Fig. 2

Re-ChIP-Seq Validation of H4K20me3 and H3K4me3 co-occupancy in ES cells. a Boxplot of density of H3K4me3 + H4K20me3 reChIP (left) or H4K20me3 + H3K4me3 reChIP (right) at H4K20me3/H3K4me3 intersecting islands. b Scatter plot of H3K4me3 + H4K20me3 reChIP and H4K20me3 density (top left), H3K4me3 + H4K20me3 reChIP and H3K4me3 density (top middle), H4K20me3 + H3K4me3 reChIP and H4K20me3 density (bottom left), and H4K20me3 + H3K4me3 and H3K4me3 density (bottom right) at H4K20me3/H3K4me3 intersecting islands. Scatter plot of H4K20me3 and H3K4me3 densities (RPKM) at 2 kb genomic bin intervals, which intersect H4K20me3/H3K4me3 ChIP bivalent regions (top right). c Average density profiles of H3K4me3 + H4K20me3 and H4K20me3 + H3K4me3 at H4K20me3/H3K4me3 intersecting islands, and (d) H3K4me3, H4K20me3, and H3K9me3 at H4K20me3/H3K4me3 intersecting regions. e Heatmaps of density of H3K4me3 + H4K20me3 and H4K20me3 + H3K4me3 at H4K20me3/H3K4me3 intersecting islands. Rows were sorted by chromosome number and position. f Browser view of H3K4me3 + H4K20me3 and H4K20me3 + H3K4me3 reChIP-Seq at individual L1/ L1Md_T repeat subfamily elements. g Percent of H4K20me3/H3K4me3 regions that overlap with H4K20me3 + H3K4me3 reChIP and H3K4me3 + H4K20me3 peaks. h Boxplot of ChIP-Seq and reChIP-Seq densities at regions marked by only H3K4me3 (left) or H4K20me3 (right). i Browser view of ChIP-Seq and reChIP-Seq signals at regions marked by H4K20me3/H3K9me3 only (left, middle) or H3K4me3 only (right)