Source: http://www.asmscience.org/content/book/10.1128/9781555816704.ch10
Timestamp: 2019-04-25 18:03:27+00:00

Document:
Levels of folding of DNA and nucleosomes that give rise to highly condensed chromatin.
Ratio of the amount of repair synthesis per unit DNA in MNase-sensitive and -resistant regions as a function of repair time after UV irradiation of cells. Note that very soon after UV irradiation, the repair synthesis label is distributed largely in MNase-sensitive regions of the genome. However, at later times the label is distributed more uniformly between MNase-sensitive and -resistant regions ( 147 ).
The methylation of DNA following NER of UV damage in confluent and in logarithmic-phase human fibroblasts is slower and less complete than in undamaged cells undergoing normal semiconservative DNA replication ( 77 ).
Effect of NER on the methylation of DNA. Repair of damage immediately in advance of a replication fork is shown on the left. If excision is initiated close to a methylated controlling sequence (A), a methylated base may be removed (B) and replaced (by repair synthesis) with a nonmethylated base (C). Replication of this region before remethylation can occur gives rise to a nonmethylated DNA duplex, which is not a substrate for the maintenance methylase. The other hemimethylated DNA duplex is normally methylated (D). Repair of damage close to a site of methylation immediately after replication is shown on the right. Excision of damage before the daughter strands have been methylated (A’ and B’) gives rise to a nonmethylated DNA molecule (C ‘), which is not a substrate for the maintenance methylase.
1. Adolphs, K. W.,, S. M. Cheng,, J. R. Paulson, and, U. K. Laemmli. 1977. Isolation of a protein scaffold from mitotic HeLa cell chromosomes. Proc. Natl. Acad. Sci. USA 74 :4937– 4941.
2. Ausio, J., and, D. W. Abbot. 2004. The role of histone variability in chromatin stability and folding, p. 241– 290. In J. Zlatanova and, S. H. Leuba (ed.), Chromatin Structure and Dynamics: State of the Art. Elsevier, Amsterdam, The Netherlands.
3. Awrey, D. E.,, R. G. Weilbaecher,, S. A. Hemming,, S. M. Orlicky,, C. M. Kane, and, A. M. Edwards. 1997. Transcription elongation through DNA arrest sites. A multistep process involving both RNA polymerase II subunit RPB9 and TFIIS. J. Biol. Chem. 272 :14747– 14754.
4. Balajee, A. S.,, A. May,, G. L. Dianov,, E. C. Friedberg, and, V. A. Bohr. 1997. Reduced RNA-polymerase II transcription in intact and per-meabilized Cockayne syndrome group B cells. Proc. Natl. Acad. Sci. USA 94 :4306– 4311.
5. Baxter, B. K., and, M. J. Smerdon. 1998. Nucleosome unfolding during DNA repair in normal and xeroderma pigmentosum (group C) human cells. J. Biol. Chem. 273 :17517– 17524.
6. Bazett-Jones, D. P., and, C. H. Eskiw. 2004. Chromatin structure and function: lessons from imaging techniques, p. 343– 368. In J. Zlatanova and, S. H. Leuba (ed.), Chromatin Structure and Dynamics: State of the Art. Elsevier, Amsterdam, The Netherlands.
7. Beaudenon, S. L.,, M. R. Huacani,, G. Wang,, D. P. McDonnell, and, J. M. Huibregtse. 1999. Rsp5 ubiquitin-protein ligase mediates DNA damage-induced degradation of the large subunit of RNA polymerase II in Saccharomyces cerevisiae. Mol. Cell. Biol. 19 :6972– 6979.
8. Benyajati, C., and, A. Worcel. 1976. Isolation, characterization, and structure of the folded interphase genome of Drosophila melanogaster. Cell 9 :393– 407.
9. Bhatia, P. K.,, R. A. Verhage,, J. Brouwer, and, E. C. Friedberg. 1996. Molecular cloning and characterization of Saccharomyces cerevisiae RAD28, the yeast homolog of the human Cockayne syndrome A (CSA) gene. J. Bacteriol. 178 :5977– 5988.
10. Bill, C. A.,, B. M. Grochan,, R. E. Meyn,, V. A. Bohr, and, P. J. Tofilon. 1991. Loss of intragenomic DNA repair heterogeneity with cellular differentiation J. Biol. Chem. 266 :21821– 21826.
11. Bird, A., 2002. DNA methylation patterns and epigenetic memory. Genes Dev. 16 :6– 21.
12. Bodell, W. J., 1977. Nonuniform distribution of DNA repair in chromatin after treatment with methyl methanesulfonate. Nucleic Acids Res. 4 :2619– 2628.
13. Bodell, W. J., and, J. E. Cleaver. 1981. Transient conformation changes in chromatin during excision repair of ultraviolet damage to DNA. Nucleic Acids Res. 9 :203– 213.
14. Bohr, V. A., 1988. DNA repair and transcriptional activity in genes. J. Cell Sci. 91 :175– 178.
15. Bohr, V. A., 1991. Gene specific DNA repair. Carcinogenesis 12 :1983– 1992.
16. Bohr, V. A.,, D. H. Phillips, and, P. C. Hanawalt. 1987. Heterogeneous DNA damage and repair in the mammalian genome. Cancer Res. 47 :6426– 6436.
17. Bohr, V. A.,, C. A. Smith,, D. S. Okumoto, and, P. C. Hanawalt. 1985. 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 :359– 369.
18. Bootsma, D., and, J. H. J. Hoeijmakers. 1993. DNA repair: engagement with transcription. Nature 363 :114– 115.
19. Bowman, K. K.,, C. A. Smith, and, P. C. Hanawalt. 1997. Excision repair patch lengths are similar for transcription-coupled repair and global genome repair in UV-irradiated human-cells. Mutat. Res. 385 :95– 105.
20. Bradbury, E. M., and, K. E. van Holde. 2004. Chromatin structure and dynamics: a historical perspective, p. 1– 11. In J. Zlatanova, and, S. H. Leuba (ed.), Chromatin Structure and Dynamics: State of the Art. Elsevier, Amsterdam, The Netherlands.
21. Bregman, D. B.,, R. Halaban,, A. J. van Gool,, K. A. Henning,, E. C. Friedberg, and, S. L. Warren. 1996. UV-induced ubiquitination of RNA polymerase II: a novel modification deficient in Cockayne syndrome cells. Proc. Natl. Acad. Sci. USA 93 :11586– 11590.
22. Bucheli, M.,, L. Lommel, and, K. Sweder. 2001. The defect in transcription-coupled repair displayed by a Saccharomyces cerevisiae rad26 mutant is dependent on carbon source and is not associated with a lack of transcription. Genetics 158 :989– 997.
23. Carothers, A. M.,, W. Zhen,, J. Mucha,, Y. J. Zhang,, R. M. Santella,, D. Grunberger, and, V. A. Bohr. 1992. DNA strand-specific repair of (+ –)-3 alpha,4 beta-dihydroxy-1 alpha,2 alpha-epoxy-1,2,3,4-tetrahydrobenzo [c]phenanthrene adducts in the hamster dihydrofolate reductase gene. Proc. Natl. Acad. Sci. USA 89 :11925– 11929.
