Fig. 6

Loss of TRPS1 alters chromatin structure and long-range interactions. a Pie charts depicting the proportion of enhancer and promoter regions among CTBP2 and HDAC3 peaks. b Venn diagrams showing the overlap of enhancer sites bound by TRPS1 and CTBP2 (left) or TRPS1 and HDAC3 (right). c Western blot for TRPS1 and YAP in MCF7 WT and TRPS1 KO cells. d, e Density profiles for CTBP2 (d) and HDAC3 (e) binding at enhancers bound by TRPS1 in MCF7 and TRPS1 KO cells. f Density profiles for H3K27ac at enhancers bound by TRPS1 in MCF7 WT and TRPS1 KO cells. g P-values that describe if enhancers bound by TRPS1 are more strongly affected by TRPS1 deletion than enhancers not bound by TRPS1. Wilcox-test, two-sided. h Venn diagram showing the number of overlapping and unique H3K27ac ChIP peaks in MCF7 WT and TRPS1 KO cells, respectively. i ChIP-Seq tracks for TRPS1, TEAD1, YAP and H3K27ac from MCF7 WT and TRPS1 KO cells at an enhancer at the given genomic location. The annotated enhancer is drawn as a pink rectangle. The 2 kb fragment that was used for the luciferase assay in j is drawn as a black rectangle. j Luciferase activity of the reporter driven by the enhancer from i in MCF7 WT and TRPS1 KO cells co-transfected with the indicated expression vectors. Increasing amounts of a FLAG-YAP 5SA construct and constant amounts of HA-TEAD construct were used. Data presented are derived from three biological replicates and error bars represent s.e.m. Student’s t-test. k 4C-Seq interaction pattern of the IGFBP3 TSS in MCF7 (WT) compared to TRPS1 KO (KO) cells. Significance was determined by the w4CSeq analysis package using a one-tailed binomial test and corrected for multiple testing yielding the adjusted P-value (P. adj). The HiC interaction map was used from a previously published ENCODE (ENCSR549MGQ) data set. Black and grey boxes mark TADs and a dashed line marks sub-TADs of the left TAD. The locations of TRPS1 ChIP-Seq peaks and annotated enhancers are given in blue and pink, respectively. TAD topologically associated domain