Repair of UV lesions in nucleosomes - Intrinsic properties and remodeling

DNA Repair

Volumn 4, Issue 8, 2005, Pages 855-869

  Thoma, Fritz ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

Chromatin; Nucleosomes; Nucleotide excision repair; Photolyase

Indexed keywords

DEOXYRIBODIPYRIMIDINE PHOTOLYASE; DNA;

CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA DAMAGE; ENZYME INHIBITION; EXCISION REPAIR; HUMAN; NONHUMAN; NUCLEOSOME; PHOTOREACTIVATION; PRIORITY JOURNAL; RADIATION EXPOSURE; SHORT SURVEY; ULTRAVIOLET RADIATION; YEAST;

EID: 21844442362     PISSN: 15687864     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dnarep.2005.04.005     Document Type: Review

References (163)

1. R.D. Kornberg, and Y. Lorch Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome Cell 98 1999 285 294
2. D. Escher, and W. Schaffner Gene activation at a distance and telomeric silencing are not affected by yeast histone H1 Mol. Gen. Genet. 256 1997 456 461
3. H.G. Patterton, C.C. Landel, D. Landsman, C.L. Peterson, and R.T. Simpson The biochemical and phenotypic characterization of Hhoip, the putative linker histone H1 of Saccharomyces cerevisiae J. Biol. Chem. 273 1998 7268 7276
4. J.A. Downs, E. Kosmidou, A. Morgan, and S.P. Jackson Suppression of homologous recombination by the Saccharomyces cerevisiae linker histone Mol. Cell 11 2003 1685 1692
5. H.S. Malik, and S. Henikoff Phylogenomics of the nucleosome Nat. Struct. Biol. 10 2003 882 891
6. M. Hild, and R. Paro Anti-silencing from the core: a histone H2A variant protects euchromatin Nat. Cell. Biol. 5 2003 278 280
7. B.D. Strahl, and C.D. Allis The language of covalent histone modifications Nature 403 2000 41 45
8. K.E. Van Holde Chromatin 1989 Springer-Verlag Berlin
9. J. Widom Structure, dynamics, and function of chromatin in vitro Annu. Rev. Biophys. Biomol. Struct. 27 1998 285 327
10. G.J. Narlikar, H.Y. Fan, and R.E. Kingston Cooperation between complexes that regulate chromatin structure and transcription Cell 108 2002 475 487
11. J.Q. Svejstrup Chromatin elongation factors Curr. Opin. Genet. Dev. 12 2002 156 161
12. M.J. Smerdon, and A. Conconi Modulation of DNA damage and DNA repair in chromatin Prog. Nucl. Acid Res. Mol. Biol. 62 1999 227 255
13. F. Thoma Light and dark in chromatin repair: repair of UV-induced DNA lesions by photolyase and nucleotide excision repair EMBO J. 18 1999 6585 6598
14. A.M. Gontijo, C.M. Green, and G. Almouzni Repairing DNA damage in chromatin Biochimie 85 2003 1133 1147
15. C.L. Peterson, and J. Cote Cellular machineries for chromosomal DNA repair Genes Dev. 18 2004 602 616
16. S.D. Cline, and P.C. Hanawalt Who's on first in the cellular response to DNA damage? Nat. Rev. Mol. Cell Biol. 4 2003 361 372
17. U.M. Muthurajan, Y.J. Park, R.S. Edayathumangalam, R.K. Suto, S. Chakravarthy, P.N. Dyer, and K. Luger Structure and dynamics of nucleosomal DNA Biopolymers 68 2003 547 556
18. T.J. Richmond, J.T. Finch, B. Rushton, D. Rhodes, and A. Klug Structure of the nucleosome core particle at 7 A resolution Nature 311 1984 532 537
19. K. Luger, A.W. Mader, R.K. Richmond, D.F. Sargent, and T.J. Richmond Crystal structure of the nucleosome core particle at 2.8 A resolution Nature 389 1997 251 260
20. T.J. Richmond, and C.A. Davey The structure of DNA in the nucleosome core Nature 423 2003 145 150
21. R.K. Suto, R.S. Edayathumangalam, C.L. White, C. Melander, J.M. Gottesfeld, P.B. Dervan, and K. Luger Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands J. Mol. Biol. 326 2003 371 380
