Interactions between DNA damage, repair, and transcription

Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis

Volumn 736, Issue 1-2, 2012, Pages 5-14

  Khobta, Andriy ^a   Epe, Bernd ^a  

^a JOHANNES GUTENBERG UNIVERSITY   (Germany)

Author keywords

DNA damage; DNA repair; Transcription

Indexed keywords

5 METHYLCYTOSINE; 8 HYDROXYGUANINE; RNA POLYMERASE;

DNA DAMAGE; DNA MODIFICATION; DNA REPAIR; DNA SYNTHESIS; EPIGENETICS; EXCISION REPAIR; GENE EXPRESSION REGULATION; GENE INTERACTION; GENE LOCUS; GENETIC TRANSCRIPTION; GENOMIC INSTABILITY; HUMAN; MUTAGENESIS; MUTATIONAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; RNA INTERFERENCE; RNA PROCESSING; RNA SYNTHESIS; RNA TRANSLATION; SHORT SURVEY; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

DNA DAMAGE; DNA REPAIR; GENE EXPRESSION REGULATION; GENOMIC INSTABILITY; HUMANS; SIGNAL TRANSDUCTION; TRANSCRIPTION, GENETIC;

EID: 84864514186     PISSN: 00275107     EISSN: 09218262     Source Type: Journal    
DOI: 10.1016/j.mrfmmm.2011.07.014     Document Type: Short Survey

References (131)

