title: 3D-DIP-Chip: a microarray-based method to measure genomic DNA damage.
abstract: Genotoxins cause DNA damage, which can result in genomic instability. The genetic changes induced have far-reaching consequences, often leading to diseases such as cancer. A wide range of genotoxins exists, including radiations and chemicals found naturally in the environment, and in man-made forms created by human activity across a variety of industries. Genomic technologies offer the possibility of unravelling the mechanisms of genotoxicity, including the repair of genetic damage, enhancing our ability to develop, test and safely use existing and novel materials. We have developed 3D-DIP-Chip, a microarray-based method to measure the prevalence of genomic genotoxin-induced DNA damage. We demonstrate the measurement of both physical and chemical induced DNA damage spectra, integrating the analysis of these with the associated changes in histone acetylation induced in the epigenome. We discuss the application of the method in the context of basic and translational sciences.
authors.affiliation: Cancer &Genetics Building, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
authors.forename: James Rees
authors.initials: JR
authors.lastname: Powell
authors.affiliation: Cancer &Genetics Building, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
authors.forename: Mark Richard
authors.initials: MR
authors.lastname: Bennett
authors.affiliation: Cancer &Genetics Building, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
authors.forename: Katie Ellen
authors.initials: KE
authors.lastname: Evans
authors.affiliation: Cancer &Genetics Building, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
authors.forename: Shirong
authors.initials: S
authors.lastname: Yu
authors.affiliation: Cancer &Genetics Building, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
authors.forename: Richard Michael
authors.initials: RM
authors.lastname: Webster
authors.affiliation: Cancer &Genetics Building, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
authors.forename: Raymond
authors.initials: R
authors.lastname: Waters
authors.affiliation: Agilent Technologies (UK) Ltd, 710 Wharfedale Road, Winnersh Triangle, Wokingham, Berkshire, RG41 5TP, UK.
authors.forename: Nigel
authors.initials: N
authors.lastname: Skinner
authors.affiliation: Cancer &Genetics Building, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
authors.forename: Simon Huw
authors.initials: SH
authors.lastname: Reed
mesh_terms: D000107:Acetylation; D004249:DNA Damage / Q000235:genetics*; D004260:DNA Repair / Q000235:genetics; D042822:Genomic Instability; D006657:Histones / Q000235:genetics; D006801:Humans; D009153:Mutagens / Q000633:toxicity*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011499:Protein Processing, Post-Translational
chemical_list: D006657:Histones; D009153:Mutagens