22. C.L. White, R.K. Suto, and K. Luger Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions EMBO J. 20 2001 5207 5218
23. R.K. Suto, M.J. Clarkson, D.J. Tremethick, and K. Luger Crystal structure of a nucleosome core particle containing the variant histone H2A.Z Nat. Struct. Biol. 7 2000 1121 1124
24. M.D. Meneghini, M. Wu, and H.D. Madhani Conserved Histone Variant H2A.Z Protects Euchromatin from the Ectopic Spread of Silent Heterochromatin Cell 112 2003 725 736
25. W. Kruger, C.L. Peterson, A. Sil, C. Coburn, G. Arents, E.N. Moudrianakis, and I. Herskowitz Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription Genes Dev. 9 1995 2770 2779
26. A. Flaus, C. Rencurel, H. Ferreira, N. Wiechens, and T. Owen-Hughes Sin mutations alter inherent nucleosome mobility EMBO J. 23 2004 343 353
27. U.M. Muthurajan, Y. Bao, L.J. Forsberg, R.S. Edayathumangalam, P.N. Dyer, C.L. White, and K. Luger Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions EMBO J. 23 2004 260 271
28. R.T. Simpson Mechanism of a reversible, thermally induced conformational change in chromatin core particles J. Biol. Chem. 254 1979 10123 10127
29. A. Prunell Periodicity of exonuclease III digestion of chromatin and the pitch of deoxyribonucleic acid on the nucleosome Biochemistry 22 1983 4887 4894
30. V.M. Studitsky, D.J. Clark, and G. Felsenfeld Overcoming a nucleosomal barrier to transcription Cell 83 1995 19 27
31. J.D. Anderson, and J. Widom Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites J. Mol. Biol. 296 2000 979 987
32. C. Wu, and A. Travers A 'one-pot' assay for the accessibility of DNA in a nucleosome core particle Nucl. Acids Res. 32 2004 e122
33. G. Li, and J. Widom Nucleosomes facilitate their own invasion Nat. Struct. Mol. Biol. 11 2004 763 769
34. P. Beard Mobility of histones on the chromosome of simian virus 40 Cell 15 1978 955 967
35. R.T. Simpson, and D.W. Stafford Structural features of a phased nucleosome core particle Proc. Natl. Acad. Sci. U.S.A. 80 1983 51 55
36. S. Pennings, G. Meersseman, and E.M. Bradbury Mobility of positioned nucleosomes on 5 S rDNA J. Mol. Biol. 220 1991 101 110
37. A. Flaus, and T.J. Richmond Positioning and stability of nucleosomes on MMTV 3′LTR sequences J. Mol. Biol. 275 1998 427 441
38. G. Meersseman, S. Pennings, and E.M. Bradbury Mobile nucleosomes-a general behavior EMBO J. 11 1992 2951 2959
39. M.J. Fedor, N.F. Lue, and R.D. Kornberg Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast J. Mol. Biol. 204 1988 109 127
40. F. Thoma, and R.T. Simpson Local protein-DNA interactions may determine nucleosome positions on yeast plasmids Nature 315 1985 250 252
41. F. Thoma Protein-DNA interactions and nuclease-sensitive regions determine nucleosome positions on yeast plasmid chromatin J. Mol. Biol. 190 1986 177 190
42. F. Thoma, and M. Zatchej Chromatin folding modulates nucleosome positioning in yeast minichromosomes Cell 55 1988 945 953
43. S. Tanaka, M. Zatchej, and F. Thoma Artificial nucleosome positioning sequences tested in yeast minichromosomes: a strong rotational setting is not sufficient to position nucleosomes in vivo EMBO J. 11 1992 1187 1193
44. X.-Y. Zhang, and W. Hörz Nucleosomes are positioned on mouse satellite DNA in multiple highly specific frames that are correlated with a diverged subrepeat of nine base-pairs J. Mol. Biol. 176 1984 105 129
45. M. Buttinelli, E. Di Mauro, and R. Negri Multiple nucleosome positioning with unique rotational setting for the Saccharomyces cerevisiae 5S rRNA gene in vitro and in vivo Proc. Natl. Acad. Sci. U.S.A. 90 1993 9315 9319