24. Chafin, D. R.,, J. M. Vitolo,, L. A. Henricksen,, R. A. Bambara, and, J. J. Hayes. 2000. Human DNA ligase I efficiently seals nicks in nucleosomes. EMBO J. 19 :5492– 5501.
25. Chen, R. H.,, V. M. Maher,, J. Brouwer,, P. van de Putte, and, J. J. McCormick. 1992. Preferential repair and strand-specific repair of benzo [a]pyrene diol epoxide adducts in the HPRT gene of diploid human fibroblasts. Proc. Natl. Acad. Sci. USA 89 :5413– 5417.
26. Chen, Y. H., and, D. F. Bogenhagen. 1993. Effects of DNA lesions on transcription elongation by T7 RNA polymerase. J. Biol. Chem. 268 :5849– 5855.
27. Christians, F. C., and, P. C. Hanawalt. 1992. Inhibition of transcription and strand-specific DNA repair by alpha-amanitin in Chinese hamster ovary cells. Mutat. Res. 274 :93– 101.
28. Christians, F. C., and, P. C. Hanawalt. 1993. Lack of transcription-coupled repair in mammalian ribosomal RNA genes. Biochemistry 32 :10512– 10518.
29. Citterio, E.,, V. van den Boom,, G. Schnitzler,, R. Kanaar,, E. Bonte,, R. E. Kingston,, J. H. J. Hoeijmakers, and, W. Vermeulen. 2000. ATP dependent chromatin remodeling by the Cockayne syndrome B DNA repair-transcription-coupling factor. Mol. Cell. Biol. 20 :7643– 7653.
30. Clark, D. J., and, G. Felsenfeld. 1991. Formation of nucleosomes on positively supercoiled DNA. EMBO J. 10 :387– 395.
31. Cleaver, J. E., 1977. Nucleosome structure controls rates of excision repair in DNA of human cells. Nature 270 :451– 453.
32. Conaway, J. W.,, A. Shilatifard,, A. Dvir, and, R. C. Conaway. 2000. Control of elongation by RNA polymerase II. Trends Biochem. Sci. 25 :375– 380.
33. Conconi, A.,, V. A. Bespalov, and, M. J. Smerdon. 2002. Transcription-coupled repair in RNA polymerase I-transcribed genes of yeast. Proc. Natl. Acad. Sci. USA 99 :649– 654.
34. Cook, P. R., 1999. The organization of replication and transcription. Science 284 :1790– 1795.
35. Cook, P. R., and, I. A. Brazell. 1975. Supercoils in human DNA. J. Cell Sci. 19 :261– 279.
36. Cramer, P.,, D. A. Bushnell, and, R. D. Kornberg. 2001. Structural basis of transcription: RNA polymerase II at 2.8 Ångstrom resolution. Science 292 :1863– 1876.
37. Dammann, R., and, G. P. Pfeifer. 1997. Lack of gene-specific and strand-specific DNA repair in RNA polymerase III-transcribed human transfer RNA genes. Mol. Cell. Biol. 17 :219– 229.
38. Davie, J. R., 2004. Histone modifications, p. 205– 240. In J. Zla-tanova and, S. H. Leuba (ed.), Chromatin Structure and Dynamics: State of the Art. Elsevier, Amsterdam, The Netherlands.
39. Doetsch, P. W., 2002. Translesion synthesis by RNA polymerases: occurrence and biological implications for transcriptional mutagenesis. Mutat. Res. 510 :131– 140.
40. Donahue, B. A.,, R. P. Fuchs,, D. Reines, and, P. C. Hanawalt. 1996. Effects of aminofluorene and acetylaminofluorene DNA adducts on transcriptional elongation by RNA polymerase II. J. Biol. Chem. 271 :10588– 10594.
41. Donahue, B. A.,, S. Yin,, J. S. Taylor,, D. Reines, and, P. C. Hanawalt. 1994. Transcript cleavage by RNA polymerase II arrested by a cyclobutane pyrimidine dimer in the DNA template. Proc. Natl. Acad. Sci. USA 91 :8502– 8506.
42. Dorigo, B.,, T. Schalch,, A. Kulangara,, S. Duda,, R. R. Schroeder, and, T. J. Richmond. 2004. Nucleosome arrays reveal the two-start organization of the chromatin fiber. Science 306 :1571– 1573.
43. Dvir, A.,, J. W. Conaway, and, R. C. Conaway. 2001. Mechanism of transcription initiation and promoter escape by RNA polymerase II. Curr. Opin. Genet. Dev. 11 :209– 214.
44. Eisen, J. A., and, P. C. Hanawalt. 1999. A phylogenomic study of DNA repair genes, proteins, and processes. Mutat. Res. DNA Repair 435 :171– 213.
45. Evans, E.,, J. Fellows,, A. Coffer, and, R. D. Wood. 1997. Open complex formation around a lesion during nucleotide excision repair provides a structure for cleavage by human XPG protein. EMBO J. 16 :625– 638.
46. Felsenfeld, G.,, D. Clark, and, V. Studitsky. 2000. Transcription through nucleosomes. Biophys. Chem. 86 :231– 237.
47. Feng, Z.,, W. Hu,, E. Komissarova,, A. Pao,, M. C. Hung,, G. M. Adair, and, M. S. Tang. 2002. Transcription-coupled DNA repair is genomic context-dependent. J. Biol. Chem. 277 :12777– 12783.
48. Ferdous, A.,, F. Gonzalez,, L. Sun,, T. Kodadek, and, S. A. Johnston. 2001. The 19S regulatory particle of the proteasome is required for efficient transcription elongation by RNA polymerase II. Mol. Cell 7 :981– 991.
49. Friedberg, E. C.,, G. C. Walker, and, W. Siede. 1995. DNA Repair and Mutagenesis. ASM Press, Washington, D.C.
50. Frit, P.,, K. Kwon,, F. Coin,, J. Auriol,, S. Dubaele,, B. Salles, and, J. M. Egly. 2002. Transcriptional activators stimulate DNA repair. Mol. Cell 10 :1391– 1401.
51. Gaillard, P.-H. L.,, J. G. Moggs,, D. M. J. Roche,, J.-P. Quivy,, P. B. Becker,, R. D. Wood, and, G. Almouzni. 1997. Initiation and bidirectional propagation of chromatin assembly from a target site for nucleotide excision repair. EMBO J. 16 :6282– 6289.
52. Gaillard, P. H. L.,, E. M. D. Martini,, P. D. Kaufman,, B. Stillman,, E. Moustacchi, and, G. Almouzni. 1996. Chromatin assembly coupled to DNA repair: a new role for chromatin assembly factor I. Cell 86 :887– 896.
53. Gale, J. M.,, K. A. Nissen, and, M. J. Smerdon. 1987. UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases. Proc. Natl. Acad. Sci. USA 84 :6644– 6648.
