Fig. 3
Oxidative damage distribution is associated with regulatory sites and repeats. a Metaprofiles of Relative Enrichments centered on CTCF and DNA binding sites within and outside DNase hypersensitive regions (DHS; nCTCFinDHS = 37,763, nCTCFnotDHS = 10,908, nTFbsInDHS = 253,613, nTFbsNotDHS = 5,463,612). Damage levels are reduced around binding sites. Shaded borders show the standard error of mean across biological replicates. b Scatter plot of average Relative Enrichments and GC contents ± 500 bp of binding sites for each transcription factor excluding those within 500 bp of a CTCF binding site as these represent a special case (see Additional file 1: Figure S5D). Binding sites are separated into within and outside DNase hypersensitive sites. Damage levels are universally reduced regardless of transcription factor, with particularly lowered levels for actively used sites in DHS regions. c Metaprofiles centered on binding sites for four selected transcription factors. d Metaprofiles centered on CpG islands, within and outside promoters and DHS regions (nDHS = 17,565, nNotDHS = 9878, nPromoter = 14850, nNotPromoter = 12,593). Damage levels are reduced regardless of location and accessibility. e Metaprofiles centered on predicted G-quadruplexes (n = 359,449). There are asymmetrically reduced damage levels for AP-sites, but not for OGG1-enriched AP-sites. f Bar plots of average Relative Enrichments in G-quadruplexes at telomeric repeats across the four treatment and processing conditions. Damage levels are increased in OGG1-enriched samples. Error bars show the standard error of mean across three biological replicates. g Genome browser views of unnormalized damage levels in ~ 30-kb locus surrounding LINC00955, including microsatellite repeats. Some groups of microsatellites accumulate large amounts of damage and reduced 8-oxoG processing. h Scatter plot displaying average damage levels in different microsatellite types for the AP-site and OGG1-enriched samples. Reverse complementary repeats were assigned to the alphabetically first repeat. Most types display similar damage levels in the two processing conditions; however, several display elevated damage in the OGG1-enriched sample. All panels display measurements for X-ray-treated samples, unless indicated otherwise. For corresponding plots of CpG islands in general and G-quadruplexes with the other treatment conditions, see Additional file 1: Figure S4E and F