Base excision repair in nucleosomes lacking histone tails

DNA Repair

Volumn 4, Issue 2, 2005, Pages 203-209

  Beard, Brian C ^a,b   Stevenson, Jill J ^a,c   Wilson, Samuel H ^d   Smerdon, Michael J ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

^c UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^d NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

AP endonuclease; Chromatin; DNA polymerase ; Glycosylase; Tailless histones

Indexed keywords

HISTONE; TRYPSIN; WERNER SYNDROME PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; CHROMATIN; DNA SEQUENCE; ENZYME ACTIVITY; ENZYME INHIBITION; EXCISION REPAIR; HUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN STRUCTURE;

DNA GLYCOSYLASES; DNA HELICASES; DNA POLYMERASE BETA; DNA REPAIR; DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; DNA-BINDING PROTEINS; HISTONES; HUMANS; NUCLEOSOMES; RECQ HELICASES; URACIL-DNA GLYCOSIDASE;

ALOCASIA MACRORRHIZOS; ZIZIPHUS MAURITIANA;

EID: 10044245884     PISSN: 15687864     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dnarep.2004.09.011     Document Type: Article

References (50)

1. J.H.J. Hoeijmakers Genome maintenance mechanisms for preventing cancer Nature 411 2001 366 374
2. E.C. Friedberg, G.C. Walker, and W. Siede DNA Repair and Mutagenesis 1995 ASM Press Washington, DC
3. D.K. Srivastava, B.J. Vande Berg, R. Prasad, J.T. Molina, W.A. Beard, A.E. Tomkinson, and S.H. Wilson Mammalian abasic site base excision repair: identification of the reaction sequence and rate-determining steps J. Biol. Chem. 273 1998 21203 21209
4. A.P. Wolffe Chromatin: Structure and Function 1998 Academic Press San Diego
5. B.C. Beard, S.H. Wilson, and M.J. Smerdon Suppressed catalytic activity of base excision repair enzymes on rotationally positioned uracil in nucleosomes Proc. Natl. Acad. Sci. USA 100 2003 7465 7470
6. C. Zheng, and J.J. Hayes Structures and interactions of the core histone tail domains Biopolymers 68 2003 539 546
7. J. Ausio, F. Dong, and K.E. van Holde Use of selectively trypsinized nucleosome core particles to analyze the role of the histone "tails" in the stabilization of the nucleosome J. Mol. Biol. 206 1989 451 463
8. J.J. Hayes, D.J. Clark, and A.P. Wolffe Histone contributions to the structure of DNA in the nucleosome Proc. Natl. Acad. Sci. USA 88 1991 6829 6833
9. K.J. Polach, P.T. Lowary, and J. Widom Effects of core histone tail domains on the equilibrium constants for dynamic DNA site accessibility in nucleosomes J. Mol. Biol. 298 2000 211 223
10. J.C. Hansen Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functions Annu. Rev. Biophys. Biomol. Struct. 31 2002 361 392
11. D.R. Chafin, J.M. Vitolo, L.A. Henricksen, R.A. Bambara, and J.J. Hayes Human DNA ligase I efficiently seals nicks in nucleosomes EMBO J. 19 2000 5492 5501
12. C. Zheng, and J.J. Hayes Intra- and inter-nucleosomal protein-DNA interactions of the core histone tail domains in a model system J. Biol. Chem. 278 2003 24217 24224
13. 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 angstrom resolution Nature 389 1997 251 260
14. T.E. Shrader, and D.M. Crothers Effects of DNA sequence and histone-histone interactions on nucleosome placement J. Mol. Biol. 216 1990 69 84
15. T.E. Shrader, and D.M. Crothers Artificial Nucleosome Positioning Sequences Proc. Natl. Acad. Sci. USA 86 1989 7418 7422
16. Q. Li, and O. Wrange Translational positioning of a nucleosomal glucocorticoid response element modulates glucocorticoid receptor affinity Genes Dev. 7 1993 2471 2482
17. Q. Li, and O. Wrange Accessibility of a glucocorticoid response element in a nucleosome depends on its rotational positioning Mol. Cell. Biol. 8 1995 4375 4384
18. J.V. Kosmoski, and M.J. Smerdon Synthesis and nucleosome structure of DNA containing a UV photoproduct at a specific site Biochemistry 38 1999 9485 9494
19. C.A. Davey, D.F. Sargent, K. Luger, A.W. Maeder, and T.J. Richmond Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution J. Mol. Biol. 319 2002 1097 1113
20. S. Khorasanizadeh The nucleosome: from genomic organization to genomic regulation Cell 116 2004 259 272
21. B.C. Beard, and M.J. Smerdon Analysis of DNA repair on nucleosome templates Methods Enzymol. 377 2004 499 507
22. X. Liu, and M.J. Smerdon Nucleotide excision repair of the 5S ribosomal RNA gene assembled into a nucleosome J. Biol. Chem. 275 2000 23729 23735
23. L.J. Libertini, and E.W. Small Salt induced transitions of chromatin core particles studied by tyrosine fluorescence anisotropy Nucleic Acids Res. 8 1980 3517 3534