54. Gillette, T. G.,, W. Huang,, S. J. Russell,, S. H. Reed,, S. A. Johnston, and, E. C. Friedberg. 2001. The 19S complex of the proteasome regulates nucleotide excision repair in yeast. Genes Dev. 15 :1528– 1539.
55. Gnatt, A. L.,, P. Cramer,, J. Fu,, D. A. Bushnell, and, R. D. Kornberg. 2001. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science 292 :1876– 1882.
56. Green, C. M., and, G. Almouzni. 2002. When repair meets chromatin. First in series on chromatin dynamics. EMBO Rep. 3 :28– 33.
57. Green, C. M., and, G. Almouzni. 2003. Local action of the chromatin assembly factor CAF-1 at sites of nucleotide excision repair in vivo. EMBO J. 22 :5163– 5174.
58. Gregory, S. M., and, K. S. Sweder. 2001. Deletion of the CSB ho- molog, RAD26, yields Spt(–) strains with proficient transcription-coupled repair. Nucleic Acids Res. 29 :3080– 3086.
59. Hanawalt, P. C., 1994. Transcription-coupled repair and human disease. Science 266 :1957– 1958.
60. Hanawalt, P. C., and, G. Spivak. 1999. Transcription-coupled DNA repair: which lesions? Which diseases? p. 169– 179. In M. Dizdaroglu and, A. Karakaya (ed.), Advances in DNA Damage and Repair. Plenum Publishing Corp., New York, N.Y.
61. Hara, R., and, A. Sancar. 2002. The SWI/SNF chromatin-remodeling factor stimulates repair by human excision nuclease in the mononucleosome core particle. Mol. Cell. Biol. 22 :6779– 6787.
62. Hara, R.,, C. P. Selby,, M. Y. Liu,, D. H. Price, and, A. Sancar. 1999. Human transcription release factor 2 dissociates RNA polymerases I and II stalled at a cyclobutane thymine dimer. J. Biol. Chem. 274 :24779– 24786.
63. Harp, J. M.,, B. L. Hanson, and, G. J. Bunick. 2004. The core particle of the nucleosome, p. 13– 44. In J. Zlatanova and, S. H. Leuba (ed.), Chromatin Structure and Dynamics: State of the Art. Elsevier, Amsterdam, The Netherlands.
64. Hemming, S. A.,, D. B. Jansma,, P. F. Macgregor,, A. Goryachev,, J. D. Friesen, and, A. M. Edwards. 2000. RNA polymerase II subunit Rpb9 regulates transcription elongation in vivo. J. Biol. Chem. 275 :35506– 35511.
65. Ho, L., and, P. C. Hanawalt. 1991. Gene-specific DNA repair in terminally differentiating rat myoblasts. Mutat. Res. 255 :123– 141.
66. Hoek, M., and, B. Stillman. 2003. Chromatin assembly factor 1 is essential and couples chromatin assembly to DNA replication in vivo. Proc. Natl. Acad. Sci. USA 100 :12183– 12188.
67. Huang, J. C., and, A. Sancar. 1994. Determination of minimum substrate size for human excinuclease. J. Biol. Chem. 269 :19034– 19040.
68. Hunting, D. J.,, S. L. Dresler, and, M. W. Lieberman. 1985. Multiple conformational states of repair in chromatin during DNA excision repair. Biochemistry 24 :3219– 3225.
69. Ishii, K., and, U. K. Laemmli. 2003. Structural and dynamic functions establish chromatin domains. Mol. Cell 11 :237– 248.
70. Jackson, D. A.,, A. S. Balajee,, L. Mullenders, and, P. R. Cook. 1994. Sites in human nuclei where DNA damaged by ultraviolet-light is repaired: visualization and localization relative to the nucleoskeleton. J. Cell Sci. 107 :1745– 1752.
71. Jackson, D. A.,, A. B. Hassan,, R. J. Errington, and, P. R. Cook. 1994. Sites in human nuclei where damage induced by ultraviolet light is repaired: localization relative to transcription sites and concentrations of proliferating cell nuclear antigen and the tumor-suppressor protein, p53. J. Cell Sci. 107 :1753– 1760.
72. Jackson, V., 2004. What happens to nucleosomes during transcription? p. 467– 491. In J. Zlatanova and, S. H. Leuba (ed.) Chromatin Structure and Dynamics: State of the Art. Elsevier, Amsterdam, The Netherlands.
73. Jansen, L. E. T.,, H. den Dulk,, R. M. Brouns,, M. de Ruijter,, J. A. Brandsma, and, J. Brouwer. 2000. Spt4 modulates Rad26 requirement in transcription-coupled nucleotide excision repair. EMBO J. 19 :6498– 6507.
74. Jenuwein, T., and, C. D. Allis. 2001. Translating the histone code. Science 293 :1074– 1080.
75. Jerzmanowski, A., 2004. The linker histones, p. 75– 102. In J. Zlatanova and, S. H. Leuba (ed.), Chromatin Structure and Dynamics: State of the Art. Elsevier, Amsterdam, The Netherlands.
76. Kamakaka, R. T.,, M. Bulger,, P. D. Kaufman,, B. Stillman, and, J. T. Kadonaga. 1996. Postreplicative chromatin assembly by Drosophila and human chromatin assembly factor 1. Mol. Cell. Biol. 16 :810– 817.
77. Kastan, M. B.,, B. J. Gowans, and, M. W. Lieberman. 1982. Methylation of deoxycytidine incorporated by excision repair synthesis of DNA. Cell 30 :509– 516.
78. Kathe, S. D.,, G. P. Shen, and, S. S. Wallace. 2004. Single-stranded breaks in DNA but not oxidative DNA base damages block transcriptional elongation by RNA polymerase II in HeLa cell nuclear extracts. J. Biol. Chem. 279 :18511– 18520.
79. Kaufman, P. D.,, R. Kobayashi, and, B. Stillman. 1997. Ultraviolet radiation sensitivity and reduction of telomeric silencing in Saccharomyces cerevisiae cells lacking chromatin assembly factor 1. Genes Dev. 11 :345– 357.
80. Kimura, H.,, Y. Tao,, R. G. Roeder, and, P. R. Cook. 1999. Quantitation of RNA polymerase II and its transcription factors in a HeLa cell: little soluble holoenzyme but significant amounts of polymerases attached to the nuclear substructure. Mol. Cell. Biol. 19 :5383– 5392.
81. Kornberg, R. D., 1974. Chromatin structure: a repeating unit of his- tones and DNA. Science 184 :868– 871.
82. Kornberg, R. D., and, Y. Lorch. 1992. Chromatin structure and transcription. Annu. Rev. Cell Biol. 8 :563– 587.
83. Kornberg, R. D., and, J. O. Thomas. 1974. Chromatin structure; oligomers of the histones. Science 184 :865– 868.
84. Kosmoski, J. V.,, E. J. Ackerman, and, M. J. Smerdon. 2001. DNA repair of a single UV photoproduct in a designed nucleosome. Proc. Natl. Acad. Sci. USA 98 :10113– 10118.
