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. 2013 Oct 3;42(1):235–248. doi: 10.1093/nar/gkt884

Figure 3.

Figure 3.

H4R3me2s accumulates at promoters and other G + C-rich regions, generally irrespective of transcriptional activity. (A) The unsupervised clustering of transcriptional start sites (TSSs) is represented as a heatmap of tag densities (0–60) per 100-bp bins, from 5 kb upstream to 5 kb downstream of mouse TSS (n = 33 876) for the indicated ChIP-seq/RNA-seq experiments in ES cells. ChIP-seq profiles for H3K4me3, H3K27me3 and RNA-seq from ES are from Marks et al. (25). The non-expressed class of TSS marked by an asterisk contains genes expressed in differentiated cells such as genes belonging to the immune response, inflammatory response or locomotory behaviour Gene Ontology terms. (B) The two class of TSS (groups 2 and 3) indicated in (A) were analysed for their G + C ratio. The two classes of promoters are represented as density plot and box-and-whisker plots in red and blue, for the groups 2 and 3, respectively. (*) Indicates Wilcoxon rank sum test with a P < 2.2e-16. (C) H4R3me2s enrichment around TSSs grouped into four different classes according to the genes’ log expression values. (D) Mean H4R3me2s enrichment levels in ES cells are represented as a function of their distance from the peak summits of H3K4me3 or H3K4me1 peaks. H4R3me2s is enriched around H3K4me3 peaks, but not around H3K4me1 peaks. However, H4R3me2s enrichment occurs both at H3K4me3-enriched regions with high H3K4me3 levels (high H3K4me3) and those with lower H3K4me3 enrichment (low H3K4me2). (E) H4R3me2s enrichment according to the G + C content of 100-bp genomic windows in ES and MEF cells showing the absence of H4R3me2s in regions with less than 50% G + C ratio. (F) Hexagonal binning of H4R3me2s-enriched regions according to their DNA methylation level assessed by MeDIP, or hydroxymethylation level assessed by hydroxyMeDIP (hMeDIP), in ES cells (24). The scales of the x- and y-axis are transformed by the following formula: asinh-1(x). Darker shades of grey indicate higher densities of bins as reported on the count scale.