Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-12

AUTHORS

Anna R. Poetsch, Simon J. Boulton, Nicholas M. Luscombe

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. More... »

PAGES

215

References to SciGraph publications

  • 2015-07. CTCF/cohesin-binding sites are frequently mutated in cancer in NATURE GENETICS
  • 2016-12. The Ensembl Variant Effect Predictor in GENOME BIOLOGY
  • 2012-08. ggbio: an R package for extending the grammar of graphics for genomic data in GENOME BIOLOGY
  • 2012-08. Chromatin organization is a major influence on regional mutation rates in human cancer cells in NATURE
  • 2015-04. Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation in NATURE
  • 2014-12. Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis in NATURE COMMUNICATIONS
  • 2015-05. Differential DNA mismatch repair underlies mutation rate variation across the human genome in NATURE
  • 2018-12. Validating the concept of mutational signatures with isogenic cell models in NATURE COMMUNICATIONS
  • 2012-11. DNA secondary structures: stability and function of G-quadruplex structures in NATURE REVIEWS GENETICS
  • 2016-12. Oxidative guanine base damage regulates human telomerase activity in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 1993-04. Instability and decay of the primary structure of DNA in NATURE
  • 2012-08. Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase in GENOME BIOLOGY
  • 2015-02. Cell-of-origin chromatin organization shapes the mutational landscape of cancer in NATURE
  • 2011-01. Integrative genomics viewer in NATURE BIOTECHNOLOGY
  • 2012-05. Evidence of non-random mutation rates suggests an evolutionary risk management strategy in NATURE
  • 2018-01. Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators in NATURE
  • 2012-04. Fast gapped-read alignment with Bowtie 2 in NATURE METHODS
  • 2017-06-09. Transposable elements in cancer in NATURE REVIEWS CANCER
  • 1988-09. The origin of mutants in NATURE
  • 2017-06-12. Identification of the elementary structural units of the DNA damage response in NATURE COMMUNICATIONS
  • 2016-10. rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome in NATURE METHODS
  • 2012-09. An integrated encyclopedia of DNA elements in the human genome in NATURE
  • 2017-03. G-quadruplex structures within the 3′ UTR of LINE-1 elements stimulate retrotransposition in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 1991-01. Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG in NATURE
  • 2017-12. Reduced mutation rate in exons due to differential mismatch repair in NATURE GENETICS
  • 2015-08. 5-Formylcytosine can be a stable DNA modification in mammals in NATURE CHEMICAL BIOLOGY
  • 2016-04. Nucleotide excision repair is impaired by binding of transcription factors to DNA in NATURE
  • 2015-02. Lagging-strand replication shapes the mutational landscape of the genome in NATURE
  • 2013-08. Signatures of mutational processes in human cancer in NATURE
  • 2016-04. Differential DNA repair underlies mutation hotspots at active promoters in cancer genomes in NATURE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13059-018-1582-2

    DOI

    http://dx.doi.org/10.1186/s13059-018-1582-2

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1110465222

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30526646


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    109 schema:description 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.
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