85. Kuraoka, I.,, M. Endou,, Y. Yamaguchi,, T. Wada,, H. Handa, and, K. Tanaka. 2003. Effects of endogenous DNA base lesions on transcription elongation by mammalian RNA polymerase II. Implications for transcription-coupled DNA repair and transcriptional mutagenesis. J. Biol. Chem. 278 :7294– 7299.
86. Lander, E. S.,, L. M. Linton,, B. Birren,, C. Nusbaum,, M. C. Zody,, J. Baldwin,, K. Devon,, K. Dewar,, M. Doyle,, W. FitzHugh,, R. Funke,, D. Gage,, K. Harris,, A. Heaford,, J. Howland,, L. Kann,, J. Lehoczky,, R. LeVine,, P. McEwan,, K. McKernan, et al., 2001. Initial sequencing and analysis of the human genome. Nature 409 :860– 921.
87. Langowski, J., and, H. Schiessel. 2004. Theory and computational modeling of the 30 nm chromatin fiber, p. 397– 420. In J. Zlatanova and, S. H. Leuba (ed.), Chromatin Structure and Dynamics: State of the Art. Elsevier, Amsterdam, The Netherlands.
88. Leadon, S. A., and, P. C. Hanawalt. 1984. Ultraviolet irradiation of monkey cells enhances the repair of DNA adducts in alpha DNA. Carcinogenesis 5 :1505– 1510.
89. Leadon, S. A.,, M. E. Zolan, and, P. C. Hanawalt. 1983. Restricted repair of aflatoxin B1 induced damage in alpha DNA of monkey cells. Nucleic Acids Res. 11 :5675– 5689.
90. Lee, K. B.,, D. Wang,, S. J. Lippard, and, P. A. Sharp. 2002. Transcription-coupled and DNA damage-dependent ubiquitination of RNA polymerase II in vitro. Proc. Natl. Acad. Sci. USA 99 :4239– 4244.
91. Lee, S. K.,, S. L. Yu,, L. Prakash, and, S. Prakash. 2001. Requirement for yeast RAD26, a homolog of the human CSB gene, in elongation by RNA polymerase II. Mol. Cell. Biol. 21 :8651– 8656.
92. Lee, S. K.,, S. L. Yu,, L. Prakash, and, S. Prakash. 2002. Requirement of yeast RAD2, a homolog of human XPG gene, for efficient RNA polymerase II transcription. Implications for Cockayne syndrome. Cell 109 :823– 834.
93. Lee, S. K.,, S. L. Yu,, L. Prakash, and, S. Prakash. 2002. Yeast RAD26, a homolog of the human CSB gene, functions independently of nucleotide excision repair and base excision repair in promoting transcription through damaged bases. Mol. Cell. Biol. 22 :4383– 4389.
94. Le Page, F.,, E. E. Kwoh,, A. Avrutskaya,, A. Gentil,, S. A. Leadon,, A. Sarasin, and, P. K. Cooper. 2000. Transcription-coupled repair of 8-oxoguanine: requirement for XPG, TFIIH, and CSB and implications for Cockayne syndrome. Cell 101 :159– 171.
95. Li, S., and, M. J. Smerdon. 2002. Rpb4 and Rpb9 mediate subpathways of transcription-coupled DNA repair in Saccharomyces cerevisiae. EMBO J. 21 :5921– 5929.
96. Li, S., and, M. J. Smerdon. 2004. Dissecting transcription-coupled and global genomic repair in the chromatin of yeast GAL1–10 genes. J. Biol. Chem. 279 :14418– 14426.
97. Li, S. S.,, M. Livingstone-Zatchej,, R. Gupta,, M. Meijer,, F. Thoma, and, M. J. Smerdon. 1999. Nucleotide excision repair in a constitutive and inducible gene of a yeast minichromosome in intact cells. Nucleic Acids Res. 27 :3610– 3620.
98. Link, C. J.,, D. L. Mitchell,, R. S. Nairn, and, V. A. Bohr. 1992. Preferential and strand-specific DNA-repair of (6–4) photoproducts detected by a photochemical method in the hamster DHFR gene. Carcinogenesis 13 :1975– 1980.
99. Liu, L. F., and, J. C. Wang. 1987. Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. USA 84 :7024– 7027.
100. Ljungman, M., and, D. P. Lane. 2004. Transcription–Guarding the genome by sensing DNA damage. Nat. Rev. Cancer 4 :727– 737.
101. Ljungman, M., and, F. Zhang. 1996. Blockage of RNA polymerase as a possible trigger for UV light-induced apoptosis. Oncogene 13 :823– 831.
102. Lommel, L.,, M. E. Bucheli, and, K. S. Sweder. 2000. Transcription-coupled repair in yeast is independent from ubiquitylation of RNA pol II: implications for Cockayne’s syndrome. Proc. Natl. Acad. Sci. USA 97 :9088– 9092.
103. Lommel, L.,, C. Carswell-Crumpton, and, P. C. Hanawalt. 1995. Preferential repair of the transcribed DNA strand in the dihydrofolate reductase gene throughout the cell cycle in UV-irradiated human cells. Mutat. Res. DNA Repair 336 :181– 192.
104. Lommel, L., and, P. C. Hanawalt. 1991. The genetic defect in the Chinese hamster ovary cell mutant UV61 permits moderate selective repair of cyclobutane pyrimidine dimers in an expressed gene. Mutat. Res. 255 :183– 191.
105. Luger, K.,, A. W. Mader,, R. K. Richmond,, D. F. Sargent, and, T. J. Richmond. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389 :251– 260.
106. Luger, K., and, T. J. Richmond. 1998. DNA binding within the nucleosome core. Curr. Opin. Struct. Biol. 8 :33– 40.
107. Luo, Z.,, J. Zheng,, Y. Lu, and, D. B. Bregman. 2001. Ultraviolet radiation alters the phosphorylation of RNA polymerase II large subunit and accelerates its proteasome-dependent degradation. Mutat. Res. 486 :259– 274.
108. Madhani, D. H.,, V. A. Bohr, and, P. C. Hanawalt. 1986. Differential DNA repair in transcriptionally active and inactive proto-oncogenes: c -abl and c-mos. Cell 45 :417– 423.
109. Mansbridge, J., and, P. Hanawalt. 1983. Domain-limited repair of DNA in ultraviolet irradiated fibroblasts from xeroderma pigmentosum complementation group C, p. 195– 207. In E. Friedberg and, B. Bridges (ed.), Cellular Responses to DNA Damage. Alan R. Liss, New York, N.Y.
110. Martini, E.,, D. M. J. Roche,, K. Marheineke,, A. Verreault, and, G. Almouzni. 1998. Recruitment of phosphorylated chromatin assembly factor 1 to chromatin after UV irradiation of human-cells. J. Cell Biol. 143 :563– 575.
111. Mauldin, S. K.,, T. M. Freeland, and, R. A. Deering. 1994. Differential repair of UV damage in a developmentally-regulated gene of Dictyostelium discoideum. Mutat. Res. 314 :187– 198.
