Fig. 3

Luminal and basal subtypes of bladder cancers show potentially distinct 3D genome organizations. a Hi-C loop analysis of luminal and basal-squamous cell lines show distinct luminal loops and basal-squamous loops. b Contacts identified in luminal and basal-squamous cell lines are shared and validated in five bladder cancer tumor samples. c Genome-browser tracks for selected luminal gene (FOXA1) and basal gene (KRT5) that contain enhancer-promoter loops are shown here. Arcs indicate the predicted chromatin loops using Hi-C data. d The type of contacts based on the overlap of contact location at either enhancer (H3K27ac at distal region) or promoter (H3K27ac and H3K4me3 at promoter) in each cell line is shown. E-P, enhancer-promoter loops; E-E, enhancer-enhancer loops; P-P, promoter-promoter loops; E-N, enhancer-non regulatory loops; P-N, promoter-non regulatory loops; None, non-regulatory loops. e Enrichment of FOXA1 (left axis) and GATA3 (right axis) binding sites in RT4 (luminal) cells is shown here at its loop anchors