46. G. Fragoso, S. John, M.S. Roberts, and G.L. Hager Nucleosome positioning on the MMTV LTR results from the frequency-biased occupancy of multiple frames Genes Dev. 9 1995 1933 1947
47. S. Tanaka, M. Livingstone-Zatchej, and F. Thoma Chromatin structure of the yeast URA3 gene at high resolution provides insight into structure and positioning of nucleosomes in the chromosomal context J. Mol. Biol. 257 1996 919 934
48. P.B. Becker, and W. Horz ATP-dependent nucleosome remodeling Annu. Rev. Biochem. 71 2002 247 273
49. P. Korber, and W. Horz SWRred not shaken; mixing the histones Cell 117 2004 5 7
50. A. Flaus, and T. Owen-Hughes Mechanisms for ATP-dependent chromatin remodelling: farewell to the tuna-can octamer? Curr. Opin. Genet. Dev. 14 2004 165 173
51. G. Felsenfeld, and M. Groudine Controlling the double helix Nature 421 2003 448 453
52. S.K. Kurdistani, and M. Grunstein Histone acetylation and deacetylation in yeast Nat. Rev. Mol. Cell. Biol. 4 2003 276 284
53. K.E. Van Holde, and T.D. Yager Nucleosome motion: evidence and models C. Nicolini P.O.P. Ts'o Structure and Function of the Genetic Apparatus 1985 Plenum Press New York, NY 35 53
54. P.B. Becker Nucleosome sliding: facts and fiction EMBO J. 21 2002 4749 4753
55. H. Park, K. Zhang, Y. Ren, S. Nadji, N. Sinha, J.S. Taylor, and C. Kang Crystal structure of a DNA decamer containing a cis-syn thymine dimer Proc. Natl. Acad. Sci. U.S.A. 99 2002 15965 15970
56. J.K. Kim, and B.S. Choi The solution structure of DNA duplex- decamer containing the (6-4) photoproduct of thymidylyl(3′->5′)thymidine by NMR and relaxation matrix refinement Eur. J. Biochem. 228 1995 849 854
57. M.M. Becker, and Z. Wang Origin of ultraviolet damage in DNA J. Mol. Biol. 210 1989 429 438
58. M.M. Becker, and J.C. Wang Use of light for footprinting DNA in vivo Nature 309 1984 682 687
59. S.B. Selleck, and J. Majors Photofootprinting in vivo detects transcription-dependent changes in yeast TATA boxes Nature 325 1987 173 177
60. G.P. Pfeifer, R. Drouin, A.D. Riggs, and G.P. Holmquist Binding of transcription factors creates hot spots for UV photoproducts in vivo Mol. Cell. Biol. 12 1992 1798 1804
61. S. Tornaletti, and G.P. Pfeifer UV light as a footprinting agent: modulation of UV-induced DNA damage by transcription factors bound at the promoters of three human genes J. Mol. Biol. 249 1995 714 728
62. Z. Wang, and M.M. Becker Selective visualization of gene structure with ultraviolet light Proc. Natl. Acad. Sci. U.S.A. 85 1988 654 658
63. U. Schieferstein, and F. Thoma Modulation of cydobutane pyrimidine dimer formation in a positioned nucleosome containing poly(dA.dT) tracts Biochemistry 35 1996 7705 7714
64. U. Schieferstein, and F. Thoma Site-specific repair of cydobutane pyrimidine dimers in a positioned nucleosome by photolyase and T4 endonuclease V in vitro EMBO J. 17 1998 306 316
65. H. Gaillard, D.J. Fitzgerald, C.L. Smith, C.L. Peterson, T.J. Richmond, and F. Thoma Chromatin remodeling activities act on UV-damaged nucleosomes and modulate DNA damage accessibility to photolyase J. Biol. Chem. 278 2003 17655 17663
66. J.M. Gale, K.A. Nissen, and M.J. Smerdon UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases Proc. Natl. Acad. Sci. U.S.A. 84 1987 6644 6648
67. J.M. Gale, and M.J. Smerdon UV induced (6-4) photoproducts are distributed differently than cydobutane dimers in nucleosomes Photochem. Photobiol. 51 1990 411 417