112. May, A.,, R. S. Nairn,, D. S. Okumoto,, K. Wassermann,, T. Stevnsner,, J. C. Jones, and, V. A. Bohr. 1993. Repair of individual DNA strands in the hamster dihydrofolate reductase gene after treatment with ultraviolet light, alkylating agents, and cisplatin J. Biol. Chem. 268 :1650– 1657.
113. McKay, B. C.,, F. Chen,, S. T. Clarke,, H. E. Wiggin,, L. M. Harley, and, M. Ljungman., 2001. UV light-induced degradation of RNA polymerase II is dependent on the Cockayne’s syndrome A and B proteins but not p53 or MLH1. Mutat. Res. DNA Repair 485 :93– 105.
114. Mellon, I.,, V. A. Bohr,, A. C. Smith, and, P. C. Hanawalt. 1986. Preferential DNA repair of an active gene in human cells. Proc. Natl. Acad. Sci. USA 83 :8878– 8882.
115. Mellon, I., and, P. C. Hanawalt. 1989. Induction of the Escherichia coli lactose operon selectively increases repair of its transcribed DNA strand. Nature 342 :95– 98.
116. Mellon, I.,, G. Spivak, and, P. C. Hanawalt. 1987. Selective removal of transcription-blocking DNA damage from the transcribed strand of the mammalian DHFR gene. Cell 51 :241– 249.
117. Moggs, J. G., and, G. Almouzni. 1999. Assays for chromatin remodeling during DNA repair. Methods Enzymol. 304 :333– 351.
118. Moggs, J. G., and, G. Almouzni. 1999. Chromatin rearrangements during nucleotide excision repair. Biochimie 81 :45– 52.
119. Moggs, J. G.,, P. Grandi,, J. P. Quivy,, Z. O. Jonsson,, U. Hubscher,, P. B. Becker, and, G. Almouzni. 2000. A CAF-1-PCNA-mediated chromatin assembly pathway triggered by sensing DNA damage. Mol. Cell. Biol. 20 :1206– 1218.
120. Mondal, N.,, Y. Zhang,, Z. Jonsson,, S. K. Dhar,, M. Kannapiran, and, J. D. Parvin. 2003. Elongation by RNA polymerase II on chromatin templates requires topoisomerase activity. Nucleic Acids Res. 31 :5016– 5024.
121. Murai, M.,, Y. Enokido,, N. Inamura,, M. Yoshino,, Y. Nakatsu,, G. T. van der Horst,, J. H. Hoeijmakers,, K. Tanaka, and, H. Hatanaka. 2001. Early postnatal ataxia and abnormal cerebellar development in mice lacking xeroderma pigmentosum group A and Cockayne syndrome group B DNA repair genes. Proc. Natl. Acad. Sci. USA 98 :13379– 13384.
122. Nakanishi, T.,, M. Shimoaraiso,, T. Kubo, and, S. Natori. 1995. Structure-function relationship of yeast S-II in terms of stimulation of RNA polymerase II, arrest relief, and suppression of 6-azauracil sensitivity. J. Biol. Chem. 270 :8991– 8995.
123. Nouspikel, T., and, P. C. Hanawalt. 2000. Terminally differentiated human neurons repair transcribed genes but display attenuated global DNA repair and modulation of repair gene expression. Mol. Cell. Biol. 20 :1562– 1570.
124. Nouspikel, T., and, P. C. Hanawalt. 2002. DNA repair in terminally differentiated cells. DNA Repair 1 :59– 75.
125. Okumoto, D. S., and, V. A. Bohr. 1987. DNA repair in the metallothionein gene increases with transcriptional activation. Nucleic Acids Res. 15 :10021– 10030.
126. Oleson, F. B.,, B. L. Mitchell,, A. Dipple, and, M. W. Lieberman. 1979. Distribution of DNA damage in chromatin and its relation to repair in human cells treated with 7-bromomethylbenz (a) anthracene. Nucleic Acids Res. 7 :1343– 1361.
127. Park, J. S.,, M. T. Marr, and, J. W. Roberts. 2002. E. coli transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation. Cell 109 :757– 767.
128. Paulson, J. R., and, U. K. Laemmli. 1977. The structure of histonedepleted metaphase chromosomes. Cell 12 :817– 828.
129. Pfaffle, P., and, V. Jackson. 1990. Studies on rates of nucleosome formation with DNA under stress. J. Biol. Chem. 265 :16821– 16829.
130. Ramanathan, B., and, M. J. Smerdon. 1989. Enhanced DNA repair synthesis in hyperacetylated nucleosomes. J. Biol. Chem. 264 :11026– 11034.
131. Ratner, J. N.,, B. Balasubramanian,, J. Corden,, S. L. Warren, and, D. B. Bregman. 1998. 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 :5184– 5189.
132. Reagan, M. S., and, E. C. Friedberg. 1997. Recovery of RNA polymerase II synthesis following DNA damage in mutants of Saccharomyces cerevisiae defective in nucleotide excision repair. Nucleic Acids Res. 25 :4257– 4263.
133. Reid, J., and, J. Q. Svejstrup. 2004. DNA damage-induced Def1-RNA polymerase II interaction and Def1 requirement for polymerase ubiquitylation in vitro. J. Biol. Chem. 279 :29875– 29878.
134. Russell, S. J.,, S. H. Reed,, W. Huang,, E. C. Friedberg, and, S. A. Johnston. 1999. The 19S regulatory complex of the proteasome functions independently of proteolysis in nucleotide excision repair. Mol. Cell 3 :687– 695.
135. Saha, A.,, J. Wittmeyer, and, B. R. Cairns. 2002. Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev. 16 :2120– 2134.
136. Scicchitano, D. A., and, P. C. Hanawalt. 1989. Repair of Nmethylpurines in specific DNA sequences in Chinese hamster ovary cells: absence of strand specificity in the dihydrofolate reductase gene. Proc. Natl. Acad. Sci. USA 86 :3050– 3054.
137. Scicchitano, D. A.,, E. C. Olesnicky, and, A. Dmitri. 2004. Transcription and DNA adducts: what happens when the message gets cut off? DNA Repair 3 :1537– 1548.
138. Scott, A. D., and, R. Waters. 1997. Inducible nucleotide excision-repair (NER) of UV-induced cyclobutane pyrimidine dimers in the cell cycle of the budding yeast Saccharomyces cerevisiae: evidence that inducible NER is confined to the G1 phase of the mitotic cell cycle. Mol. Gen. Genet. 254 :43– 53.
139. Selby, C. P.,, R. Drapkin,, D. Reinberg, and, A. Sancar. 1997. RNA polymerase II stalled at a thymine dimer: footprint and effect on excision repair. Nucleic Acids Res. 25 :787– 793.
140. Selby, C. P., and, A. Sancar. 1997. Cockayne syndrome group B protein enhances elongation by RNA polymerase II. Proc. Natl. Acad. Sci. USA 94 :11205– 11209.
