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Fig. 4 | Genome Biology

Fig. 4

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

Fig. 4

Oxidative damage patterns follow chromatin changes at chromatin loop anchors. a Loop anchors are defined by overlaps of a canonical CTCF motif with CTCF peaks as well as the cohesin components RAD21 and SMC3. Loop anchor sites (n = 18,242) were localized to the center of the CTCF motif and oriented accordingly. b Mean read coverage around the loop anchors is depicted for all three components. c AP-site distribution, determined as Relative Enrichment of AP-sites after X-ray treatment. For corresponding plots depicting the other treatment conditions, see Additional file 1: Figure S4G. d Based on the orientation of the loop anchor, chromatin status was determined outside (− 10 kb) and inside (+ 10 kb) of the chromatin loop. e As markers of active and inactive chromatin, the log2 ratios of H3K36me3 and H3K27me3 read coverage outside and inside the loop are depicted relative to the loop anchors. Their ratio is taken as a cut-off to categorize the insulation properties of the loop anchor. Loop anchors with a differential log2 ratio of 1.2 are defined as anchors that lead to a swap from inactive to active chromatin “swap ON” (n = 2021). A differential log2 ratio below − 1.2 is separating anchors that lead to a swap from active to inactive chromatin “swap OFF” (n = 1767). Neutral loop anchors were differentiated further as depicted in f. Neutral loop anchors that do not lead to a change in chromatin are differentiated by their mean H3K36me3 and H3K27me3 coverage ± 10 kb. Loops are defined to be in inactive chromatin “OFF” (n = 10,479), if log2(H3K27me3/H3K36me3) exceeds 2. Otherwise, loop anchors are considered to be in open chromatin “ON” (n = 3975). g H3K27me3 and H3K36me3 mean coverage distribution over the loop anchor classification illustrates the changes of chromatin states. Comparison to AP-sites, determined as relative enrichment after X-ray treatment (mean ± standard error of the mean), shows a reduction of AP-sites at a change into active chromatin. Loop anchors in inactive chromatin are low in AP-sites, despite inactive chromatin adjacent to active chromatin showing the highest damage levels. AP-sites are quantified in h as mean relative enrichment at the loop anchors ± 10 kb, and changes in AP-site prevalence are quantified in i as the mean relative differential enrichment at loop anchor + 10 kb minus loop anchor − 10 kb with significantly different changes of damage levels between the “swap ON” and “swap OFF” categories, p < 0.001 by Wilcoxon rank test, indicated by asterisks

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