Extended Data Fig. 8: Features and validation of enhancer–promoter interaction.
From: RIC-seq for global in situ profiling of RNA–RNA spatial interactions
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.