68. J.R. Pehrson Thymine dimer formation as a probe of the path of DNA in and between nucleosomes in intact chromatin Proc. Natl. Acad. Sci. U.S.A. 86 1989 9149 9153
69. J.R. Pehrson Probing the conformation of nucleosome linker DNA in situ with pyrimidine dimer formation J. Biol. Chem. 270 1995 22440 22444
70. D.W. Brown, L.J. Libertini, C. Suquet, E.W. Small, and M.J. Smerdon Unfolding of nucleosome cores dramatically changes the distribution of ultraviolet photoproducts in DNA Biochemistry 32 1993 10527 10531
71. C. Suquet, and M.J. Smerdon UV damage to DNA strongly influences its rotational setting on the histone surface of reconstituted nucleosomes J. Biol. Chem. 268 1993 23755 23757
72. D.B. Mann, D.L. Springer, and M.J. Smerdon DNA damage can alter the stability of nucleosomes: effects are dependent on damage type Proc. Natl. Acad. Sci. U.S.A. 94 1997 2215 2220
73. R. Lucchini, R.E. Wellinger, and J.M. Sogo Nucleosome positioning at the replication fork EMBO J. 20 2001 7294 7302
74. B. Suter, M. Livingstone-Zatchej, and F. Thoma Chromatin structure modulates DNA repair by photolyase in vivo EMBO J. 16 1997 2150 2160
75. M. Livingstone-Zatchej, B. Suter, and F. Thoma Photolyase: a molecular tool to characterize chromatin structure in yeast P. Becker Methods in Molecular Biology "Chromatin" vol. 119 1999 245 259
76. E.C. Friedberg, G.C. Walker, and W. Siede DNA repair and mutagenesis 1995 ASM Press Washington, DC
77. E.C. Friedberg The discovery of enzymatic photoreactivation and the question of priority: the letters of Salvador Luria and Albert Kelner Biochimie 81 1999 7 13
78. A. Sancar Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors Chem. Rev. 103 2003 2203 2238
79. M. Byrdin, V. Sartor, A.P. Eker, M.H. Vos, C. Aubert, K. Brettel, and P. Mathis Intraprotein electron transfer and proton dynamics during photoactivation of DNA photolyase from E. coli: review and new insights from an "inverse" deuterium isotope effect Biochim. Biophys. Acta 1655 2004 64 70
80. T. Carell, L.T. Burgdorf, L.M. Kundu, and M. Cichon The mechanism of action of DNA photolyases Curr. Opin. Chem. Biol. 5 2001 491 498
81. G.B. Sancar, and F.W. Smith Interactions between yeast photolyase and nucleotide excision repair proteins in Saccharomyces cerevisiae and Escherichia coli Mol. Cell. Biol. 9 1989 4767 4776
82. J.V. Kosmoski, E.J. Ackerman, and M.J. Smerdon DNA repair of a single UV photoproduct in a designed nucleosome Proc. Natl. Acad. Sci. U.S.A. 98 2001 10113 10118
83. L.K. Gordon, and W.A. Haseltine Comparison of the cleavage of pyrimidine dimers by the bacteriophage T4 and Micrococcus luteus UV-specific endonucleases J. Biol. Chem. 255 1980 12047 12050
84. D.G. Vassylyev, T. Kashiwagi, Y. Mikami, M. Ariyoshi, S. Iwai, E. Ohtsuka, and K. Morikawa Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition Cell 83 1995 773 782
85. M. Baer, and G.B. Sancar Photolyases from Saccharomyces cerevisiae and Escherichia coli recognize common binding determinants in DNA containing pyrimidine dimers Mol. Cell. Biol. 9 1989 4777 4788
86. G.B. Sancar Enzymatic photoreactivation: 50 years and counting Mutat. Res. 451 2000 25 37
87. Y.H. You, D.H. Lee, J.H. Yoon, S. Nakajima, A. Yasui, and G.P. Pfeifer Cyclobutane pyrimidine dimers are responsible for the vast majority of mutations induced by UVB irradiation in mammalian cells J. Biol. Chem. 276 2001 44688 44694
88. M.E. Fitch, S. Nakajima, A. Yasui, and J.M. Ford In vivo recruitment of XPC to UV-induced cyclobutane pyrimidine dimers by the DDB2 gene product J. Biol. Chem. 278 2003 46906 46910
