Base excision repair in nucleosome substrates

Chromosome Research

Volumn 14, Issue 1, 2006, Pages 27-37

  Jagannathan, Indu ^a   Cole, Hope A ^a   Hayes, Jeffrey J ^a  

^a UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

Author keywords

Base excision repair; Chromatin; Nucleosome

Indexed keywords

GENOMIC DNA;

CATALYSIS; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA BINDING; DNA DAMAGE; DNA HELIX; DNA HISTONE INTERACTION; DNA REPAIR; DNA REPLICATION; DNA TRANSCRIPTION; EXCISION REPAIR; GENE EXPRESSION; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN INTERACTION; REVIEW; STATISTICAL SIGNIFICANCE;

DNA DAMAGE; DNA REPAIR; DNA REPAIR ENZYMES; DNA-BINDING PROTEINS; HISTONES; HUMANS; NUCLEOSOMES;

EUKARYOTA;

EID: 33644626974     PISSN: 09673849     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10577-005-1020-7     Document Type: Review

References (43)

1. Angelov D, Vitolo JM, Mutskov V, Dimitrov S, Hayes JJ (2001) Preferential interaction of the core histone tail domains with linker DNA. PNAS 98: 6599-6604.
2. Beard BC, Wilson SH, Smerdon MJ (2003) Suppressed catalytic activity of base excision repair enzymes on rotationally positioned uracil in nucleosomes. PNAS 100: 7465-7470.
3. Beard BC, Stevenson JJ, Wilson SH, Smerdon MJ (2005) Base excision repair in nucleosomes lacking histone tails. DNA Repair 4: 203-209.
4. Chafin DR, Vitolo JM, Henricksen LA, Bambara RA, Hayes JJ (2000) Human DNA ligase I efficiently seals nicks in nucleosomes. The EMBO J 19: 5492-5501.
5. Chafin DR, Hayes JJ (2001) Site-directed cleavage of DNA by linker histone-Fe(II) EDTA conjugates. Meth Mol Biol 148: 275-290.
6. Doetsch PW (2002) Translesion synthesis by RNA polymerases: occurrence and biological implications for transcriptional mutagenesis. Mutat Res 510: 131-140.
7. Edayathumangalam RS, Weyermann P, Dervan PB, Gottesfeld JM, Luger K (2005) Nucleosomes in solution exist as a mixture of twist-defect states. J Mol Biol 345: 103-114.
8. Friedberg EC (2003) DNA damage and repair. Nature 421: 436-440.
9. Gowher H, Stockdale CJ, Goyal R, Ferreira H, Owen-Hughes T, Jeltsch A (2005) De novo methylation of nucleosomal DNA by the mammalian Dnmt1 and Dnmt3A DNA methyltransferases. Biochemistry 44: 9899-9904.
10. Hasan S, Hassa PO, Imhof R, Hottiger MO (2001a) Transcription coactivator p300 binds PCNA and may have a role in DNA repair synthesis. Nature 410: 387-391.
11. Hasan S, Stucki M, Hassa PO et al. (2001b) Regulation of human flap endonuclease-1 activity by acetylation through the transcriptional coactivator p300. Mol Cell 7: 1221-1231.
12. Hayes JJ, Tullius TD, Wolffe AP (1990) The structure of DNA in a nucleosome. PNAS 87: 7405-7409.
13. He Z, Ingles CJ (1997) Isolation of human complexes proficient in nucleotide excision repair. Nucleic Acids Res 25: 1136-1141.
14. Henricksen LA, Bambara RA (1998) Multiprotein reactions in mammalian DNA replication. Leuk Res 22: 1-5
15. Hosfield DJ, Daniels DS, Mol CD, Putnam CD, Parikh SS, Tainer JA (2001) DNA damage recognition and repair pathway coordination revealed by the structural biochemistry of DNA repair enzymes. Prog Nucleic Acid Res Mol Biol 68: 315-347.
16. Huggins CF, Chafin DR, Aoyagi S, Henricksen LA, Bambara RA, Hayes JJ (2002) Flap endonuclease I efficiently cleaves base excision repair and DNA replication intermediates assembled into nucleosomes. Mol Cell 10: 1201-1211.
17. Krokan HE, Standal R, Slupphaug G (1997) DNA glycosylases in the base excision repair of DNA. Biochem J 325: 1-16.
18. Kysela B, Chovanec M, Jeggo PA (2005) Phosphorylation of linker histones by DNA-dependent protein kinase is required for DNA ligaseIV-dependent ligation in the presence of histone H1. PNAS 102: 1877-1882.