1. Troelstra C., van Gool A., de Wit J., Vermeulen W., Bootsma D., Hoeijmakers J.H. ERCC6, a member of a subfamily of putative helicases, is involved in Cockayne's syndrome and preferential repair of active genes. Cell 1992, 71:939-953.
2. Henning K.A, Li L., Iyer N., McDaniel L.D., Reagan M.S., Legerski R., Schultz R.A., Stefanini M., Lehmann A.R., Mayne L.V., Friedberg E.C. 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 1995, 82:555-564.
3. Mayne L.V., Lehmann A.R. 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. 1982, 42:1473-1478.
4. O'Hagan H.M., Mohammad H.P., Baylin S.B. Double strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG island. PLoS Genet. 2008, 4:e1000155.
5. Khobta A., Anderhub S., Kitsera N., Epe B. Gene silencing induced by oxidative DNA base damage: association with local decrease of histone H4 acetylation in the promoter region. Nucleic Acids Res. 2010, 38:4285-4295.
6. Polo S.E., Almouzni G. DNA damage leaves its mark on chromatin. Cell Cycle 2007, 6:2355-2359.
7. Niehrs C. Active DNA demethylation and DNA repair. Differentiation 2009, 77:1-11.
8. Zhu J.K. Active DNA demethylation mediated by DNA glycosylases. Annu. Rev. Genet. 2009, 43:143-166.
9. Fuda N.J., Ardehali M.B., Lis J.T. Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature 2009, 461:186-192.
10. Tornaletti S. Transcription arrest at DNA damage sites. Mutat. Res. 2005, 577:131-145.
11. Verri A., Mazzarello P., Biamonti G., Spadari S., Focher F. The specific binding of nuclear protein(s) to the cAMP responsive element (CRE) sequence (TGACGTCA) is reduced by the misincorporation of U and increased by the deamination of C. Nucleic Acids Res. 1990, 18:5775-5780.
12. Ghosh R., Mitchell D.L. Effect of oxidative DNA damage in promoter elements on transcription factor binding. Nucleic Acids Res. 1999, 27:3213-3218.
13. Marietta C., Gulam H., Brooks P.J. A single 8 5'-cyclo-2'-deoxyadenosine lesion in a TATA box prevents binding of the TATA binding protein and strongly reduces transcription in vivo. DNA Repair (Amst.) 2002, 1:967-975.
14. Hailer-Morrison M.K., Kotler J.M., Martin B.D., Sugden K.D. Oxidized guanine lesions as modulators of gene transcription. Altered p50 binding affinity and repair shielding by 7,8-dihydro-8-oxo-2'-deoxyguanosine lesions in the NF-kappaB promoter element. Biochemistry 2003, 42:9761-9770.
15. Ramon O., Sauvaigo S., Gasparutto D., Faure P., Favier A., Cadet J. Effects of 8-oxo-7,8-dihydro-2'-deoxyguanosine on the binding of the transcription factor Sp1 to its cognate target DNA sequence (GC box). Free Radical Res. 1999, 31:217-229.
16. Weitzman S.A., Turk P.W., Milkowski D.H., Kozlowski K. Free radical adducts induce alterations in DNA cytosine methylation. Proc. Natl. Acad. Sci. U. S. A. 1994, 91:1261-1264.
17. Zhai X., Beckmann H., Jantzen H.M., Essigmann J.M. Cisplatin-DNA adducts inhibit ribosomal RNA synthesis by hijacking the transcription factor human upstream binding factor. Biochemistry 1998, 37:16307-16315.
18. Coin F., Frit P., Viollet B., Salles B., Egly J.M. TATA binding protein discriminates between different lesions on DNA, resulting in a transcription decrease,. Mol. Cell. Biol. 1998, 18:3907-3914.
19. Nocentini S., Coin F., Saijo M., Tanaka K., Egly J.M. DNA damage recognition by XPA protein promotes efficient recruitment of transcription factor II H. J. Biol. Chem. 1997, 272:22991-22994.
20. Vichi P., Coin F., Renaud J.P., Vermeulen W., Hoeijmakers J.H., Moras D., Egly J.M. Cisplatin- and UV-damaged DNA lure the basal transcription factor TFIID/TBP. EMBO J. 1997, 16:7444-7456.
21. Park C.H., Mu D., Reardon J.T., Sancar A. The general transcription-repair factor TFIIH is recruited to the excision repair complex by the XPA protein independent of the TFIIE transcription factor. J. Biol. Chem. 1995, 270:4896-4902.
22. Hanawalt P.C. Transcription-coupled repair and human disease. Science 1994, 266:1957-1958.
