Fig. 1: Overview of the 66 epigenomes and 18 chromatin states during mouse embryogenesis.

a Twelve tissues at 4–7 developmental timepoints have ChIP-seq data for eight histone marks (green boxes), ATAC-seq data, and DNA methylation (DNAme) data, totaling 66 complete epigenomes. Twenty-one of these epigenomes also have DNase-seq data (green dots). Embryonic stem cells (orange box) have ChIP-seq data for seven histone marks, and are missing H3K4me2, ATAC-seq, and DNAme. b Eighteen chromatin states are defined by ChromHMM across the 66 complete epigenomes. c Histone-mark probabilities, genome coverage (averaged over 66 epigenomes, posterior probability > 0.5), and overlapping genomic features including gene expression, regulatory features (EP300 binding, CTCF binding, and DNase I hypersensitive sites), and distances to the TSSs of expressed and repressed genes are shown for each chromatin state. The enrichments for the categories are the averaged values across tissues and timepoints. d Jaccard similarities between the partial epigenomes with each mark omitted and the ten-mark E13.5 midbrain epigenome. e The Dlx1 locus is displayed with chromatin states (color-coded as in b) in the forebrain and the liver for all seven timepoints. Also shown are the signals of several histone marks (scale: 0–50) that differ between forebrain and liver (for E11.5, E13.5, E15.5, and P0 only, due to space constraints), along with ATAC and DNA methylation signals. A transgenic mouse embryo is shown on top of the enhancer region, indicating the forebrain-specific activity of this enhancer. A CpG island that overlaps with the bivalent region at the TSS of Dlx1 is shown at the bottom of the panel.