141. Selby, C. P., and, A. Sancar. 1997. Human transcription-repair coupling factor CSB/ERCC6 is a DNA-stimulated ATPase but is not a helicase and does not disrupt the ternary transcription complex of stalled RNApolymerase II. J. Biol. Chem. 272 :1885– 1890.
142. Singer, M. F., 1982. Highly repeated sequences in mammalian genomes. Int. Rev. Cytol. 76 :67– 112.
143. Sitaram, A.,, G. Plitas,, W. Wang, and, D. A. Scicchitano. 1997. Functional nucleotide excision repair is required for the preferential removal of N-ethylpurines from the transcribed strand of the dihydrofolate reductase gene of Chinese hamster ovary cells. Mol. Cell. Biol. 17 :564– 570.
144. Smerdon, M. J., 1986. Completion of excision repair in human cells. Relationship between ligation and nucleosome formation. J. Biol. Chem. 261 :244– 252.
145. Smerdon, M. J., 1991. DNA repair and the role of chromatin structure. Curr. Opin. Cell Biol. 3 :422– 428.
146. Smerdon, M. J.,, M. B. Kastan, and, M. W. Lieberman. 1979. Distribution of repair-incorporated nucleotides and nucleosome rearrangement in the chromatin of normal and xeroderma pigmentosum human fibroblasts. Biochemistry 18 :3732– 3739.
147. Smerdon, M. J., and, M. W. Lieberman. 1978. Nucleosome rearrangement in human chromatin during UV-induced DNA repair synthesis. Proc. Natl. Acad. Sci. USA 75 :4238– 4241.
148. Smerdon, M. J.,, T. D. Tlsty, and, M. W. Lieberman. 1978. Distribution of ultraviolet-induced DNA repair synthesis in nuclease sensitive and resistant regions of human chromatin. Biochemistry 17 :2377– 2386.
149. Smerdon, M. J.,, J. F. Watkins, and, M. W. Lieberman. 1982. Effect of histone H1 removal on the distribution of ultraviolet-induced deoxyribonucleic acid repair synthesis within chromatin. Biochemistry 21 :3879– 3885.
150. Smith, P. J., 1986. n-Butyrate alters chromatin accessibility to DNA repair enzymes. Carcinogenesis 7 :423– 429.
151. Smith, S., and, B. Stillman. 1989. Purification and characterization of CAF-I, a human cell factor required for chromatin assembly during DNA replication in vitro. Cell 58 :15– 25.
152. Spivak, G., and, P. C. Hanawalt. 1992. Translesion DNA-synthesis in the dihydrofolate-reductase domain of UV-irradiated CHO cells. Biochemistry 31 :6794– 6800.
153. Strahl, B. D., and, C. D. Allis. 2000. The language of covalent histone modifications. Nature 403 :41– 45.
154. Svejstrup, J. Q., 2001. Transcription-coupled DNA repair without the transcription-coupling repair factor. Trends Biochem. Sci. 26 :151.
155. Svejstrup, J. Q., 2002. Chromatin elongation factors. Curr. Opin. Genet. Dev. 12 :156– 161.
156. Svejstrup, J. Q., 2002. Mechanisms of transcription-coupled DNA repair. Nat. Rev. Mol. Cell Biol. 3 :21– 40.
157. Svejstrup, J. Q., 2003. Rescue of arrested RNA polymerase II complexes. J. Cell Sci. 116 :447– 451.
158. Svetlova, M. P.,, L. V. Solovjeva,, N. A. Pleskach, and, N. V. Tomilin. 1999. Focal sites of DNA repair synthesis in human chromosomes. Biochem. Biophys. Res. Commun. 257 :378– 383.
159. Sweder, K. S., and, P. C. Hanawalt. 1992. Preferential repair of cyclobutane pyrimidine dimers in the transcribed strand of a gene in yeast chromosomes and plasmids is dependent on transcription. Proc. Natl. Acad. Sci. USA 89 :10696– 10700.
160. Tang, J. Y.,, B. J. Hwang,, J. M. Ford,, P. C. Hanawalt, and, G. Chu. 2000. Xeroderma pigmentosum p48 gene enhances global genomic repair and suppresses UV-induced mutagenesis. Mol. Cell 5 :737– 744.
161. Tang, M. S.,, V. A. Bohr,, X. S. Zhang,, J. Pierce, and, P. C. Hanawalt. 1989. Quantification of aminofluorene adduct formation and repair in defined DNA sequences in mammalian cells using the UvrABC nuclease. J. Biol. Chem. 264 :4455– 4462.
162. Tantin, D., 1998. 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 :27794– 27799.
163. Tantin, D.,, A. Kansal, and, M. Carey. 1997. Recruitment of the putative transcription repair coupling factor CSB/ERCC6 to RNA polymerase II elongation complexes. Mol. Cell. Biol. 17 :6803– 6814.
164. Teng, Y., and, R. Waters. 2000. Excision repair at the level of the nucleotide in the upstream control region, the coding sequence and in the region where transcription terminates of the Saccharomyces cerevisiae MFA2 gene and the role of RAD26. Nucleic Acids Res. 28 :1114– 1119.
165. Terleth, C.,, P. van de Putte, and, J. Brouwer. 1991. New insights in DNA repair: preferential repair of transcriptionally active DNA. Mutagenesis 6 :103– 111.
166. Thoma, F., 1991. Structural changes in nucleosomes during transcription: strip, split or flip? Trends Genet. 7 :175– 177.
167. Thoma, F., 1999. Light and dark in chromatin repair: repair of UVinduced DNA lesions by photolyase and nucleotide excision repair. EMBO J. 18 :6585– 6598.
168. Thomas, D. C.,, D. S. Okumoto,, A. Sancar, and, V. A. Bohr. 1989. Preferential DNA repair of (6–4) photoproducts in the dihydrofolate reductase gene of Chinese hamster ovary cells. J. Biol. Chem. 264 :8005– 8010.
169. Tijsterman, M., and, J. Brouwer. 1999. Rad26, the yeast homolog of the Cockayne syndrome B gene product, counteracts inhibition of DNA repair due to RNA polymerase II transcription. J. Biol. Chem. 274 :1199– 1202.
170. Tijsterman, M.,, R. de Pril,, J. G. Tasseron-de Jong, and, J. Brouwer. 1999. RNA polymerase II transcription suppresses nucleosomal modulation of UV-induced (6–4) photoproduct and cyclobutane pyrimidine dimer repair in yeast. Mol. Cell. Biol. 19 :934– 940.
171. Tijsterman, M.,, J. G. Tasseron-de Jong,, P. van de Putte, and, J. Brouwer. 1996. Transcription-coupled and global genome repair in the Saccharomyces cerevisiae RPB2 gene at nucleotide resolution. Nucleic Acids Res. 24 :3499– 3506.
172. Tijsterman, M.,, R. A. Verhage,, P. van de Putte,, J. G. Tasseronde Jong, and, J. Brouwer. 1997. 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 :8027– 8032.
173. Tlsty, T. D., and, M. W. Lieberman. 1978. The distribution of DNA repair synthesis in chromatin and its rearrangement following damage with N-acetoxy-2-acetylaminofluorene. Nucleic Acids Res. 5 :3261– 3273.
