Fig. 6
From: Links between DNA methylation and nucleosome occupancy in the human genome
Characterization of chromatin at CpG islands. a Boxplots display the distribution of nucleosome occupancy as a function of the number of methylated CpGs. b, c Nucleosome with midpoints within CpG islands was divided into two groups, non-TSS and TSS. For each nucleosome, nucleosome occupancy and DNA methylation values were plotted in the 2D color-coded scatterplots. Using NOMe-seq and Roadmap ChIP-seq data from IMR90 cells, nucleosome occupancy, DNA methylation levels, and Z-scores from 12 histone modifications and the histone variant H2A.Z were aligned to TSSs that overlapped CpG Islands (d) and to the centers of CpG islands located in gene bodies and intergenic regions (e). Heatmap values were computed in 101 21-bp bins surrounding the TSSs and non-TSS CpG island centers, and sites (heatmap rows) were sorted by nucleosome occupancy