Fig. 6

DNA methylation separates embryonic and adult programs through blocking high CG density adult enhancers.(A and B) Heatmaps showing H3K4me3, H3K27ac (A), and mCG (B) around distal ectopic H3K4me3 in embryos and adult tissues (45). Peaks with H3K27ac signals are defined as active enhancers (A) (red). LMRs are defined as putative enhancers (B) (red). (C) Pie chart showing distribution of distal ectopic H3K4me3 overlapping with embryonic (red), active adult (green; “ac”, distal H3K27ac), decommissioned adult (green; “A”, ATAC-seq; “L”, LMRs; without H3K27ac) enhancers, and the rest ectopic H3K4me3 sites (orange). (D) Box plot showing distance from center of distal ectopic H3K4me3 peaks to up-regulated (red), down-regulated (blue), and non-DEGs (green) at shield stage. (E and F) UCSC Genome Browser snapshots (E) and line chart (F) showing Sox2 binding and H3K4me3 (E) and Sox2 binding distribution around ectopic H3K4me3 acquiring Sox2 (F) in control (blue) and dnmt1 mKD (red) embryos. (G) Venn diagram showing overlap between embryonic (dome and shield) and adult tissues (45) enhancers. (H) Line charts showing H3K27ac, mCG, and CG densities in dome (red), shield (dark red) embryos, and adult tissues 45) (green; line, average value; shade, range of all tissues) around putative enhancers defined at each stage. (I) Heatmaps showing average CG density, mCG, H3K4me3, H3K27ac, H3K4me1, and ATAC-seq of putative enhancers. Classification of enhancer (left): red/crossed red, embryonic-specific enhancer with/without distal ectopic H3K4me3; green/crossed green, adult enhancers with [defined in (C)]/without distal ectopic H3K4me3; orange, the rest distal ectopic H3K4me3. Bar chart shows the ratios of enriched TF motifs (P < 1 × 10⁻²⁰) in putative enhancers containing CGs (right). (J) Line chart showing CG densities around embryonic specific enhancers with (red line)/without (red dashed line) distal ectopic H3K4me3, as well as adult enhancer with (green line)/without (green dashed line) distal ectopic H3K4me3.