23. Hanawalt P.C., Spivak G. Transcription-coupled DNA repair: two decades of progress and surprises. Nat. Rev. Mol. Cell Biol. 2008, 9:958-970.
24. Kathe S.D., Shen G.P., Wallace S.S. 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. 2004, 279:18511-18520.
25. Tornaletti S., Patrick S.M., Turchi J.J., Hanawalt P.C. Behavior of T7 RNA polymerase and mammalian RNA polymerase II at site-specific cisplatin adducts in the template DNA. J. Biol. Chem. 2003, 278:35791-35797.
26. Damsma G.E., Alt A., Brueckner F., Carell T., Cramer P. Mechanism of transcriptional stalling at cisplatin-damaged DNA. Nat. Struct. Mol. Biol. 2007, 14:1127-1133.
27. Brueckner F., Hennecke U., Carell T., Cramer P. CPD damage recognition by transcribing RNA polymerase II. Science 2007, 315:859-862.
28. Tornaletti S., Maeda L.S., Kolodner R.D., Hanawalt P.C. Effect of 8-oxoguanine on transcription elongation by T7 RNA polymerase and mammalian RNA polymerase II. DNA Repair (Amst.) 2004, 3:483-494.
29. Saxowsky T.T., Doetsch P.W. RNA polymerase encounters with DNA damage: transcription-coupled repair or transcriptional mutagenesis?. Chem. Rev. 2006, 106:474-488.
30. Doetsch P.W. Translesion synthesis by RNA polymerases: occurrence and biological implications for transcriptional mutagenesis. Mutat. Res. 2002, 510:131-140.
31. Bregeon D., Doddridge Z.A., You H.J., Weiss B., Doetsch P.W. Transcriptional mutagenesis induced by uracil and 8-oxoguanine in Escherichia coli. Mol. Cell 2003, 12:959-970.
32. Viswanathan A., You H.J., Doetsch P.W. Phenotypic change caused by transcriptional bypass of uracil in nondividing cells. Science 1999, 284:159-162.
33. Saxowsky T.T., Meadows K.L., Klungland A., Doetsch P.W. 8-Oxoguanine-mediated transcriptional mutagenesis causes Ras activation in mammalian cells. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:18877-18882.
34. Bregeon D., Peignon P.A., Sarasin A. Transcriptional mutagenesis induced by 8-oxoguanine in mammalian cells. PLoS Genet. 2009, 5:e1000577.
35. Clauson C.L., Oestreich K.J., Austin J.W., Doetsch P.W. Abasic sites and strand breaks in DNA cause transcriptional mutagenesis in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:3657-3662.
36. Granneman S., Baserga S.J. Crosstalk in gene expression: coupling and co-regulation of rDNA transcription, pre-ribosome assembly and pre-rRNA processing,. Curr. Opin. Cell Biol. 2005, 17:281-286.
37. Bentley D.L Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors,. Curr. Opin. Cell Biol. 2005, 17:251-256.
38. Pandit S., Wang D., Fu X.D. Functional integration of transcriptional and RNA processing machineries. Curr. Opin. Cell Biol. 2008, 20:260-265.
39. de la Mata M., Alonso C.R., Kadener S., Fededa J.P., Blaustein M., Pelisch F., Cramer P., Bentley D., Kornblihtt A.R. A slow RNA polymerase II affects alternative splicing in vivo. Mol. Cell 2003, 12:525-532.
40. Lacadie S.A., Tardiff D.F., Kadener S., Rosbash M. In vivo commitment to yeast cotranscriptional splicing is sensitive to transcription elongation mutants. Genes Dev. 2006, 20:2055-2066.
41. Howe K.J., Kane C.M., Ares M. Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. RNA 2003, 9:993-1006.
42. Luco R.F., Pan Q., Tominaga K., Blencowe B.J., Pereira-Smith O.M., Misteli T. Regulation of alternative splicing by histone modifications. Science 2010, 327:996-1000.
43. Munoz M.J., Perez Santangelo M.S., Paronetto M.P., de la Mata M., Pelisch F., Boireau S., Glover-Cutter K., Ben-Dov C., Blaustein M., Lozano J.J., Bird G., Bentley D., Bertrand E., Kornblihtt A.R. DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation. Cell 2009, 137:708-720.
44. Boeger H., Bushnell D.A., Davis R., Griesenbeck J., Lorch Y., Strattan J.S., Westover K.D., Kornberg R.D. Structural basis of eukaryotic gene transcription. FEBS Lett. 2005, 579:899-903.
