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Fig.1 | Genome Biology


From: Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis


Oxidative damage is heterogeneously distributed at different scales of resolution. a Schematic of AP-seq, a new protocol to detect apurinic-sites (AP-sites). DNA containing these sites are biotin-tagged using an aldehyde reactive probe (ARP), fragmented, and pulled down with streptavidin. The enriched DNA is processed for sequencing and mapped to the reference genome. The damage level across the genome is quantified by assessing the number of mapped reads. To check for unprocessed 8-oxoG in addition to AP-sites, we perform an in vitro digest of extracted genomic DNA with OGG1 and repeat the AP-site pulldown. b Genome-wide map of AP-site distribution after X-ray treatment. The color scale represents the log2 fold change of normalized AP-seq enrichment over input (Relative Enrichment) in 100-kb bins across the human genome, averaged across biological replicates. Gray regions represent undefined sequences in the human genome, such as centromeres and telomeres. Damage levels are highly correlated between treatment conditions at 100-kb resolution. c More detailed view of AP-site distribution on Chromosome 16. Plot lines depict the average Relative Enrichment for AP-sites in samples after X-ray treatment (green) and without treatment (blue). Shaded boundaries show standard error of the mean for three biological replicates. Untreated and X-ray-treated samples display very similar damage profiles. d Genome browser views of damage distributions for untreated and X-ray-treated samples and their corresponding input samples across an 8-kb region upstream of MALT1. Damage levels are represented as unnormalized sequencing depth of the pooled biological replicates. At high resolution, it becomes apparent how sharp the damage levels rise over background at Alu elements after X-ray treatment, which leads to more distinct patterns than the broader distributed untreated control. e Scatterplots of the correlation in average Relative Enrichments of samples with differing treatment and OGG1-enrichment conditions. Damage levels are highly correlated across all conditions

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