High-resolution characterization of CPD hotspot formation in human fibroblasts

Nucleic Acids Research

Volumn 42, Issue 2, 2014, Pages 893-905

  Zavala, Anamaria G ^a   Morris, Robert T ^a   Wyrick, John J ^a   Smerdon, Michael J ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL DNA; PYRIMIDINE DIMER;

ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMOSOME 1; CHROMOSOME 6; CHROMOSOME MAP; CONTROLLED STUDY; DNA ADDUCT; DNA DAMAGE; DNA REPAIR; DNA SEQUENCE; FIBROBLAST; GENE REARRANGEMENT; HUMAN; HUMAN CELL; HUMAN GENOME; IRRADIATION; MOLECULAR DYNAMICS; NUCLEOSOME; PRIORITY JOURNAL; RADIATION INJURY; RADIATION INJURY REPAIR;

CHROMOSOMES, HUMAN, PAIR 1; CHROMOSOMES, HUMAN, PAIR 6; DNA; DNA ADDUCTS; FIBROBLASTS; HUMANS; IMMUNOPRECIPITATION; NUCLEOSOMES; POLY T; PYRIMIDINE DIMERS; REPETITIVE SEQUENCES, NUCLEIC ACID;

EID: 84893293856     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt912     Document Type: Article

References (56)

