Fig. 3

Correlation analysis enriched sites of H3K4 methylation, DNA methyl binding proteins (MBD3, MBD2, MECP2 MBD1A, MBD4 and MBD1B), DNA 5mC and 5hmC. (a) Violin plots of the DNA methylation distribution (y-axis) within peaks of H3K4me1, H3K4me3, and MBD proteins. The vertical white segments inside the violins connect the first (Q1) and the third quartile (Q3), and the white point represents the median (Med) of the DNA methylation level of the peaks. (b) Bar plot of the fraction of the highly methylated peaks (DNA methylation >95%) among all peaks of H3K4me1 and H3K4me3, and MBD binding regions. (c) Heat map of number of pairwise overlaps between peaks of two signals (chromatin marks or protein binding), O _SiSj (eq. 2), in %. The peak frequencies are shown in parentheses in the row labels. Alternations in (d) H3K4me1 and (e) H3K4me3 enrichment (y-axes) in the absence (−) or presence (+) of either 5mC or 5hmC (y-axes)