45. Frederico L.A., Kunkel T.A., Shaw B.R. A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy. Biochemistry 1990, 29:2532-2537.
46. Koster D.A., Crut A., Shuman S., Bjornsti M.A., Dekker N.H. Cellular strategies for regulating DNA supercoiling: a single-molecule perspective. Cell 2010, 142:519-530.
47. Armstrong J.A. Negotiating the nucleosome: factors that allow RNA polymerase II to elongate through chromatin. Biochem. Cell Biol. 2007, 85:426-434.
48. Sims R.J., Mandal S.S., Reinberg D. Recent highlights of RNA-polymerase-II-mediated transcription. Curr. Opin. Cell Biol. 2004, 16:263-271.
49. Beletskii A., Bhagwat A.S. Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 1996, 93:13919-13924.
50. Datta A., Jinks-Robertson S. Association of increased spontaneous mutation rates with high levels of transcription in yeast. Science 1995, 268:1616-1619.
51. Kim N., Abdulovic A.L., Gealy R., Lippert M.J., Jinks-Robertson S. Transcription-associated mutagenesis in yeast is directly proportional to the level of gene expression and influenced by the direction of DNA replication. DNA Repair (Amst.) 2007, 6:1285-1296.
52. Li X., Manley J.L. Cotranscriptional processes and their influence on genome stability. Genes Dev. 2006, 20:1838-1847.
53. Aguilera A., Gomez-Gonzalez B. Genome instability: a mechanistic view of its causes and consequences. Nat. Rev. Genet. 2008, 9:204-217.
54. Tsai A.G., Lieber M.R. Mechanisms of chromosomal rearrangement in the human genome. BMC Genom. 2010, 1(11 Suppl.):S1.
55. Aguilera A. The connection between transcription and genomic instability. EMBO J. 2002, 21:195-201.
56. Voelkel-Meiman K., Keil R.L., Roeder G.S. Recombination-stimulating sequences in yeast ribosomal DNA correspond to sequences regulating transcription by RNA polymerase I. Cell 1987, 48:1071-1079.
57. Thomas B.J., Rothstein R. Elevated recombination rates in transcriptionally active DNA. Cell 1989, 56:619-630.
58. Huertas P., Aguilera A. Co-transcriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. Mol. Cell 2003, 12:711-721.
59. Huertas P., Garcia-Rubio M.L., Wellinger R.E., Luna R., Aguilera A. An hpr1 point mutation that impairs transcription and mRNP biogenesis without increasing recombination. Mol. Cell Biol. 2006, 26:7451-7465.
60. Garcia-Rubio M., Huertas P., Gonzalez-Barrera S., Aguilera A. Recombinogenic effects of DNA-damaging agents are synergistically increased by transcription in Saccharomyces cerevisiae. New insights into transcription-associated recombination,. Genetics 2003, 165:457-466.
61. Hendriks G., Calleja F., Vrieling H., Mullenders L.H., Jansen J.G., de Wind N. Gene transcription increases DNA damage-induced mutagenesis in mammalian stem cells. DNA Repair (Amst.) 2008, 7:1330-1339.
62. Roy D., Zhang Z., Lu Z., Hsieh C.L., Lieber M.R. Competition between the RNA transcript and the nontemplate DNA strand during R-loop formation in vitro: a nick can serve as a strong R-loop initiation site. Mol. Cell Biol. 2010, 30:146-159.
63. Belotserkovskii B.P., Liu R., Tornaletti S., Krasilnikova M.M., Mirkin S.M., Hanawalt P.C. Mechanisms and implications of transcription blockage by guanine-rich DNA sequences. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:12816-12821.
64. Hraiky C., Raymond M.A., Drolet M. RNase H overproduction corrects a defect at the level of transcription elongation during rRNA synthesis in the absence of DNA topoisomerase I in Escherichia coli. J. Biol. Chem. 2000, 275:11257-11263.
65. El Hage A., French S.L., Beyer A.L., Tollervey D. Loss of topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis. Genes Dev. 2010, 24:1546-1558.
66. Trigueros S., Roca J. Failure to relax negative supercoiling of DNA is a primary cause of mitotic hyper-recombination in topoisomerase-deficient yeast cells. J. Biol. Chem. 2002, 277:37207-37211.