24. R.T. Simpson, and P. Kunzler Chromatin and core particle formed from the inner histones and synthetic polydeoxyribonucleotides of defined sequence Nucleic Acids Res. 6 1979 1387 1415
25. 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. USA 94 1997 2215 2220
26. H.R. Widlund, J.M. Vitolo, C. Thiriet, and J.J. Hayes DNA sequence-dependent contributions of core histone tails to nucleosome stability: differential effects of acetylation and proteolytic tail removal Biochemistry 39 2000 3835 3841
27. L.M. Carruthers, C. Tse, K.P. Walker 3rd, and J.C. Hansen Assembly of defined nucleosomal and chromatin arrays from pure components Methods Enzymol. 304 1999 19 35
28. H. Nilsen, T. Lindahl, and A. Verreault DNA base excision repair of uracil residues in reconstituted nucleosome core particles EMBO J. 21 2002 5943 5952
29. Y. Matsumoto, and K. Kim Excision of deoxyribose phosphate residues by DNA polymerase beta during DNA repair Science 269 1995 699 702
30. C.E. Piersen, R. Prasad, S.H. Wilson, and R.S. Lloyd Evidence for an imino intermediate in the DNA polymerase beta deoxyribose phosphate excision reaction J. Biol. Chem. 271 1996 17811 17815
31. B.C. Beard Base Excision Repair of Dynamic Chromatin Substrates, School of Molecular Biosciences 2003 Washington State University Pullman, Washington p. 212
32. J.A. Harrigan, P.L. Opresko, C. von Kobbe, P.S. Kedar, R. Prasad, S.H. Wilson, and V.A. Bohr The Werner syndrome protein stimulates DNA polymerase beta strand displacement synthesis via its helicase activity J. Biol. Chem. 278 2003 22686 22695
33. H.R. Widlund, H. Cao, S. Simonsson, E. Magnusson, T. Simonsson, P.E. Nielsen, J.D. Kahn, D.M. Crothers, and M. Kubista Identification and characterization of genomic nucleosome-positioning sequences J. Mol. Biol. 267 1997 807 817
34. Y. Wang, W. Fischle, W. Cheung, S. Jacobs, S. Khorasanizadeh, and C.D. Allis Beyond the double helix: writing and reading the histone code Novartis Found Symp. 259 2004 3 17 (discussion 17-21, 163-169)
35. R.T. Simpson Structure of the chromatosome, a chromatin core particle containing 160 base pairs of DNA and all the histones Biochemistry 17 1978 5524 5531
36. J.D. Anderson, A. Thastrom, and J. Widom Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation Mol. Cell. Biol. 22 2002 7147 7157
37. J.D. Anderson, P.T. Lowary, and J. Widom Effects of histone acetylation on the equilibrium accessibility of nucleosomal DNA target sites J. Mol. Biol. 307 2001 977 985
38. C.L. Peterson Chromatin remodeling enzymes: taming the machines EMBO Rep. 3 2002 319 322
39. P.B. Becker, and W. Horz ATP-dependent nucleosome remodeling Annu. Rev. Biochem. 71 2002 247 273
40. K. Ura, and J.J. Hayes Nucleotide excision repair and chromatin remodeling Eur. J. Biochem. 269 2002 2288 2293
41. V.A. Bohr, N.S. Pinto, S.G. Nyaga, G. Dianov, K. Kraemer, M.M. Seidman, and R.M. Brosh DNA Repair and mutagenesis in werner syndrome Environ. Mol. Mutagen. 38 2001 227 234
42. Y. Kubota, R.A. Nash, A. Klungland, P. Schar, D.E. Barnes, and T. Lindahl Reconstitution of DNA base excision-repair with purified human proteins: interaction between DNA polymerase beta and the XRCC1 protein EMBO J. 15 1996 6662 6670
43. A. Marintchev, A. Robertson, E.K. Dimitriadis, R. Prasad, S.H. Wilson, and G.P. Mullen Domain specific interaction in the XRCC1-DNA polymerase beta complex Nucleic Acids Res. 28 2000 2049 2059
44. A.E. Vidal, S. Boiteux, I.D. Hickson, and J.P. Radicella XRCC1 coordinates the initial and late stages of DNA abasic site repair through protein-protein interactions EMBO J. 20 2001 6530 6539
45. J. Griesenbeck, S.L. Oei, P. Mayer-Kuckuk, M. Ziegler, G. Buchlow, and M. Schweiger Protein-protein interaction of the human poly(ADP-ribosyl) transferase depends on the functional state of the enzyme Biochemistry 36 1997 7297 7304
46. C. Bernstein, H. Bernstein, C.M. Payne, and H. Garewal DNA repair/pro-apoptotic dual-role proteins in five major DNA repair pathways: fail-safe protection against carcinogenesis Mutat. Res. 511 2002 145 178
47. M. Masson, C. Niedergang, V. Schreiber, S. Muller, J. Menissier-de Murcia, and G. de Murcia XRCC1 is specifically associated with poly(ADP-ribose) polymerase and negatively regulates its activity following DNA damage Mol. Cell. Biol. 18 1998 3563 3571
48. 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
49. 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
50. 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