Fig. 2

LADs correspond closely with KDDs. A Example track view of H3K9me2 enrichment and associated KDDs in all 12 cell types assayed. KDD states as defined by HMM per cell type shown above each H3K9me2 track. T1-KDDs in dark green; T2-KDDs in light green. Regions highlighted in gray span differential H3K9me2/KDD regions between cell types. Y-axis indicated on the first track is consistent across all tracks shown. B LB1 occupancy per KDD state in all 12 cell types. T1-KDDs (dark green) are the most enriched, and nonKDDs (gray) are the least enriched for LB1. C Mean proportion of genes expressed (TPM > 5) per LAD category for cell types with matched RNA-seq data (cardiac myocytes, early somites, mesoderm progenitors, mid-hindgut, definitive ectoderm, and endothelial progenitors). Error bars indicate standard deviation. D Enrichment (positive z-score) or depletion (negative z-score) of genes. Cell types in key are as follows: Row 1 (L-R): ESC, liver progenitors, epicardium, endothelial progenitors; Row 2 (L-R): mid-hindgut, border ectoderm, anterior primitive streak, midbrain; Row 3 (L-R): cardiac myocytes, definitive ectoderm, early somite, mesoderm progenitors. E Enrichment of ATAC-seq peaks [39], and B compartment (B comp.) from matched cell types [40] (see “Methods”)