Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin
- Shirong Yu1,3,4,
- Katie Evans1,3,
- Patrick van Eijk1,
- Mark Bennett1,
- Richard M. Webster1,
- Matthew Leadbitter1,
- Yumin Teng1,5,
- Raymond Waters1,
- Stephen P. Jackson2 and
- Simon H. Reed1
- 1Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom;
- 2Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, United Kingdom
- Corresponding author: reedsh1{at}cardiff.ac.uk
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↵3 These authors are joint first authors and contributed equally to this work.
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.209106.116.
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Freely available online through the Genome Research Open Access option.
- Received April 28, 2016.
- Accepted July 27, 2016.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