174. Tornaletti, S., and, P. C. Hanawalt. 1999. Effect of DNA lesions on transcription elongation. Biochimie 81 :139– 146.
175. Tornaletti, S.,, L. S. Maeda,, R. D. Kolodner, and, P. C. Hanawalt. 2004. Effect of 8-oxoguanine on transcription elongation by T7 RNA polymerase and mammalian RNA polymerase II. DNA Repair 3 :483– 494.
176. Tornaletti, S.,, L. S. Maeda,, D. R. Lloyd,, D. Reines, and, P. C. Hanawalt. 2001. Effect of thymine glycol on transcription elongation by T7 RNA polymerase and mammalian RNA polymerase II. J. Biol. Chem. 276 :45367– 45371.
177. Travers, A. A., and, T. Owen-Hughes. 2004. Nucleosome remodeling, p. 421– 465. In J. Zlatanova and, S. H. Leuba (ed.), Chromatin Structure and Dynamics: State of the Art. Elsevier, Amsterdam, The Netherlands.
178. Tremeau-Bravard, A.,, T. Riedl,, J. M. Egly, and, M. E. Dahmus. 2004. Fate of RNA polymerase II stalled at a cisplatin lesion. J. Biol. Chem. 279 :7751– 7759.
179. Troelstra, C.,, A. van Gool,, J. De Wit,, W. Vermeulen,, D. Bootsma, and, J. H. J. Hoeijmakers. 1992. ERCC6, a member of a subfamily of putative helicases, is involved in Cockayne’s syndrome and preferential repair of active genes. Cell 71 :939– 953.
180. Tu, Y.,, S. Bates, and, G. P. Pfeifer. 1998. The transcription repair coupling factor CSA is required for efficient repair only during the elongation stages of RNA polymerase II transcription. Mutat. Res. 400 :143– 151.
181. Tu, Y. Q.,, S. Bates, and, G. P. Pfeifer. 1997. Sequence-specific and domain specific DNA repair in xeroderma pigmentosum and Cockayne syndrome cells. J. Biol. Chem. 272 :20747– 20755.
182. Tu, Y. Q.,, S. Tornaletti, and, G. P. Pfeifer. 1996. DNA repair domains within a human gene: selective repair of sequences near the transcription initiation site. EMBO J. 15 :675– 683.
183. Turner, B. M., 2002. Cellular memory and the histone code. Cell 111 :285– 291.
184. Turner, B. M., 2004. Nucleosome modifications and their interactions: searching for a histone code, p. 291– 308. In J. Zlatanova and, S. H. Leuba (ed.), Chromatin Structure and Dynamics: State of the Art. Elsevier, Amsterdam, The Netherlands.
185. Tyler, J. K.,, C. R. Adams,, S. R. Chen,, R. Kobayashi,, R. T. Kamakaka, and, J. T. Kadonaga. 1999. The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature 402 :555– 560.
186. Tyler, J. K.,, K. A. Collins,, J. Prasad-Sinha,, E. Amiott,, M. Bulger,, P. J. Harte,, R. Kobayashi, and, J. T. Kadonaga. 2001. Interaction between the Drosophila CAF-1 and ASF1 chromatin assembly factors. Mol. Cell. Biol. 21 :6574– 6584.
187. Ura, K.,, M. Araki,, H. Saeki,, C. Masutani,, T. Ito,, S. Iwai,, T. Mizukoshi,, Y. Kaneda, and, F. Hanaoka. 2001. ATP-dependent chromatin remodeling facilitates nucleotide excision repair of UV-induced DNA lesions in synthetic dinucleosomes. EMBO J. 20 :2004– 2014.
188. Ura, K., and, J. J. Hayes. 2002. Nucleotide excision repair and chromatin remodeling. Eur. J. Biochem. 269 :2288– 2293.
189. van den Boom, V.,, N. G. Jaspers, and, W. Vermeulen. 2002. When machines get stuck: obstructed RNA polymerase II: displacement, degradation or suicide. Bioessays 24 :780– 784.
190. van Gool, A. J.,, E. Citterio,, S. Rademakers,, R. Vanos,, W. Vermeulen,, A. Constantinou,, J. M. Egly,, D. Bootsma, and, J. H. J. Hoeijmakers. 1997. The Cockayne syndrome B protein, involved in transcription-coupled DNA repair, resides in an RNA polymerase II-containing complex. EMBO J. 16 :5955– 5965.
191. van Gool, A. J.,, R. Verhage,, S. M. A. Swagemakers,, P. van de Putte,, J. Brouwer,, C. Troelstra,, D. Bootsma, and, J. H. J. Hoeijmakers. 1994. Rad26, the functional Saccharomyces cerevisiae homolog of the Cockayne syndrome B gene ERCC6. EMBO J. 13 :5361– 5369.
192. van Hoffen, A.,, A. T. Natarajan,, L. V. Mayne,, A. A. van Zeeland,, L. H. F. Mullenders, and, J. Venema. 1993. Deficient repair of the transcribed strand of active genes in Cockayne’s syndrome cells. Nucleic Acids Res. 21 :5890– 5895.
193. van Hoffen, A.,, J. Venema,, R. Meschini,, A. A. van Zeeland, and, L. H. F. Mullenders. 1995. Transcription-coupled repair removes both cyclobutane pyrimidine dimers and 6–4 photoproducts with equal efficiency and in a sequential way from transcribed DNA in xeroderma pigmentosum group C fibroblasts. EMBO J. 14 :360– 367.
194. van Holde, K. E., 1988. Chromatin. Springer-Verlag, New York, N.Y.
195. van Holde, K. E.,, D. E. Lohr, and, C. Robert. 1992. What happens to nucleosomes during transcription? J. Biol. Chem. 267 :2837– 2840.
196. van Oosterwijk, M. F.,, R. Filon,, A. J. L. de Groot,, A. A. van Zee-land, and, L. H. F. Mullenders. 1998. Lack of transcription-coupled repair of acetylaminofluorene DNA-adducts in human fibroblasts contrasts their efficient inhibition of transcription. J. Biol. Chem. 273 :13599– 13604.
197. van Oosterwijk, M. F.,, R. Filon,, W. H. Kalle,, L. H. Mullenders, and, A. A. van Zeeland. 1996. The sensitivity of human fibroblasts to N-acetoxy-2-acetylaminofluorene is determined by the extent of transcription-coupled repair, and/or their capability to counteract RNA synthesis inhibition. Nucleic Acids Res. 24 :4653– 4659.
198. Vaquero, A.,, A. Loyola, and, D. Reinberg. 2003. The constantly changing face of chromatin. Sci. Aging Knowledge Environ. 2003 :RE4.
199. Venema, J.,, L. H. F. Mullenders,, A. T. Natarajan,, A. A. Van Zeeland, and, L. V. Mayne. 1990. The genetic defect in Cockayne syndrome is associated with a defect in repair of UV-induced DNA damage in transcriptionally active DNA. Proc. Natl. Acad. Sci. USA 87 :4707– 4711.
