Abstract
BackgroundDNA 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.ResultsTo 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.ConclusionsOur 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.
Highlights
The integrity of DNA is constantly challenged by damaging agents and chemical modifications
apurinic site (AP-site) are removed through backbone incision by AP-lyase (APEX1), and end processing through flap-endonuclease 1 (FEN1), and the base is subsequently replaced with an undamaged nucleotide
Under neutral conditions, 1 h at 37 °C, the probe is highly specific for the aldehydes occurring at AP-sites, which is the experimental condition we use; 5-fC is generated through the TET enzymes primarily in CpG islands and enhancers during early development, while the genome is demethylated [47, 48]
Summary
The integrity of DNA is constantly challenged by damaging agents and chemical modifications. A human cell is estimated to undergo 100 to 500 such modifications per day, most commonly resulting in 8-oxo-7,8-dihydroguanine (8-oxoG) and related products [1], which are processed into repair intermediates. Up to 2400 8-oxoG sites per cell are reported [2]. Oxidative damage is processed in a two-step process through the base excision repair (BER) pathway [11]. Other sources of AP-sites include spontaneous depurination and excision of non-oxidative base modifications, such as uracil. Cells are reported to typically present with a steady state of ~ 15,000 to ~ 30,000 AP-sites per cell, which includes the associated beta-elimination product [2, 13]. DNA is subject to constant chemical modification and damage, which eventually results in variable mutation rates throughout the genome. Detailed molecular mechanisms of DNA damage and repair are well understood, damage impact and execution of repair across a genome remain poorly defined
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