89. W. Schul, J. Jans, Y.M. Rijksen, K.H. Klemann, A.P. Eker, J. de Wit, O. Nikaido, S. Nakajima, A. Yasui, J.H. Hoeijmakers, and G.T. van der Horst Enhanced repair of cyclobutane pyrimidine dimers and improved UV resistance in photolyase transgenic mice EMBO J. 21 2002 4719 4729
90. S. Prakash, and L. Prakash Nucleotide excision repair in yeast Mutat. Res. 451 2000 13 24
91. B. Suter, and F. Thoma DNA-repair by photolyase reveals dynamic properties of nucleosome positioning in vivo J. Mol. Biol. 319 2002 395 406
92. A. Aboussekhra, and F. Thoma Nucleotide excision repair and photolyase preferentially repair the nontranscribed strand of RNA polymerase Ill-transcribed genes in Saccharomyces cerevisiae Genes Dev. 12 1998 411 421
93. B. Suter, G. Schnappauf, and F. Thoma Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo Nucl. Acids Res. 28 2000 4083 4089
94. N.R. Morse, V. Meniel, and R. Waters Photoreactivation of UV-induced cyclobutane pyrimidine dimers in the MFA2 gene of Saccharomyces cerevisiae Nucl. Acids Res. 30 2002 1799 1807
95. B. Suter, R.E. Wellinger, and F. Thoma DNA repair in a yeast origin of replication: contributions of photolyase and nucleotide excision repair Nucl. Acids Res. 28 2000 2060 2068
96. C. Capiaghi, T.V. Ho, and F. Thoma Kinetochores prevent repair of UV damage in Saccharomyces cerevisiae centromeres Mol. Cell. Biol. 24 2004 6907 6918
97. M. Livingstone-Zatchej, R. Marcionelli, K. Moller, R. De Pril, and F. Thoma Repair of UV lesions in silenced chromatin provides in vivo evidence for a compact chromatin structure J. Biol. Chem. 278 2003 37471 37479
98. M. Livingstone-Zatchej, A. Meier, B. Suter, and F. Thoma RNA polymerase II transcription inhibits DNA repair by photolyase in the transcribed strand of active yeast genes Nucl. Acids Res. 25 1997 3795 3800
99. A. Meier, M. Livingstone-Zatchej, and F. Thoma Repair of active and silenced rDNA in yeast: the contributions of photolyase and transcription- coupled nucleotide excision repair J. Biol. Chem. 277 2002 11845 11852
100. J. Bedoyan, R. Gupta, F. Thoma, and M.J. Smerdon Transcription, nucleosome stability, and DNA repair in a yeast minichromosome J. Biol. Chem. 267 1992 5996 6005
101. R.D. Phair, and T. Misteli High mobility of proteins in the mammalian cell nucleus Nature 404 2000 604 609
102. C.P. Rubbi, and J. Milner p53 is a chromatin accessibility factor for nucleotide excision repair of DNA damage EMBO J. 22 2003 975 986
103. X. Shen, G. Mizuguchi, A. Hamiche, and C. Wu A chromatin remodelling complex involved in transcription and DNA processing Nature 406 2000 541 544
104. H. Koyama, M. Itoh, K. Miyahara, and E. Tsuchiya Abundance of the RSC nucleosome-remodeling complex is important for the cells to tolerate DNA damage in Saccharomyces cerevisiae FEBS Lett. 531 2002 215 221
105. N.A. Kent, N. Karabetsou, P.K. Politis, and J. Mellor In vivo chromatin remodeling by yeast ISWI homologs Isw1p and Isw2p Genes Dev. 15 2001 619 626
106. T.G. Fazzio, and T. Tsukiyama Chromatin remodeling in vivo: evidence for a nucleosome sliding mechanism Mol. Cell 12 2003 1333 1340
107. T. Tsukiyama, J. Palmer, C.C. Landel, J. Shiloach, and C. Wu Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae Genes Dev. 13 1999 686 697
108. D.J. Fitzgerald, C. DeLuca, I. Berger, H. Gaillard, R. Sigrist, K. Schimmele, and T.J. Richmond Reaction cycle of the yeast Isw2 chromatin remodeling complex EMBO J. 23 2004 3836 3843
