Fig. 3

Hierarchical TADs are more active than singletons. a An illustration of hierarchical levels of TADs. The levels are assigned from external to internal. The TADs covered by the cyan dash line are assigned to level 1, by blue dash line are assigned to level 2, by orange dash line are assigned to level 3, and singletons are also assigned to level 1 (cyan). b mean CTCF signal at the boundaries specific to hierarchical TADs (light green), specific to singletons (cyan), and shared between hierarchical TADs and singletons (orange). The boundaries of hierarchical TADs have the highest enrichment of CTCF signal. c, d Enrichment of epigenetic states at the regions covered by different levels of TADs. The enrichment (fold change) of active states (marked in orange in c) increases as the TAD level increases. The trend is visualized for the states of Tss, Enh, and PromCtcf in d. The whole-genome average is used as the background for calculating enrichments. e, f Density of expressed gene in different levels of TADs in GM12878 (e) and K562 (f)