200. Venema, J.,, A. van Hoffen,, V. Karcagi,, A. T. Natarajan,, A. A. van Zeeland, and, L. H. F. Mullenders. 1991. Xeroderma pigmentosum complementation group C cells remove pyrimidine dimers selectively from the transcribed strand of active genes. Mol. Cell. Biol. 11 :4128– 4134.
201. Venema, J.,, A. van Hoffen,, A. T. Natarajan,, A. A. Van Zeeland, and, L. H. F. Mullenders. 1990. The residual repair capacity of xeroderma pigmentosum complementation group C fibroblasts is highly specific for transcriptionally active DNA. Nucleic Acids Res. 18 :443– 448.
202. Venter, J. C.,, M. D. Adams,, E. W. Myers,, P. W. Li,, R. J. Mural,, G. G. Sutton,, H. O. Smith,, M. Yandell,, C. A. Evans,, R. A. Holt,, J. D. Go-cayne,, P. Amanatides,, R. M. Ballew,, D. H. Huson,, J. R. Wortman,, Q. Zhang,, C. D. Kodira,, X. H. Zheng,, L. Chen,, M. Skupski, et al., 2001. The sequence of the human genome. Science 291 :1304– 1351.
203. Verhage, R.,, A. Zeeman,, N. de Groot,, F. Gleig,, D. Bang,, P. van de Putte, and, J. Brouwer. 1994. 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 :6135– 6142.
204. Verhage, R. A.,, P. van de Putte, and, J. Brouwer. 1996. Repair of rDNA in Saccharomyces cerevisiae: RAD4-independent strand-specific nucleotide excision repair of RNA polymerase I transcribed genes. Nucleic Acids Res. 24 :1020– 1025.
205. Vidali, G.,, L. C. Boffa,, E. M. Bradbury, and, V. G. Allfrey. 1978. Butyrate suppression of histone deacetylation leads to accumulation of multiacetylated forms of histones H3 and H4 and increased DNase I sensitivity of the associated DNA sequences. Proc. Natl. Acad. Sci. USA 75 :2239– 2243.
206. Vignali, M.,, A. H. Hassan,, K. E. Neely, and, J. L. Workman. 2000. ATP-dependent chromatin-remodeling complexes. Mol. Cell. Biol. 20 :1899– 1910.
207. Viswanathan, A., and, P. W. Doetsch. 1998. Effects of nonbulky DNA base damages on Escherichia coli RNA polymerase-mediated elongation and promoter clearance. J. Biol. Chem. 273 :21276– 21281.
208. Vos, J. M. H., and, E. L. Wauthier. 1991. Differential introduction of DNA damage and repair in mammalian genes transcribed by RNA polymerase I and polymerase II. Mol. Cell. Biol. 11 :2245– 2252.
209. Wang, W.,, A. Sitaram, and, D. A. Scicchitano. 1995. 3- Methyladenine and 7-methylguanine exhibit no preferential removal from the transcribed strand of the dihydrofolate reductase gene in Chinese hamster ovary B11 cells. Biochemistry 34 :1798– 1804.
210. Wang, Z.,, X. Wu, and, E. C. Friedberg. 1991. Nucleotide excision repair of DNA by human cell extracts is suppressed in reconstituted nu- cleosomes. J. Biol. Chem. 266 :22472– 22478.
211. Wellinger, R. E., and, F. Thoma. 1997. Nucleosome structure and positioning modulate nucleotide excision repair in the nontranscribed strand of an active gene. EMBO J. 16 :5046– 5056.
212. Williams, J. I., and, E. C. Friedberg. 1979. Deoxyribonucleic acid excision repair in chromatin after ultraviolet irradiation of human fibro-blasts in culture. Biochemistry 18 :3965– 3972.
213. Williams, J. I., and, E. C. Friedberg. 1982. Increased levels of unscheduled DNA synthesis in UV-irradiated human fibroblasts pretreated with sodium butyrate. Photochem. Photobiol. 36 :423– 427.
214. Wilson, V. L., and, P. A. Jones. 1983. Inhibition of DNA methylation by chemical carcinogens in vitro. Cell 32 :239– 246.
215. Wittschieben, B. ∅.,, G. Otero,, T. de Bizemont,, J. Fellows,, H. Erdjument-Bromage,, R. Ohba,, Y. Li,, C. D. Allis,, P. Tempst, and, J. Q. Svejstrup. 1999. A novel histone acetyltransferase is an integral subunit of elongating RNA polymerase II holoenzyme. Mol. Cell 4 :123– 128.
216. Wolffe, A. P., 1998. Chromatin: Structure and Function, 3rd ed. Academic Press, Inc. San Diego, Calif.
217. Woudstra, E. C.,, C. Gilbert,, J. Fellows,, L. Jansen,, J. Brouwer,, H. Erdjument-Bromage,, P. Tempst, and, J. Q. Svejstrup. 2002. A Rad26-Def1 complex coordinates repair and RNA pol II proteolysis in response to DNA damage. Nature 415 :929– 933.
218. Yamaizumi, M., and, T. Sugano. 1994. UV-induced nuclear accumulation of p53 is evoked through DNA damage of actively transcribed genes independent of the cell cycle. Oncogene 9 :2775– 2784.
219. Yasuhira, S.,, M. Morimyo, and, A. Yasui. 1999. Transcription dependence and the roles of two excision repair pathways for UV damage in fission yeast Schizosaccharomyces pombe. J. Biol. Chem. 274 :26822– 26827.
220. Yu, A.,, H. Y. Fan,, D. Liao,, A. D. Bailey, and, A. M. Weiner. 2000. 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 :801– 810.
221. Zawel, L.,, K. P. Kumar, and, D. Reinberg. 1995. Recycling of general transcription factors during RNA polymerase II transcription. Genes Dev. 9 :1479– 1490.
222. Zheng, Y.,, A. Pao,, G. M. Adair, and, M. Tang. 2001. Cyclobutane pyrimidine dimers and bulky chemical DNA adducts are efficiently repaired in both strands of either a transcriptionally active or promoter- deleted APRT gene. J. Biol. Chem. 276 :16786– 16796.
223. Zlatanova, J.,, S. H. Leuba, and, K. van Holde. 1999. Chromatin structure revisited. Crit. Rev. Eukaryot. Gene Expression 9 :245– 255.
224. Zolan, M. E.,, G. A. Cortopassi,, C. A. Smith, and, P. C. Hanawalt. 1982. Deficient repair of chemical adducts in alpha DNA of monkey cells. Cell 28 :613– 619.
225. Zolan, M. E.,, C. A. Smith,, N. M. Calvin, and, P. C. Hanawalt. 1982. Rearrangement of mammalian chromatin structure following excision repair. Nature 299 :462– 464.
226. Zolan, M. E.,, C. A. Smith, and, P. C. Hanawalt. 1984. Formation and repair of furocoumarin adducts in alpha deoxyribonucleic and bulk deoxyribonucleic acid of monkey cells. Biochemistry 23 :63– 68.

References: V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V.