Fig. 3

Distribution of ChIP-seq reads around the TSS for gene promoters of different CpG density. Genes were divided into different groups based on the presence or absence of a promoter-associated CpG island. CpG-island genes were further sub-classified by CpG density into quintiles, with the highest CpG density (81–100 percentile, a), and lowest density (0–20 percentile, b) CpG-island genes shown. Gene promoters without CpG islands are shown in c. For each plot, genes were additionally characterized for gene expression, with genes belonging to lowest (0–20 percentile) or highest (81–100 percentile) expression depicted in black and red, respectively. ChIP-seq reads were binned at 10 bp intervals. Y-axis represents average ChIP-seq read profiles normalized to corresponding average of the input. 1^st row, H3K4me3 ChIP-seq reads plotted as outlined above. 2^nd row, H3K27me3 ChIP-seq reads. 3^rd row, Sequential ChIP (H3K27me3 → H3K4me3)-seq reads. 4^th row, H2A.Z ChIP-seq reads