67. Tian M., Alt F.W. Transcription-induced cleavage of immunoglobulin switch regions by nucleotide excision repair nucleases in vitro. J. Biol. Chem. 2000, 275:24163-24172.
68. Mugal C.F., von Grunberg H.H., Peifer M. Transcription-induced mutational strand bias and its effect on substitution rates in human genes. Mol. Biol. Evol. 2009, 26:131-142.
69. Francino M.P., Ochman H. Deamination as the basis of strand-asymmetric evolution in transcribed Escherichia coli sequences. Mol. Biol. Evol. 2001, 18:1147-1150.
70. Yu S.L., Lee S.K., Johnson R.E., Prakash L., Prakash S. The stalling of transcription at abasic sites is highly mutagenic. Mol. Cell Biol. 2003, 23:382-388.
71. Kim N., Jinks-Robertson S. Abasic sites in the transcribed strand of yeast DNA are removed by transcription-coupled nucleotide excision repair. Mol. Cell Biol. 2010, 30:3206-3215.
72. Hendriks G., Calleja F., Besaratinia A., Vrieling H., Pfeifer G.P., Mullenders L.H., Jansen J.G., de Wind N. Transcription-dependent cytosine deamination is a novel mechanism in ultraviolet light-induced mutagenesis. Curr. Biol. 2010, 20:170-175.
73. Hendriks G., Jansen J.G., Mullenders L.H., de Wind N. Transcription and replication: far relatives make uneasy bedfellows. Cell Cycle 2010, 9:2300-2304.
74. Kim N., Jinks-Robertson S. dUTP incorporation into genomic DNA is linked to transcription in yeast. Nature 2009, 459:1150-1153.
75. Chaudhuri J., Tian M., Khuong C., Chua K., Pinaud E., Alt F.W. Transcription-targeted DNA deamination by the AID antibody diversification enzyme. Nature 2003, 422:726-730.
76. Pavri R., Gazumyan A., Jankovic M., Di Virgilio M., Klein I., Ansarah-Sobrinho C., Resch W., Yamane A., San-Martin B.R., Barreto V., Nieland T.J., Root D.E., Casellas R., Nussenzweig M.C. Activation-induced cytidine deaminase targets DNA at sites of RNA polymerase II stalling by interaction with Spt5. Cell 2010, 143:122-133.
77. Muramatsu M., Kinoshita K., Fagarasan S., Yamada S., Shinkai Y., Honjo T. Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell 2000, 102:553-563.
78. Revy P., Muto T., Levy Y., Geissmann F., Plebani A., Sanal O., Catalan N., Forveille M., Dufourcq-Labelouse R., Gennery A., Tezcan I., Ersoy F., Kayserili H., Ugazio A.G., Brousse N., Muramatsu M., Notarangelo L.D., Kinoshita K., Honjo T., Fischer A., Durandy A. Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the hyper-IgM syndrome (HIGM2),. Cell 2000, 102:565-575.
79. Pham P., Bransteitter R., Petruska J., Goodman M.F. Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation. Nature 2003, 424:103-107.
80. Rada C., Williams G.T., Nilsen H., Barnes D.E., Lindahl T., Neuberger M.S. Immunoglobulin isotype switching is inhibited and somatic hypermutation perturbed in UNG-deficient mice. Curr. Biol. 2002, 12:1748-1755.
81. Schrader C.E., Linehan E.K., Mochegova S.N., Woodland R.T., Stavnezer J. Inducible DNA breaks in Ig S regions are dependent on AID and UNG. J. Exp. Med. 2005, 202:561-568.
82. Stavnezer J., Schrader C.E. Mismatch repair converts AID-instigated nicks to double-strand breaks for antibody class-switch recombination. Trends Genet. 2006, 22:23-28.
83. Robbiani D.F., Bothmer A., Callen E., Reina-San-Martin B., Dorsett Y., Difilippantonio S., Bolland D.J., Chen H.T., Corcoran A.E., Nussenzweig A., Nussenzweig M.C. AID is required for the chromosomal breaks in c-myc that lead to c-myc/IgH translocations. Cell 2008, 135:1028-1038.
84. Tsai A.G., Lu H., Raghavan S.C., Muschen M., Hsieh C.L., Lieber M.R. Human chromosomal translocations at CpG sites and a theoretical basis for their lineage and stage specificity. Cell 2008, 135:1130-1142.
85. Okazaki I.M., Hiai H., Kakazu N., Yamada S., Muramatsu M., Kinoshita K., Honjo T. Constitutive expression of AID leads to tumorigenesis. J. Exp. Med. 2003, 197:1173-1181.
86. Chiu Y.L., Greene W.C. The APOBEC3 cytidine deaminases: an innate defensive network opposing exogenous retroviruses and endogenous retroelements. Annu. Rev. Immunol. 2008, 26:317-353.
