A Novel Method for the Genome-wide High Resolution Analysis of DNA Damage

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2010 Nov 11

PMID 21062813

Citations 26

Authors

Yumin Teng

Mark Bennett

Katie E Evans

Huayun Zhuang-Jackson

Andy Higgs

Simon H Reed

Raymond Waters

Affiliations

Soon will be listed here.

Abstract

DNA damage occurs via endogenous and exogenous genotoxic agents and compromises a genome's integrity. Knowing where damage occurs within a genome is crucial to understanding the repair mechanisms which protect this integrity. This paper describes a new development based on microarray technology which uses ultraviolet light induced DNA damage as a paradigm to determine the position and frequency of DNA damage and its subsequent repair throughout the entire yeast genome.

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Methods and applications of genome-wide profiling of DNA damage and rare mutations.

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Gene architecture is a determinant of the transcriptional response to bulky DNA damages.

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Damage mapping techniques and the light they have shed on canonical and atypical UV photoproducts.

Bohm K, Wyrick J Front Genet. 2023; 13:1102593.

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References

Prakash L . Repair of pyrimidine dimers in radiation-sensitive mutants rad3, rad4, rad6 and rad9 of Saccharomyces cerevisiae. Mutat Res. 1977; 45(1):13-20. DOI: 10.1016/0027-5107(77)90038-0. View

Waters R, Teng Y, Yu Y, Yu S, Reed S . Tilting at windmills? The nucleotide excision repair of chromosomal DNA. DNA Repair (Amst). 2008; 8(2):146-52. DOI: 10.1016/j.dnarep.2008.11.001. View

Mitchell D, Jen J, Cleaver J . Sequence specificity of cyclobutane pyrimidine dimers in DNA treated with solar (ultraviolet B) radiation. Nucleic Acids Res. 1992; 20(2):225-9. PMC: 310358. DOI: 10.1093/nar/20.2.225. View

Tornaletti S, Rozek D, Pfeifer G . The distribution of UV photoproducts along the human p53 gene and its relation to mutations in skin cancer. Oncogene. 1993; 8(8):2051-7. View

Teng Y, Yu Y, Ferreiro J, Waters R . Histone acetylation, chromatin remodelling, transcription and nucleotide excision repair in S. cerevisiae: studies with two model genes. DNA Repair (Amst). 2005; 4(8):870-83. DOI: 10.1016/j.dnarep.2005.04.006. View

Spivak G, Pfeifer G, Hanawalt P . In vivo assays for transcription-coupled repair. Methods Enzymol. 2006; 408:223-46. DOI: 10.1016/S0076-6879(06)08014-1. View

Clayton D, Doda J, Friedberg E . The absence of a pyrimidine dimer repair mechanism in mammalian mitochondria. Proc Natl Acad Sci U S A. 1974; 71(7):2777-81. PMC: 388554. DOI: 10.1073/pnas.71.7.2777. View

Verhage R, Zeeman A, De Groot N, Gleig F, Bang D, Van de Putte P . 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. 1994; 14(9):6135-42. PMC: 359140. DOI: 10.1128/mcb.14.9.6135-6142.1994. View

Pokholok D, Harbison C, Levine S, Cole M, Hannett N, Lee T . Genome-wide map of nucleosome acetylation and methylation in yeast. Cell. 2005; 122(4):517-27. DOI: 10.1016/j.cell.2005.06.026. View

10.

Teng Y, Yu S, Reed S, Waters R . Lux ex tenebris: nucleotide resolution DNA repair and nucleosome mapping. Methods. 2009; 48(1):23-34. DOI: 10.1016/j.ymeth.2009.02.017. View

11.

Teng Y, Li S, Waters R, Reed S . Excision repair at the level of the nucleotide in the Saccharomyces cerevisiae MFA2 gene: mapping of where enhanced repair in the transcribed strand begins or ends and identification of only a partial rad16 requisite for repairing upstream control.... J Mol Biol. 1997; 267(2):324-37. DOI: 10.1006/jmbi.1996.0908. View

12.

Mockler T, Chan S, Sundaresan A, Chen H, Jacobsen S, Ecker J . Applications of DNA tiling arrays for whole-genome analysis. Genomics. 2004; 85(1):1-15. DOI: 10.1016/j.ygeno.2004.10.005. View

13.

Waters R, MOUSTACCHI E . The fate of ultraviolet-induced pyrimidine dimers in the mitochondrial DNA of Saccharomyces cerevisiae following various post-irradiation cell treatments. Biochim Biophys Acta. 1974; 366(3):241-50. DOI: 10.1016/0005-2787(74)90282-2. View