a, Pie chart shows the strand preference of eRNAs interacting with promoter RNAs. b, eRNAs tend to interact with other RNAs within TADs. Colour intensity indicates read density in 40-kb windows. The purple line denotes the boundary of TADs. c, Circos plot showing whole-genome enhancer–promoter contacts on the basis of their pairwise-interacting RNAs. Red circle, super-enhancers; blue circle, typical enhancers; yellow circle, promoters. Red and light green arc lines illustrate inferred super-enhancer–promoter and typical-enhancer–promoter interactions, respectively. d, qPCR validation of enhancer–promoter interactions at four typical enhancers upon depletion of eRNAs with LNA ASOs. Specific-enhancer-linked promoter reads are shown as blue arc lines above the genes at positive and negative strands. C5AR1, LRSAM1, AK1, SPTAN1, ZDHHC12, LINC02398, SLCO1C1 and SLCO1B1 served as locus-specific controls. The relative fold change is normalized to the LNA control. e, Inferred enhancer–promoter and promoter–promoter interaction networks on chromosome 8. qPCR showing the expression level of super-enhancer-638-linked genes (box) upon depletion of super-enhancer RNAs with LNA ASOs. PCAT1 and GSDMC served as locus-specific negative controls. Data in d, e are mean ± s.d.; n = 3 biological replicates, two-tailed, unpaired t-test.