubunit transcription factor IIH J. Biol. Chem. 273 1998 7134 7140
33. M. Ljungman, and D.P. Lane Transcription - guarding the genome by sensing DNA damage Nat. Rev. Cancer 4 2004 727 737
34. E. Maldonado, R. Drapkin, and D. Reinberg Purification of human RNA polymerase II and general transcription factors Methods Enzymol. 274 1996 72 100
35. L.V. Mayne, and A.R. Lehmann Failure of RNA synthesis to recover after UV irradiation. An early defect in cells from individuals with Cockayne's syndrome and xeroderma pigmentosum Cancer Res. 42 1982 1473 1478
36. I. Mellon, G. Spivak, and P.C. Hanawalt Selective removal of transcription-blocking DNA damage from the transcribed strand of the mammalian DHFR gene Cell 51 1987 241 249
37. A. Nicholls, K.A. Sharp, and B. Honig Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons Proteins 11 1991 281 296
38. T. Nouspikel, P. Lalle, S.A. Leadon, P.K. Cooper, and S.G. Clarkson A common mutational pattern in Cockayne syndrome patients from xeroderma pigmentosum group G: implications for a second XPG function Proc. Natl. Acad. Sci. USA 94 1997 3116 3121
39. I. Rapin, Y. Lindenbaum, D.W. Dickson, K.H. Kraemer, and J.H. Robbins Cockayne syndrome and xeroderma pigmentosum Neurology 55 2000 1442 1449
40. C.P. Selby, and A. Sancar Cockayne syndrome group B protein enhances elongation by RNA polymerase II Proc. Natl. Acad. Sci. USA 94 1997 11205 11209
41. C.P. Selby, R. Drapkin, D. Reinberg, and A. Sancar RNA polymerase II stalled at a thymine dimer: footprint and effect on excision repair Nucleic Acids Res. 25 1997 787 793
42. R.R. Selzer, S. Nyaga, J. Tuo, A. May, M. Muftuoglu, M. Christiansen, E. Citterio, R.M. Brosh Jr., and V.A. Bohr Differential requirement for the ATPase domain of the Cockayne syndrome group B gene in the processing of UV-induced DNA damage and 8-oxoguanine lesions in human cells Nucleic Acids Res. 30 2002 782 793
43. N. Shiomi, S. Kito, M. Oyama, T. Matsunaga, Y.N. Harada, M. Ikawa, M. Okabe, and T. Shiomi Identification of the XPG region that causes the onset of Cockayne syndrome by using Xpg mutant mice generated by the cDNA-mediated knock-in method Mol. Cell. Biol. 24 2004 3712 3719
44. N. Shiomi, M. Mori, S. Kito, Y.N. Harada, K. Tanaka, and T. Shiomi Severe growth retardation and short life span of double-mutant mice lacking Xpa and exon 15 of Xpg DNA Repair (Amst.) 4 2005 351 357
45. M.K. Shivji, J.G. Moggs, I. Kuraoka, and R.D. Wood Dual-incision assays for nucleotide excision repair using DNA with a lesion at a specific site Methods Mol. Biol. 113 1999 373 392
46. I. Sidorenkov, N. Komissarova, and M. Kashlev Crucial role of the RNA:DNA hybrid in the processivity of transcription Mol. Cell 2 1998 55 64
47. J.Q. Svejstrup Mechanisms of transcription-coupled DNA repair Nat. Rev. Mol. Cell Biol. 3 2002 21 29
48. J.Q. Svejstrup Rescue of arrested RNA polymerase II complexes J. Cell Sci. 116 2003 447 451
49. D. Tantin RNA polymerase II elongation complexes containing the Cockayne syndrome group B protein interact with a molecular complex containing the transcription factor IIH components xeroderma pigmentosum B and p62 J. Biol. Chem. 273 1998 27794 27799
50. D. Tantin, A. Kansal, and M. Carey Recruitment of the putative transcription-repair coupling factor CSB/ERCC6 to RNA polymerase II elongation complexes Mol. Cell. Biol. 17 1997 6803 6814
51. F. Thorel, A. Constantinou, I. Dunand-Sauthier, T. Nouspikel, P. Lalle, A. Raams, N.G. Jaspers, W. Vermeulen, M.K. Shivji, R.D. Wood, and S.G. Clarkson Definition of a short region of XPG necessary for TFIIH interaction and stable recruitment to sites of UV damage Mol. Cell. Biol. 24 2004 10670 10680
52. M. Tian, D.A. Jones, M. Smith, R. Shinkura, and F.W. Alt Deficiency in the nuclease activity of xeroderma pigmentosum G in mice leads to hypersensitivity to UV irradiation Mol. Cell. Biol. 24 2004 2237 2242
53. M. Tijsterman, R.A. Verhage, P. van de Putte, J.G. Tasseron-de Jong, and J. Brouwer Transitions in the coupling of transcription and nucleotide excision repair within RNA polymerase II-transcribed genes of Saccharomyces cerevisiae Proc. Natl. Acad. Sci. USA 94 1997 8027 8032
54. F. Tirode, D. Busso, F. Coin, and J.M. Egly Reconstitution of the transcription factor TFIIH: assignment of functions for the three enzymatic subunits, XPB, XPD, and cdk7 Mol. Cell 3 1999 87 95
55. S. Tornaletti, and P.C. Hanawalt Effect of DNA lesions on transcription elongation Biochimie 81 1999 139 146
56. S. Tornaletti, D. Reines, and P.C. Hanawalt Structural characterization of RNA polymerase II complexes arrested by a cyclobutane pyrimidine dimer in the transcribed strand of template DNA J. Biol. Chem. 274 1999 24124 24130
57. A. Tremeau-Bravard, T. Riedl, J.M. Egly, and M.E. Dahmus Fate of RNA polymerase II stalled at a cisplatin lesion J. Biol. Chem. 279 2004 7751 7759
58. Y. Tu, S. Bates, and G.P. Pfeifer Sequence-specific and domain-specific DNA repair in xeroderma pigmentosum and Cockayne syndrome cells J. Biol. Chem. 272 1997 20747 20755
59. A.J. van Gool, E. Citterio, S. Rademakers, R. van Os, W. Vermeulen, A. Constantinou, J.M. Egly, D. Bootsma, and J.H. Hoeijmakers The Cockayne syndrome B protein, involved in transcription-coupled DNA repair, resides in an RNA polymerase II-containing complex EMBO J. 16 1997 5955 5965
60. A. van Hoffen, A.T. Natarajan, L.V. Mayne, A.A. van Zeeland, L.H. Mullenders, and J. Venema Deficient repair of the transcribed strand of active genes in Cockayne's syndrome cells Nucleic Acids Res. 21 1993 5890 5895
61. K.D. Westover, D.A. Bushnell, and R.D. Kornberg Structural basis of transcription: separation of RNA from DNA by RNA polymerase II Science 303 2004 1014 1016
62. 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
63. X. Wu, J. Li, X. Li, C.L. Hsieh, P.M. Burgers, and M.R. Lieber Processing of branched DNA intermediates by a complex of human FEN-1 and PCNA Nucleic Acids Res. 24 1996 2036 2043
64. A. Yu, H.Y. Fan, D. Liao, A.D. Bailey, and A.M. Weiner Activation of p53 or loss of the Cockayne syndrome group B repair protein causes metaphase fragility of human U1, U2, and 5S genes Mol. Cell 5 2000 801 810