87. Beale R.C., Petersen-Mahrt S.K., Watt I.N., Harris R.S., Rada C., Neuberger M.S. Comparison of the differential context-dependence of DNA deamination by APOBEC enzymes: correlation with mutation spectra in vivo. J. Mol. Biol. 2004, 337:585-596.
88. Harris R.S., Petersen-Mahrt S.K., Neuberger M.S. RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators. Mol. Cell 2002, 10:1247-1253.
89. Landry S., Narvaiza I., Linfesty D.C., Weitzman M.D. APOBEC3A can activate the DNA damage response and cause cell-cycle arrest. EMBO Rep. 2011, 12:444-450.
90. Misteli T. Beyond the sequence: cellular organization of genome function. Cell 2007, 128:787-800.
91. Pomerantz R.T., O'Donnell M. Direct restart of a replication fork stalled by a head-on RNA polymerase. Science 2010, 327:590-592.
92. Pomerantz R.T., O'Donnell M. The replisome uses mRNA as a primer after colliding with RNA polymerase. Nature 2008, 456:762-766.
93. Prado F., Aguilera A. Impairment of replication fork progression mediates RNA polII transcription-associated recombination. EMBO J. 2005, 24:1267-1276.
94. Takeuchi Y., Horiuchi T., Kobayashi T. Transcription-dependent recombination and the role of fork collision in yeast rDNA. Genes Dev. 2003, 17:1497-1506.
95. Omberg L., Meyerson J.R., Kobayashi K., Drury L.S., Diffley J.F., Alter O. Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression. Mol. Syst. Biol. 2009, 5:312.
96. Rudolph C.J., Dhillon P., Moore T., Lloyd R.G. Avoiding and resolving conflicts between DNA replication and transcription. DNA Repair (Amst.) 2007, 6:981-993.
97. Larrea A.A., Lujan S.A., McElhinny S.A., Mieczkowski P.A., Resnick M.A., Gordenin D.A., Kunkel T.A. Genome-wide model for the normal eukaryotic DNA replication fork. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:17674-17679.
98. Svejstrup J.Q. The interface between transcription and mechanisms maintaining genome integrity. Trends Biochem. Sci. 2010, 35:333-338.
99. Burgers P.M. Polymerase dynamics at the eukaryotic DNA replication fork. J. Biol. Chem. 2009, 284:4041-4045.
100. Hubscher U., Seo Y.S. Replication of the lagging strand: a concert of at least 23 polypeptides. Mol. Cell 2001, 12:149-157.
101. Bohr V.A., Smith C.A., Okumoto D.S., Hanawalt P.C. 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 1985, 40:359-369.
102. Mellon I., Spivak G., Hanawalt P.C. Selective removal of transcription-blocking DNA damage from the transcribed strand of the mammalian DHFR gene. Cell 1987, 51:241-249.
103. Laine J.P., Egly J.M. Initiation of DNA repair mediated by a stalled RNA polymerase II. EMBO J. 2006, 25:387-397.
104. Drapkin R., Sancar A., Reinberg D. Where transcription meets repair. Cell 1994, 77:9-12.
105. de Laat W.L., Jaspers N.G., Hoeijmakers J.H. Molecular mechanism of nucleotide excision repair. Genes Dev. 1999, 13:768-785.
106. Laine J.P., Egly J.M. When transcription and repair meet: a complex system. Trends Genet. 2006, 22:430-436.
107. Drapkin R., Reardon J.T., Ansari A., Huang J.C., Zawel L., Ahn K., Sancar A., Reinberg D. Dual role of TFIIH in DNA excision repair and in transcription by RNA polymerase II. Nature 1994, 368:769-772.
108. Fousteri M., Vermeulen W., van Zeeland A.A., Mullenders L.H. Cockayne syndrome A and B proteins differentially regulate recruitment of chromatin remodeling and repair factors to stalled RNA polymerase II in vivo. Mol. Cell 2006, 23:471-482.
109. Selby C.P., Sancar A. Cockayne syndrome group B protein enhances elongation by RNA polymerase II. Proc. Natl. Acad. Sci. U. S. A. 1997, 94:11205-11209.
110. Lee S.K., Yu S.L., Prakash L., Prakash S. Requirement for yeast RAD26, a homolog of the human CSB gene, in elongation by RNA polymerase II,. Mol. Cell Biol. 2001, 21:8651-8656.
111. Le May N., Mota-Fernandes D., Velez-Cruz R., Iltis I., Biard D., Egly J.M. NER factors are recruited to active promoters and facilitate chromatin modification for transcription in the absence of exogenous genotoxic attack. Mol. Cell 2010, 38:54-66.
