Fig. 3: AR-bound enhancers only increase contact frequency to AR-regulated gene promoters.

A Kernel density estimation of the number of significantly called loop anchoring promoters (left; AR-regulated promoters are in red; AR-independent promoter backgrounds are in black) or enhancers (right; AR-bound enhancers are in yellow; AR-free CRE background are in gray) at each time point (H3K27ac HiChIP). Each row represents the significantly called loops at each time point separately, and not reference loops. B Schematic representation of fold change in contact frequency calculation for a given gene set (left), from its promoter’s viewpoint (middle), from its enhancers’ viewpoint (right). The query loop sets are compared to the same reference loop set. Promoter view: The AR-regulated gene promoter loops (red sticks) and a random set of AR-independent gene promoter loops (black sticks) are compared to the reference loops, which are selected from AR-independent promoter loops (denominator black sticks). Enhancer view: The loops of AR-bound enhancers (yellow sticks) and AR-free enhancers (gray sticks), and loops of AR-free enhancers (black sticks) that interact with AR-independent gene promoters are compared to the reference loops which are selected from AR-independent promoters that interact with AR-free enhancers (denominator black sticks). C Fold change in chromatin loop contact frequency of AR-regulated gene promoters (P + AR; red) and highly expressed AR-independent gene promoters (P-AR; black). D Fold change in contact frequency of AR-bound enhancers that loop to AR-regulated genes (E + AR; yellow), AR-free enhancers looping to AR-regulated genes (E-AR; gray), and AR-free enhancers looping to highly expressed AR-independent genes (E-ARi; black). E Fold change in contact frequency in AR-bound enhancers looping to AR-downregulated genes (E+dAR; blue), and AR-free enhancers looping to highly expressed genes (E-ARi; black). F Min-max normalized standard deviation (SD) following androgen treatment for AR, FOXA1, H3K27ac, and H3K4me3 ChIP-seq, ATAC-seq and H3K27ac and H3K4me3 HiChIP contact frequency (CF) are depicted for AR-bound (E + AR; orange) and AR-free (E-AR; gray) CREs of six selected AR-regulated genes (KLK2, KLK3, NKX3-1, UAP1, ABBCC4, and DHCR24). For all line plots (C–E), the solid line represents the mean, and the error bars indicate the 95% confidence.