19. Lee KM, Hayes JJ (1998) Linker DNA and H1-dependent reorganization of histone-DNA interactions within the nucleosome. Biochemistry 37: 8622-8628.
20. Li S, Smerdon MJ (2002) Nucleosome structure and repair of N-methyl purines in the GAL-10 genes of Saccharomyces cerevisiae. J Biol Chem 277: 44651-44659.
21. Li G, Levitus M, Bustamante C, Widom J (2005) Rapid spontaneous accessibility of nucleosomal DNA. Nature Struct Mol Biol 12: 46-53.
22. Liu X, Smerdon MJ (2000) Nucleotide excision repair of the 5S ribosomal RNA gene assembled into a nucleosome. J Biol Chem 275: 23729-23735.
23. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389: 251-260.
24. McCullough AK, Dodson ML, Lloyd RS (1999) Initiation of base excision repair: Glycosylase mechanisms and structures. Annu Rev Biochem 68: 255-285.
25. Memisoglu A, Samson L (2000) Base excision repair in yeast and mammals. Mutat Res 451: 39-51.
26. Mol CD, Izumi T, Mitra S, Tainer JA (2000) DNA-bound structures and mutants reveal abasic DNA binding by APE1 DNA repair and coordination. Nature 403: 451-456.
27. Negri R, Buttinelli M, Panetta G, De Arcangelis V, Di Mauro E, Travers A (2001) Sequence dependence of translational positioning of core nucleosomes. J Mol Biol 307: 987-999.
28. Nilsen H, Lindahl T, Verreault A (2002) DNA base excision repair of uracil residues in reconstituted nucleosome core particles. EMBO J 21: 5943-5952.
29. Parikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE, Tainer JA (1998) Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA. EMBO J 17: 5214-5226.
30. Parikh SS, Putnam CD, Tainer JA (2000) Lessons learned from structural results on uracil-DNA glycosylase. Mutat Res 460: 183-199.
31. Peterson CL, Cote J (2004) Cellular machineries for chromosomal DNA repair. Genes Dev 18: 602-616.
32. Polach KJ, Widom J (1995) Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J Mol Biol 254: 130-149.
33. Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H (1997) Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: Evidence for an induced fit mechanism. Biochemistry 36: 11205-11215.
34. Seeberg E, Eide L, Bjoras M (1995) The base excision repair pathway. Trends Biol Sci 20: 391-397.
35. Shrader TE, Crothers DM (1989) Artificial nucleosome positioning sequences. Proc Natl Acad Sci USA 86: 7418-7422.
36. Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA (1996) A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature 384: 87-92.
37. Smerdon MJ, Conconi A (1999) Modulation of DNA damage and DNA repair in chromatin. Prog Nucleic Acid Res Mol Biol 62: 227-255.
38. Sokhansanj BA, Rodrigue GR, Fitch JP, Wilson DM 3rd (2002) A quantitative model of human base excision repair. I. Mechanistic insights. Nucleic Acids Res 30: 1817-1825.
39. Tini M, Benecke A, Um SJ, Torchia J, Evans RM, Chambon P (2002) Association of CBP/p300 acetylase and thymine DNA glycosylase links DNA repair and transcription. Mol Cell 9: 265-277.
40. Tuo J, Jaruga P, Rodriguez H, Dizdaroglu M, Bohr VA (2002a) The cockayne syndrome group B gene product is involved in cellular repair of 8-hydroxyadenine in DNA. J Biol Chem 277: 30832-30837.
41. Tuo J, Chen C, Zeng X, Christiansen M, Bohr VA (2002b) Functional crosstalk between hOgg1 and the helicase domain of Cokayne syndrome group B protein. DNA Repair 1: 913-927.
42. Ura K, Hayes JJ (2002) Nucleotide excision repair and chromatin remodeling. Eur J Biochem 269: 2288-2293.
43. Woodcock CL, Dimitrov S (2001) Higher-order structure of chromatin and chromosomes. Curr Opin Genet Dev 11: 130-135.