109. J.H. Hoeijmakers Genome maintenance mechanisms for preventing cancer Nature 411 2001 366 374
110. P.C. Hanawalt Subpathways of nucleotide excision repair and their regulation Oncogene 21 2002 8949 8956
111. W.L. de Laat, N.G. Jaspers, and J.H. Hoeijmakers Molecular mechanism of nucleotide excision repair Genes Dev. 13 1999 768 785
112. M. Wakasugi, and A. Sancar Order of assembly of human DNA repair excision nuclease J. Biol. Chem. 274 1999 18759 18768
113. 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
114. K. Sugasawa, J.M. Ng, C. Masutani, S. Iwai, P.J. van der Spek, A.P. Eker, F. Hanaoka, D. Bootsma, and J.H. Hoeijmakers Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair Mol. Cell 2 1998 223 232
115. R. Dip, U. Camenisch, and H. Naegeli Mechanisms of DNA damage recognition and strand discrimination in human nucleotide excision repair DNA Rep. (Amsterdam) 3 2004 1409 1423
116. M.J. Smerdon, and M.W. Lieberman Nucleosome rearrangement in human chromatin during UV-induced DNA-reapir synthesis Proc. Natl. Acad. Sci. U.S.A. 75 1978 4238 4241
117. M.J. Smerdon, and M.W. Lieberman Distribution within chromatin of deoxyribonucleic acid repair synthesis occurring at different times after ultraviolet radiation Biochemistry 19 1980 2992 3000
118. K.A. Nissen, S.Y. Lan, and M.J. Smerdon Stability of nucleosome placement in newly repaired regions of DNA J. Biol. Chem. 261 1986 8585 8588
119. K.A. Jensen, and M.J. Smerdon DNA repair within nucleosome cores of UV-irradiated human cells Biochemistry 29 1990 4773 4782
120. J.C. Huang, and A. Sancar Determination of minimum substrate size for human excinuclease J. Biol. Chem. 269 1994 19034 19040
121. J.C. Huang, D.L. Svoboda, J.T. Reardon, and A. Sancar Human nucleotide excision nuclease removes thymine dimers from DNA by incising the 22nd phosphodiester bond 5′ and the 6th phosphodiester bond 3′ to the photodimer Proc. Natl. Acad. Sci. U.S.A. 89 1992 3664 3668
122. P.H. Gaillard, E.M. Martini, P.D. Kaufman, B. Stillman, E. Moustacchi, and G. Almouzni Chromatin assembly coupled to DNA repair: a new role for chromatin assembly factor I Cell 86 1996 887 896
123. P.H. Gaillard, J.G. Moggs, D.M. Roche, J.P. Quivy, P.B. Becker, R.D. Wood, and G. Almouzni Initiation and bidirectional propagation of chromatin assembly from a target site for nucleotide excision repair EMBO J. 16 1997 6281 6289
124. C.M. Green, and G. Almouzni Local action of the chromatin assembly factor CAF-1 at sites of nucleotide excision repair in vivo EMBO J. 22 2003 5163 5174
125. P.D. Kaufman, R. Kobayashi, and B. Stillman Ultraviolet radiation sensitivity and reduction of telomeric silencing Saccharomyces cerevisiae cells lacking chromatin assembly factor-I Gene Dev. 11 1997 345 357
126. J.K. Tyler, C.R. Adams, S.R. Chen, R. Kobayashi, R.T. Kamakaka, and J.T. Kadonaga The RCAF complex mediates chromatin assembly during DNA replication and repair Nature 402 1999 555 560
127. M. Volker, M.J. Mone, P. Karmakar, A. van Hoffen, W. Schul, W. Vermeulen, J.H. Hoeijmakers, R. van Driel, A.A. van Zeeland, and L.H. Mullenders Sequential assembly of the nucleotide excision repair factors in vivo Mol. Cell 8 2001 213 224
128. M. Wakasugi, A. Kawashima, H. Morioka, S. Linn, A. Sancar, T. Mori, O. Nikaido, and T. Matsunaga DDB accumulates at DNA damage sites immediately after UV irradiation and directly stimulates nucleotide excision repair J. Biol. Chem. 277 2002 1637 1640
