1
|
van Eijk P, Teng Y, Bennet MR, Evans KE, Powell JR, Webster RM, Reed SH. Integrated Microarray-based Tools for Detection of Genomic DNA Damage and Repair Mechanisms. Methods Mol Biol 2018; 1672:77-99. [PMID: 29043618 DOI: 10.1007/978-1-4939-7306-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
The genetic information contained within the DNA molecule is highly susceptible to chemical and physical insult, caused by both endogenous and exogenous sources that can generate in the order of thousands of lesions a day in each of our cells (Lindahl, Nature 362(6422):709-715, 1993). DNA damages interfere with DNA metabolic processes such as transcription and replication and can be potent inhibitors of cell division and gene expression. To combat these regular threats to genome stability, a host of DNA repair mechanisms have evolved. When DNA lesions are left unrepaired due to defects in the repair pathway, mutations can arise that may alter the genetic information of the cell. DNA repair is thus fundamental to genome stability and defects in all the major repair pathways can lead to cancer predisposition. Therefore, the ability to accurately measure DNA damage at a genomic scale and determine the level, position, and rates of removal by DNA repair can contribute greatly to our understanding of how DNA repair in chromatin is organized throughout the genome. For this reason, we developed the 3D-DIP-Chip protocol described in this chapter. Conducting such measurements has potential applications in a variety of other fields, such as genotoxicity testing and cancer treatment using DNA damage inducing chemotherapy. Being able to detect and measure genomic DNA damage and repair patterns in individuals following treatment with chemotherapy could enable personalized medicine by predicting response to therapy.
Collapse
Affiliation(s)
- Patrick van Eijk
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Yumin Teng
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Mark R Bennet
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Katie E Evans
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - James R Powell
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Richard M Webster
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Simon H Reed
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
| |
Collapse
|
2
|
Yu S, Evans K, van Eijk P, Bennett M, Webster RM, Leadbitter M, Teng Y, Waters R, Jackson SP, Reed SH. Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin. Genome Res 2016; 26:1376-1387. [PMID: 27470111 PMCID: PMC5052058 DOI: 10.1101/gr.209106.116] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/27/2016] [Indexed: 01/08/2023]
Abstract
The rates at which lesions are removed by DNA repair can vary widely throughout the genome, with important implications for genomic stability. To study this, we measured the distribution of nucleotide excision repair (NER) rates for UV-induced lesions throughout the budding yeast genome. By plotting these repair rates in relation to genes and their associated flanking sequences, we reveal that, in normal cells, genomic repair rates display a distinctive pattern, suggesting that DNA repair is highly organized within the genome. Furthermore, by comparing genome-wide DNA repair rates in wild-type cells and cells defective in the global genome-NER (GG-NER) subpathway, we establish how this alters the distribution of NER rates throughout the genome. We also examined the genomic locations of GG-NER factor binding to chromatin before and after UV irradiation, revealing that GG-NER is organized and initiated from specific genomic locations. At these sites, chromatin occupancy of the histone acetyl-transferase Gcn5 is controlled by the GG-NER complex, which regulates histone H3 acetylation and chromatin structure, thereby promoting efficient DNA repair of UV-induced lesions. Chromatin remodeling during the GG-NER process is therefore organized into these genomic domains. Importantly, loss of Gcn5 significantly alters the genomic distribution of NER rates; this has implications for the effects of chromatin modifiers on the distribution of mutations that arise throughout the genome.
Collapse
Affiliation(s)
- Shirong Yu
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Katie Evans
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Patrick van Eijk
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Mark Bennett
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Richard M Webster
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Matthew Leadbitter
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Yumin Teng
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Raymond Waters
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Stephen P Jackson
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, United Kingdom
| | - Simon H Reed
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| |
Collapse
|