Fig. 3

Genomic characterization of LAD subtypes indicates T1- and T2-LAD distinction. A Enrichment of transposable elements (top) and replication timing (RT) domains (bottom) in T1- and T2-LADs across the atlas. Transposable elements differentially enriched in T1- and T2-LADs highlighted in gray. 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. B,C CTCF binding at transitions from B nonLADs to T2-LADs (including mirrored T2-LAD to nonLAD boundaries) and C T2-LADs to T1-LADs (including mirrored T1-LAD to T2-LAD boundaries) shows CTCF enrichment at T2-LAD boundaries. D Percentage of single cells with LB1 occupancy per LAD locus in mesoderm progenitor cells shows greater overlap with T1-LADs. E chromHMM feature enrichments in LADs from four cell types, as indicated. Asterisks (*) indicate adjusted p-value < 0.01. F H3K9me2 occupancy per LAD state in selected cell types, as indicated (full set in Additional file 2: Fig. S6A). T1-LADs (dark purple) are the most enriched and nonLADs (gray) are least enriched for H3K9me2