Extended Data Fig. 1: Chromatin domains reflect a similar domain-wide epigenetic profile across different cell types.

a, Overlaps between common TAD boundaries in this manuscript and TAD boundaries from ENCODE cancer cell lines. Horizontal bars represent the total number of TAD boundaries per cell type. Vertical bars represent the number of intersecting boundaries between cell types. Combination matrix (below), circles indicate that denote cell types are part of the intersection for each vertical bar. b, Aggregate plots show average cell-type specific enrichment levels for Insulation score, CTCF binding sites, DNAseI hypersensitivity regions and H3K9me3 ChIP-seq enrichment levels from GM12878 cell line around common TAD boundaries. c, Classification of subcompartments (domains) based on chromatin state coverage. Heatmap shows domain-length normalized coverage of each chromatin state from Roadmap Epigenome aggregate data (rows) for each domain (columns). Chromatin states are clustered based on co-enrichments within domains. Domains are classified into five groups: heterochromatin (purple), inactive (gray), repressed (blue), active (orange), and active-2 (red) according to dominant chromatin state combinations. d, Box plots represent the enrichment of selected ChromHMM chromatin states in each domain type. These states are selected based on their highest enrichment in the heatmap plotted in Extended Data Fig. 1c. In these and all other boxplots, the center line is the median; box limits are the upper and lower quantiles; whiskers represent 1.5x the interquartile range. Heterochromatin:180, Inactive:1219:, Repressed:969, Active:1086, Active-2:593. e, Heatmaps represent domain-length normalized coverage of cell-type specific ChromHMM chromatin states within domain for representative Roadmap Epigenome cell types. Cell type’s name and the Roadmap Epigenome IDs are denoted on top of each heatmap. Domain-state matrices are not clustered but sorted based on our five domain annotations. These annotations are denoted as colored bars beneath the heatmap. Box plots below represent the domain-length normalized coverage of chromatin states for the corresponding cell type. Domain numbers are Heterochromatin:180, Inactive:1219:, Repressed:969, Active:1086, Active-2:593.