129. M. Brand, J.G. Moggs, M. Oulad-Abdelghani, F. Lejeune, F.J. Dilworth, J. Stevenin, G. Almouzni, and L. Tora UV-damaged DNA-binding protein in the TFTC complex links DNA damage recognition to nucleosome acetylation EMBO J. 20 2001 3187 3196
130. D. Hoogstraten, A.L. Nigg, H. Heath, L.H. Mullenders, R. van Driel, J.H. Hoeijmakers, W. Vermeulen, and A.B. Houtsmuller Rapid Switching of TFIIH between RNA polymerase I and II transcription and DNA repair in vivo Mol. Cell 10 2002 1163 1174
131. A.B. Houtsmuller, S. Rademakers, A.L. Nigg, D. Hoogstraten, J.H. Hoeijmakers, and W. Vermeulen Action of DNA repair endonuclease ERCC1/XPF in living cells Science 284 1999 958 961
132. Z.G. Wang, X.H. Wu, and E.C. Friedberg Nucleotide excision repair of DNA by human cell extracts is suppressed in reconstituted nucleosomes J. Biol. Chem. 266 1991 22472 22478
133. M. Araki, C. Masutani, T. Maekawa, Y. Watanabe, A. Yamada, R. Kusumoto, D. Sakai, K. Sugasawa, Y. Ohkuma, and F. Hanaoka Reconstitution of damage DNA excision reaction from SV40 minichromosomes with purified nucleotide excision repair proteins Mutat. Res. 459 2000 147 160
134. X. Liu, and M.J. Smerdon Nucleotide excision repair of the 5 S ribosomal RNA gene assembled into a nucleosome J. Biol. Chem. 275 2000 23729 23735
135. K. Ura, M. Araki, H. Saeki, C. Masutani, T. Ito, S. Iwai, T. Mizukoshi, Y. Kaneda, and F. Hanaoka ATP-dependent chromatin remodeling facilitates nucleotide excision repair of UV-induced DNA lesions in synthetic dinucleosomes EMBO J. 20 2001 2004 2014
136. R. Hara, J. Mo, and A. Sancar DNA damage in the nucleosome core is refractory to repair by human excision nuclease Mol. Cell Biol. 20 2000 9173 9181
137. R. Hara, and A. Sancar Effect of damage type on stimulation of human excision nuclease by SWI/SNF chromatin remodeling factor Mol. Cell Biol. 23 2003 4121 4125
138. R. Hara, and A. Sancar The SWI/SNF chromatin-remodeling factor stimulates repair by human excision nuclease in the mononucleosome core particle Mol. Cell. Biol. 22 2002 6779 6787
139. R.E. Wellinger, and F. Thoma Nucleosome structure and positioning modulate nucleotide excision repair in the non-transcribed strand of an active gene EMBO J. 16 1997 5046 5056
140. M. Tijsterman, R. de Pril, J.G. Tasseron-de Jong, and J. Brouwer RNA polymerase II transcription suppresses nucleosomal modulation of UV-induced (6-4) photoproduct and cyclobutane pyrimidine dimer repair in yeast Mol. Cell. Biol. 19 1999 934 940
141. J.A. Ferreiro, N.G. Powell, N. Karabetsou, N.A. Kent, J. Mellor, and R. Waters Cbf1p modulates chromatin structure, transcription and repair at the Saccharomyces cerevisiae MET16 locus Nucl. Acids Res. 32 2004 1617 1626
142. N.G. Powell, J. Ferreiro, N. Karabetsou, J. Mellor, and R. Waters Transcription, nucleosome positioning and protein binding modulate nucleotide excision repair of the Saccharomyces cerevisiae MET17 promoter DNA Rep. (Amsterdam) 2 2003 375 386
143. S. Li, and M.J. Smerdon Nucleosome structure and repair of N- methylpurines in the GAL1-10 genes of Saccharomyces cerevisiae J. Biol. Chem. 277 2002 44651 44659
144. S. Li, M. Livingstone-Zatchej, R. Gupta, M. Meijer, F. Thoma, and M.J. Smerdon Nucleotide excision repair in a constitutive and inducible gene of a yeast minichromosome in intact cells Nucl. Acids Res. 27 1999 3610 3620
145. S.G. Bavykin, S.I. Usachenko, A.I. Lishanskaya, V.V. Shick, A.V. Belyavsky, I.M. Undritsov, A.A. Strokov, I.A. Zalenskaya, and A.D. Mirzabekov Primary organization of nucleosomal core particles is invariable in repressed and active nuclei from animal, plant and yeast cells Nucl. Acids Res. 13 1985 3439 3459