1. Hanawalt, P.C. (1998) Genomic instability: environmental invasion and the enemies within. Mutat. Res., 400, 117-125.
2. Douki, T. and Cadet, J. (2001) Individual determination of the yield of the main UV-induced dimeric pyrimidine photoproducts in DNA suggests a high mutagenicity of CC photolesions. Biochemistry, 40, 2495-2501.
3. Tornaletti, S., Rozek, D. and Pfeifer, G.P. (1993) The distribution of UV photoproducts along the human p53 gene and its relation to mutations in skin cancer. Oncogene, 8, 2051-2057.
4. Gale, J.M., Nissen, K.A. and Smerdon, M.J. (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.
5. Smerdon, M.J. and Conconi, A. (1999) Modulation of DNA damage and DNA repair in chromatin. Prog. Nucleic Acid Res. Mol. Biol., 62, 227-255.
6. Cleaver, J.E. (2000) Common pathways for ultraviolet skin carcinogenesis in the repair and replication defective groups of xeroderma pigmentosum. J. Dermatol. Sci., 23, 1-11.
7. Gong, F., Kwon, Y. and Smerdon, M.J. (2005) Nucleotide excision repair in chromatin and the right of entry. DNA Repair, 4, 884-896.
8. Gillet, L.C. and Scharer, O.D. (2006) Molecular mechanisms of mammalian global genome nucleotide excision repair. Chem. Rev., 106, 253-276.
9. Liu, X. and Smerdon, M.J. (2000) Nucleotide excision repair of the 5 S ribosomal RNA gene assembled into a nucleosome. J. Biol. Chem., 275, 23729-23735.
10. Nag, R., Kyriss, M., Smerdon, J.W., Wyrick, J.J. and Smerdon, M.J. (2010) A cassette of N-terminal amino acids of histone H2B are required for efficient cell survival, DNA repair and Swi/Snf binding in UV irradiated yeast. Nucleic Acids Res., 38, 1450-1460.
11. Chaudhuri, S., Wyrick, J.J. and Smerdon, M.J. (2009) Histone H3 Lys79 methylation is required for efficient nucleotide excision repair in a silenced locus of Saccharomyces cerevisiae. Nucleic Acids Res., 37, 1690-1700.
12. Gong, F., Fahy, D., Liu, H., Wang, W. and Smerdon, M.J. (2008) Role of the mammalian SWI/SNF chromatin remodeling complex in the cellular response to UV damage. Cell Cycle, 7, 1067-1074.
13. You, Y.H., Szabo, P.E. and Pfeifer, G.P. (2000) Cyclobutane pyrimidine dimers form preferentially at the major p53 mutational hotspot in UVB-induced mouse skin tumors. Carcinogenesis, 21, 2113-2117.
14. Tommasi, S., Oxyzoglou, A.B. and Pfeifer, G.P. (2000) Cell cycleindependent removal of UV-induced pyrimidine dimers from the promoter and the transcription initiation domain of the human CDC2 gene. Nucleic Acids Res., 28, 3991-3998.
15. Strickland, P.T. and Gentile, C. (1991) Separation of carcinogendamaged DNA fragments from undamaged DNA. Nucleic Acids Res., 19, 6955.
16. Rochette, P.J. and Brash, D.E. (2010) Human telomeres are hypersensitive to UV-induced DNA Damage and refractory to repair. PLoS Genet., 6, e1000926.
17. Teng, Y., Bennett, M., Evans, K.E., Zhuang-Jackson, H., Higgs, A., Reed, S.H. and Waters, R. (2011) A novel method for the genomewide high resolution analysis of DNA damage. Nucleic Acids Res., 39, e10.
18. King, N.M., Nikolaishvili-Feinberg, N., Bryant, M.F., Luche, D.D., Heffernan, T.P., Simpson, D.A., Hanaoka, F., Kaufmann, W.K. and Cordeiro-Stone, M. (2005) Overproduction of DNA polymerase eta does not raise the spontaneous mutation rate in diploid human fibroblasts. DNA Repair, 4, 714-724.
19. Adair, J.E., Kwon, Y., Dement, G.A., Smerdon, M.J. and Reeves, R. (2005) Inhibition of nucleotide excision repair by high mobility group protein HMGA1. J. Biol. Chem., 280, 32184-32192.
20. Smerdon, M.J., Kastan, M.B. and Lieberman, M.W. (1979) Distribution of repair-incorporated nucleotides and nucleosome rearrangement in the chromatin of normal and xeroderma pigmentosum human fibroblasts. Biochemistry, 18, 3732-3739.
21. Perdiz, D., Grof, P., Mezzina, M., Nikaido, O., Moustacchi, E. and Sage, E. (2000) Distribution and repair of bipyrimidine photoproducts in solar UV-irradiated mammalian cells. Possible role of Dewar photoproducts in solar mutagenesis. J. Biol. Chem., 275, 26732-26742.
22. Lee, T.I., Johnstone, S.E. and Young, R.A. (2006) Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat. Protoc., 1, 729-748.
23. Ozturk, N., Kao, Y.T., Selby, C.P., Kavakli, I.H., Partch, C.L., Zhong, D. and Sancar, A. (2008) Purification and characterization of a type III photolyase from Caulobacter crescentus. Biochemistry, 47, 10255-10261.
24. Duan, M.R. and Smerdon, M.J. (2010) UV damage in DNA promotes nucleosome unwrapping. J. Biol. Chem., 285, 26295-26303.
25. Richard-Foy, H. and Hager, G.L. (1987) Sequence-specific positioning of nucleosomes over the steroid-inducible MMTV promoter. EMBO J., 6, 2321-2328.
26. Judy, J.T. and Ji, H. (2009) TileProbe: modeling tiling array probe effects using publicly available data. Bioinformatics, 25, 2369-2375.
27. Ji, H., Jiang, H., Ma, W., Johnson, D.S., Myers, R.M. and Wong, W.H. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol., 26, 1293-1300.
28. Johnson, W.E., Li, W., Meyer, C.A., Gottardo, R., Carroll, J.S., Brown, M. and Liu, X.S. (2006) Model-based analysis of tilingarrays for ChIP-chip. Proc. Natl Acad. Sci. USA, 103, 12457-12462.
