Figure 2. YAP/TAZ are required for BRD4 recruitment to chromatin.

a) Comparison of BRD4 ChIP-seq signal (expressed as normalized read density, RPKM) in active enhancers with or without YAP/TAZ peaks (n=5169 and n=30281, respectively) in MDA-MB-231 cells treated with DMSO or JQ1 (1µM, 6h), or transfected with YAP/TAZ siRNAs (48h). Data are presented as box-and-whiskers plots (whiskers extend from the 5^th to the 95^th percentile; the box extends from the 25^th to the 75^th percentile; the line within the box represents the median). **** p<10^-10 (one-tailed Mann-Whitney U test); ⁺⁺⁺⁺ p<10^-10 (one-tailed Wilcoxon matched-pairs signed rank test)

b) Average signal of BRD4 ChIP-seq reads in enhancers with YAP/TAZ peaks (n=5169) in a window of ±1 kb centered on the summit of YAP/TAZ peaks.

c) Genome browser view of YAP, BRD4 and H3K4me1 binding profiles at representative active enhancers in MDA-MB-231 cells. Both JQ1 and YAP/TAZ siRNA induce a strong decrease in BRD4 binding.

d) Box plot of BRD4 ChIP-seq signal (RPKM) comparing promoters of genes not activated by YAP/TAZ (n=8026) or of YAP/TAZ target genes (YT targets, n=616) in MDA-MB-231 cells (treated with DMSO). Data are presented as in a. **** p<10^-10 (one-tailed Mann-Whitney U test)

e) Treatment with JQ1 (left) and YAP/TAZ depletion (right) induce preferential loss of BRD4 at promoters of YAP/TAZ target genes (n=616) vs. promoters of not YAP/TAZ targets (n=8026). Fold change in BRD4 binding is calculated as RPKM_{(JQ1 or siYT)}/RPKM_(DMSO). Data are presented as box-and-whiskers plots (whiskers extend from the 5^th to the 95^th percentile; the box extends from the 25^th to the 75^th percentile; the line within the box represents the median). **** p<10^-10 (one-tailed Mann-Whitney U test)

f) Heatmap showing BRD4 binding on the promoters of YAP/TAZ targets in MDA-MB-231 cells, in a window of ±1.5kb centered on the transcription start site (TSS).

g) Average signal of BRD4 ChIP-seq reads on the promoters of YAP/TAZ target genes (n=616) in MDA-MB-231 cells, in a window of ±1.5 kb centered on TSS.

h) YAP, BRD4 and H3K4me3 binding profiles at representative promoters of YAP/TAZ target genes or not-YAP/TAZ targets. Arrows indicate BRD4 enrichment at the TSS. JQ1 and siYAP/TAZ induce a strong decrease in BRD4 binding on YAP/TAZ targets, whereas there is no overt variation of BRD4 binding on the TSS of not YAP/TAZ targets. GINS1 exemplifies direct YAP/TAZ target genes with YAP/TAZ binding sites in both enhancers and the TSS; E2F3 exemplifies direct YAP/TAZ target genes regulated by YAP/TAZ exclusively from distal enhancers.

i) YAP, BRD4 and H3K4me1/H3K4me3 binding profiles on a distal enhancer and on CDCA5 promoter. JQ1 (1µM, 6h) and siYAP/TAZ (48h) induce a strong decrease in BRD4 binding both on the enhancer, containing YAP/TAZ peak, and on TSS of CDCA5.