Fig. 5

Analysis of nucleosome occupancy and mCpG density in differentially marked chromatin across the genome. Using MNase-seq, NOMe-seq, and Roadmap ChIP-seq data from IMR90 cells, average occurrences of CpGs (a), mHCG/HCG fractions (b), and uGCH/GCH fractions (c) were computed from forward and reverse complement sequences aligned to MNase-seq derived nucleosome midpoints within several histone modification peaks indicated in the key. The 12 histone modifications (and variant H2A.Z) in the key are ordered by decreasing average DNA methylation at the nucleosome midpoint. d Using data between positions −61 to +61 relative to the nucleosome midpoint, the average nucleosome occupancy for each histone modification was plotted against the corresponding average number of methylated CpGs in the central 123 base pairs of the nucleosome. e–g Nucleosome occupancy (e) and mCpGs density (f) were weighted by ChIP-seq Z-scores for both single and paired histone modifications (see “Methods” section). g Plots of nucleosome occupancy and mCpG density from the heatmaps in e and f show that H3K9me3-modified chromatin (blue dots) deviates from the correlation observed in the genome-wide data