112. Barnes D.E., Lindahl T. Repair and genetic consequences of endogenous DNA base damage in mammalian cells. Annu. Rev. Genet. 2004, 38:445-476.
113. Guillet M., Boiteux S. Endogenous DNA abasic sites cause cell death in the absence of Apn1, Apn2 and Rad1/Rad10 in Saccharomyces cerevisiae. EMBO J. 2002, 21:2833-2841.
114. Guillet M., Boiteux S. Origin of endogenous DNA abasic sites in Saccharomyces cerevisiae. Mol. Cell Biol. 2003, 23:8386-8394.
115. Khobta A., Kitsera N., Speckmann B., Epe B. 8-Oxoguanine DNA glycosylase (Ogg1) causes a transcriptional inactivation of damaged DNA in the absence of functional Cockayne syndrome B (Csb) protein. DNA Repair (Amst.) 2009, 8:309-317.
116. Kitsera N., Stathis D., Luhnsdorf B., Muller H., Carell T., Epe B.A. Khobta, 8-Oxo-7,8-dihydroguanine in DNA does not constitute a barrier to transcription, but is converted into transcription-blocking damage by OGG1. Nucleic Acids Res. 2011, 39:5926-5934.
117. Kunz C., Focke F., Saito Y., Schuermann D., Lettieri T., Selfridge J., Schar P. Base excision by thymine DNA glycosylase mediates DNA-directed cytotoxicity of 5-fluorouracil. PLoS Biol. 2009, 7:e91.
118. Liu J., Doetsch P.W. Template strand gap bypass is a general property of prokaryotic RNA polymerases: implications for elongation mechanisms. Biochemistry 1996, 35:14999-15008.
119. Roy D., Lieber M.R. G clustering is important for the initiation of transcription-induced R-loops in vitro, whereas high G density without clustering is sufficient thereafter. Mol. Cell Biol. 2009, 29:3124-3133.
120. Fortini P., Parlanti E., Sidorkina O.M., Laval J., Dogliotti E. The type of DNA glycosylase determines the base excision repair pathway in mammalian cells,. J. Biol. Chem. 1999, 274:15230-15236.
121. Frosina G., Fortini P., Rossi O., Carrozzino F., Raspaglio G., Cox L.S., Lane D.P., Abbondandolo A., Dogliotti E. Two pathways for base excision repair in mammalian cells. J. Biol. Chem. 1996, 271:9573-9578.
122. Klungland A., Lindahl T. Second pathway for completion of human DNA base excision-repair: reconstitution with purified proteins and requirement for DNase IV (FEN1). EMBO J. 1997, 16:3341-3348.
123. Garg P., Stith C.M., Sabouri N., Johansson E., Burgers P.M. Idling by DNA polymerase delta maintains a ligatable nick during lagging-strand DNA replication. Genes Dev. 2004, 18:2764-2773.
124. Dianov G., Bischoff C., Piotrowski J., Bohr V.A. Repair pathways for processing of 8-oxoguanine in DNA by mammalian cell extracts. J. Biol. Chem. 1998, 273:33811-33816.
125. Sung J.S., DeMott M.S., Demple B. Long-patch base excision DNA repair of 2-deoxyribonolactone prevents the formation of DNA-protein cross-links with DNA polymerase beta. J. Biol. Chem. 2005, 280:39095-39103.
126. Khobta A., Lingg T., Schulz I., Warken D., Kitsera N., Epe B. Mouse CSB protein is important for gene expression in the presence of a single-strand break in the non-transcribed DNA strand. DNA Repair (Amst.) 2010, 9:985-993.
127. Rusyn I., Fry R.C., Begley T.J., Klapacz J., Svensson J.P., Ambrose M., Samson L.D. Transcriptional networks in S. cerevisiae linked to an accumulation of base excision repair intermediates. PLoS One 2007, 2:e1252.
128. Shanbhag N.M., Rafalska-Metcalf I.U., Balane-Bolivar C., Janicki S.M., Greenberg R.A. ATM-dependent chromatin changes silence transcription in cis to DNA double-strand breaks. Cell 2010, 141:970-981.
129. Huen M.S., Chen J. ATM creates a veil of transcriptional silence. Cell 2010, 141:924-926.
130. Polo S.E., Roche D., Almouzni G. New histone incorporation marks sites of UV repair in human cells. Cell 2006, 127:481-493.
131. Osley M.A., Tsukuda T., Nickoloff J.A. ATP-dependent chromatin remodeling factors and DNA damage repair. Mutat. Res. 2007, 618:65-80.