146. J.R. Davie, C.A. Saunders, J.M. Walsh, and S.C. Weber Histone modifications in the yeast S. cerevisiae Nucl. Acids Res. 9 1981 3205 3215
147. R.H. Morse, D.S. Pederson, A. Dean, and R.T. Simpson Yeast nucleosomes allow thermal untwisting of DNA Nucl. Acids Res. 15 1987 10311 10330
148. M. Pineiro, C. Puerta, and E. Palacian Yeast nucleosomal particles: structural and transcriptional properties Biochemistry 30 1991 5805 5810
149. F. Thoma, T. Koller, and A. Klug Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin J. Cell. Biol. 83 1979 403 427
150. S. Pennings, G. Meersseman, and E.M. Bradbury Linker histones H1 and H5 prevent the mobility of positioned nucleosomes Proc. Natl. Acad. Sci. U.S.A. 91 1994 10275 10279
151. M.J. Smerdon, S.Y. Lan, R.E. Calza, and R. Reeves Sodium butyrate stimulates DNA repair in UV-irradiated normal and xeroderma pigmentosum human fibroblasts J. Biol. Chem. 257 1982 13441 13447
152. Y. Teng, Y. Yu, and R. Waters The Saccharomyces cerevisiae histone acetyltransferase Gcn5 has a role in the photoreactivation and nucleotide excision repair of UV-induced cyclobutane pyrimidine dimers in the MFA2 gene J. Mol. Biol. 316 2002 489 499
153. A. Mees, T. Klar, P. Gnau, U. Hennecke, A.P. Eker, T. Carell, and L.O. Essen Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair Science 306 2004 1789 1793
154. R.D. Miller, L. Prakash, and S. Prakash Defective excision of pyrimidine dimers and interstrand DNA crosslinks in rad7 and rad23 mutants of Saccharomyces cerevisiae Mol. Gen. Genet. 188 1982 235 239
155. R. Verhage, A.M. Zeeman, N. de Groot, F. Gleig, D.D. Bang, P. van de Putte, and J. Brouwer The RAD7 and RAD16 genes, which are essential for pyrimidine dimer removal from the silent mating type loci, are also required for repair of the nontranscribed strand of an active gene in Saccharomyces cerevisiae Mol. Cell. Biol. 14 1994 6135 6142
156. R.A. Verhage, A.M. Zeeman, M. Lombaerts, P. van de Putte, and J. Brouwer Analysis of gene- and strand-specific repair in the moderately UV- sensitive Saccharomyces cerevisiae rad23 mutant Mutat. Res. 362 1996 155 165
157. J.P. Mueller, and M.J. Smerdon Repair of plasmid and genomic DNA in a rad7 delta mutant of yeast Nucl. Acids Res. 23 1995 3457 3464
158. Y. Teng, S. Li, R. Waters, and S.H. Reed Excision repair at the level of the nucleotide in the Saccharomyces cerevisiae MFA2 gene: mapping of where enhanced repair in the transcribed strand begins or ends and identification of only a partial rad16 requisite for repairing upstream control sequences J. Mol. Biol. 267 1997 324 337
159. S. Yu, T. Owen-Hughes, E.C. Friedberg, R. Waters, and S.H. Reed The yeast Rad7/Rad16/ABf1 complex generates superhelical torsion in DNA that is required for nucleotide excision repair DNA Rep. 3 2004 277 287
160. J.T. Reardon, and A. Sancar Molecular anatomy of the human excision nuclease assembled at sites of DNA damage Mol. Cell. Biol. 22 2002 5938 5945
161. J.T. Reardon, and A. Sancar Recognition and repair of the cyclobutane thymine dimer, a major cause of skin cancers, by the human excision nuclease Genes Dev. 17 2003 2539 2551
162. J.Y. Tang, B.J. Hwang, J.M. Ford, P.C. Hanawalt, and G. Chu Xeroderma pigmentosum p48 gene enhances global genomic repair and suppresses UV-induced mutagenesis Mol. Cell 5 2000 737 744
163. J. Tang, and G. Chu Xeroderma pigmentosum complementation group E and UV-damaged DNA-binding protein DNA Rep. (Amsterdam) 1 2002 601 616