Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis
Abstract Background DNA is subject to constant chemical modification and damage, which eventually results in variable mutation rates throughout the genome. Although detailed molecular mechanisms of DNA damage and repair are well understood, damage impact and execution of repair across a genome remai...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-12-01
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| Series: | Genome Biology |
| Online Access: | http://link.springer.com/article/10.1186/s13059-018-1582-2 |
| _version_ | 1828531399157612544 |
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| author | Anna R. Poetsch Simon J. Boulton Nicholas M. Luscombe |
| author_facet | Anna R. Poetsch Simon J. Boulton Nicholas M. Luscombe |
| author_sort | Anna R. Poetsch |
| collection | DOAJ |
| description | Abstract Background DNA is subject to constant chemical modification and damage, which eventually results in variable mutation rates throughout the genome. Although detailed molecular mechanisms of DNA damage and repair are well understood, damage impact and execution of repair across a genome remain poorly defined. Results To bridge the gap between our understanding of DNA repair and mutation distributions, we developed a novel method, AP-seq, capable of mapping apurinic sites and 8-oxo-7,8-dihydroguanine bases at approximately 250-bp resolution on a genome-wide scale. We directly demonstrate that the accumulation rate of apurinic sites varies widely across the genome, with hot spots acquiring many times more damage than cold spots. Unlike single nucleotide variants (SNVs) in cancers, damage burden correlates with marks for open chromatin notably H3K9ac and H3K4me2. Apurinic sites and oxidative damage are also highly enriched in transposable elements and other repetitive sequences. In contrast, we observe a reduction at chromatin loop anchors with increased damage load towards inactive compartments. Less damage is found at promoters, exons, and termination sites, but not introns, in a seemingly transcription-independent but GC content-dependent manner. Leveraging cancer genomic data, we also find locally reduced SNV rates in promoters, coding sequence, and other functional elements. Conclusions Our study reveals that oxidative DNA damage accumulation and repair differ strongly across the genome, but culminate in a previously unappreciated mechanism that safeguards the regulatory and coding regions of genes from mutations. |
| first_indexed | 2024-12-11T22:38:00Z |
| format | Article |
| id | doaj.art-b808cdefed6f4717bf3209a1105d052b |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-11T22:38:00Z |
| publishDate | 2018-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-b808cdefed6f4717bf3209a1105d052b2022-12-22T00:47:54ZengBMCGenome Biology1474-760X2018-12-0119112310.1186/s13059-018-1582-2Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesisAnna R. Poetsch0Simon J. Boulton1Nicholas M. Luscombe2The Francis Crick InstituteThe Francis Crick InstituteThe Francis Crick InstituteAbstract Background DNA is subject to constant chemical modification and damage, which eventually results in variable mutation rates throughout the genome. Although detailed molecular mechanisms of DNA damage and repair are well understood, damage impact and execution of repair across a genome remain poorly defined. Results To bridge the gap between our understanding of DNA repair and mutation distributions, we developed a novel method, AP-seq, capable of mapping apurinic sites and 8-oxo-7,8-dihydroguanine bases at approximately 250-bp resolution on a genome-wide scale. We directly demonstrate that the accumulation rate of apurinic sites varies widely across the genome, with hot spots acquiring many times more damage than cold spots. Unlike single nucleotide variants (SNVs) in cancers, damage burden correlates with marks for open chromatin notably H3K9ac and H3K4me2. Apurinic sites and oxidative damage are also highly enriched in transposable elements and other repetitive sequences. In contrast, we observe a reduction at chromatin loop anchors with increased damage load towards inactive compartments. Less damage is found at promoters, exons, and termination sites, but not introns, in a seemingly transcription-independent but GC content-dependent manner. Leveraging cancer genomic data, we also find locally reduced SNV rates in promoters, coding sequence, and other functional elements. Conclusions Our study reveals that oxidative DNA damage accumulation and repair differ strongly across the genome, but culminate in a previously unappreciated mechanism that safeguards the regulatory and coding regions of genes from mutations.http://link.springer.com/article/10.1186/s13059-018-1582-2 |
| spellingShingle | Anna R. Poetsch Simon J. Boulton Nicholas M. Luscombe Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis Genome Biology |
| title | Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis |
| title_full | Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis |
| title_fullStr | Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis |
| title_full_unstemmed | Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis |
| title_short | Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis |
| title_sort | genomic landscape of oxidative dna damage and repair reveals regioselective protection from mutagenesis |
| url | http://link.springer.com/article/10.1186/s13059-018-1582-2 |
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