29. Ji, H. and Wong, W.H. (2005) TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics, 21, 3629-3636.
30. Johns, H.E., Rapaport, S.A. and Delbrueck, M. (1962) Photochemistry of thymine dimers. J. Mol. Biol., 4, 104-114.
31. Albig, W. and Doenecke, D. (1997) The human histone gene cluster at the D6S105 locus. Hum. Genet., 101, 284-294.
32. Wang, Y.H. (2006) Chromatin structure of human chromosomal fragile sites. Cancer Lett., 232, 70-78.
33. Smit, A.F. (1999) Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev., 9, 657-663.
34. Toth, G., Gaspari, Z. and Jurka, J. (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res., 10, 967-981.
35. Mitchell, D.L., Jen, J. and Cleaver, J.E. (1992) Sequence specificity of cyclobutane pyrimidine dimers in DNA treated with solar (ultraviolet B) radiation. Nucleic Acids Res., 20, 225-229.
36. Dechering, K.J., Cuelenaere, K., Konings, R.N. and Leunissen, J.A. (1998) Distinct frequency-distributions of homopolymeric DNA tracts in different genomes. Nucleic Acids Res., 26, 4056-4062.
37. Widlund, H.R., Cao, H., Simonsson, S., Magnusson, E., Simonsson, T., Nielsen, P.E., Kahn, J.D., Crothers, D.M. and Kubista, M. (1997) Identification and characterization of genomic nucleosome-positioning sequences. J. Mol. Biol., 267, 807-817.
38. Tomita, N., Fujita, R., Kurihara, D., Shindo, H., Wells, R.D. and Shimizu, M. (2002) Effects of triplet repeat sequences on nucleosome positioning and gene expression in yeast minichromosomes. Nucleic Acids Res. Suppl., 2002, 231-232.
39. Tanaka, Y., Yamashita, R., Suzuki, Y. and Nakai, K. (2010) Effects of Alu elements on global nucleosome positioning in the human genome. BMC Genomics, 11, 309.
40. Kosmoski, J.V. and Smerdon, M.J. (1999) Synthesis and nucleosome structure of DNA containing a UV photoproduct at a specific site. Biochemistry, 38, 9485-9494.
41. Wellinger, R.E. and Thoma, F. (1997) Nucleosome structure and positioning modulate nucleotide excision repair in the nontranscribed strand of an active gene. EMBO J., 16, 5046-5056.
42. Powell, N.G., Ferreiro, J., Karabetsou, N., Mellor, J. and Waters, R. (2003) Transcription, nucleosome positioning and protein binding modulate nucleotide excision repair of the Saccharomyces cerevisiae MET17 promoter. DNA Repair, 2, 375-386.
43. Nag, R., Kyriss, M., Smerdon, J.W., Wyrick, J.J. and Smerdon, M.J. (2009) A cassette of N-terminal amino acids of histone H2B are required for efficient cell survival, DNA repair and Swi/Snf binding in UV irradiated yeast. Nucleic Acids Res., 38, 1450-1460.
44. Argueso, J.L., Westmoreland, J., Mieczkowski, P.A., Gawel, M., Petes, T.D. and Resnick, M.A. (2008) Double-strand breaks associated with repetitive DNA can reshape the genome. Proc. Natl Acad. Sci. USA, 105, 11845-11850.
45. Parsons, R., Myeroff, L.L., Liu, B., Willson, J.K., Markowitz, S.D., Kinzler, K.W. and Vogelstein, B. (1995) Microsatellite instability and mutations of the transforming growth factor beta type II receptor gene in colorectal cancer. Cancer Res., 55, 5548-5550.
46. Liu, B., Farrington, S.M., Petersen, G.M., Hamilton, S.R., Parsons, R., Papadopoulos, N., Fujiwara, T., Jen, J., Kinzler, K.W., Wyllie, A.H. et al. (1995) Genetic instability occurs in the majority of young patients with colorectal cancer. Nat. Med., 1, 348-352.
47. Englander, E.W. and Howard, B.H. (1997) Alu-mediated detection of DNA damage in the human genome. Mutat. Res., 385, 31-39.
48. Suter, B., Schnappauf, G. and Thoma, F. (2000) Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo. Nucleic Acids Res., 28, 4083-4089.
49. Field, Y., Kaplan, N., Fondufe-Mittendorf, Y., Moore, I.K., Sharon, E., Lubling, Y., Widom, J. and Segal, E. (2008) Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput. Biol., 4, e1000216.
50. Yuan, G.C., Liu, Y.J., Dion, M.F., Slack, M.D., Wu, L.F., Altschuler, S.J. and Rando, O.J. (2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science, 309, 626-630.
51. Ozsolak, F., Song, J.S., Liu, X.S. and Fisher, D.E. (2007) Highthroughput mapping of the chromatin structure of human promoters. Nat. Biotechnol., 25, 244-248.
52. Brash, D.E., Seetharam, S., Kraemer, K.H., Seidman, M.M. and Bredberg, A. (1987) Photoproduct frequency is not the major determinant of UV base substitution hot spots or cold spots in human cells. Proc. Natl Acad. Sci. USA, 84, 3782-3786.
53. Mann, D.B., Springer, D.L. and Smerdon, M.J. (1997) DNA damage can alter the stability of nucleosomes: effects are dependent on damage type. Proc. Natl Acad. Sci. USA, 94, 2215-2220.
54. Hakimi, M.A., Bochar, D.A., Schmiesing, J.A., Dong, Y., Barak, O.G., Speicher, D.W., Yokomori, K. and Shiekhattar, R. (2002) A chromatin remodelling complex that loads cohesin onto human chromosomes. Nature, 418, 994-998.
55. Erdel, F., Schubert, T., Marth, C., Langst, G. and Rippe, K. (2010) Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites. Proc. Natl Acad. Sci. USA, 107, 19873-19878.
56. Erdel, F. and Rippe, K. (2011) Binding kinetics of human ISWI chromatin-remodelers to DNA repair sites elucidate their target location mechanism. Nucleus, 2, 105-112.