Fig. 3: BET inhibition has minimal effects on enhancer–promoter interactions.

a Capture-C from the MYC promoter (above) or enhancer (below) following 90 min DMSO treatment (purple) or 90 min or 24 h 1 µM IBET treatment (green). Only the promoter and enhancer regions are shown. Differential tracks show the change in profile in IBET-treated samples compared to DMSO treatment for the same time period: pink bars show increases; blue bars show decreases. Mean of three biological replicates. b Capture-C from the MYC promoter following 24 h DMSO (purple) or 1 µM AT1 treatment (green), as in (a). c, d Capture-C from the BCL2 promoter or enhancer, as in a, b. e Capture-C traces from gene promoters following treatment with DMSO (purple line), IBET for 90 min (left, green line), AT1 for 24 h (middle left, orange line) or EPZ-5676 for 7d (DOT1Li, middle right, blue line). Ribbon shows ±1 SD for three replicates. Vertical gray bar indicates the capture point for each gene. Horizontal bars show 10 kb region around BRD4 ChIP-seq peaks. Shading highlights effect of IBET treatment on promoter interaction frequency within that window: pink bars indicate statistically significant increases; blue bars indicate decreases; gray bars indicate no significant difference (Holm–Bonferroni adjusted p-value < 0.05, paired Mann–Whitney test; adjusted P-values are given in Supplementary Data 3). Scale bars show 100 kb. Transcriptional effect of the drug treatment on the gene is indicated. Right: Nascent RNA-seq levels for each gene under control or indicated treatment conditions. ****FDR < 0.0001, **FDR < 0.01, *FDR < 0.05, ns no significant change; FDR values are given in Supplementary Data 2. Mean of three biological replicates; error bars show SEM. DOT1Li Capture-C and RNA-seq data are taken from³⁰. f Left: change in interaction frequency (mean logFC of three replicates) between promoters and BRD4 peaks (10 kb windows) of significantly affected (Holm–Bonferroni adjusted p-value < 0.05, paired Mann–Whitney test; adjusted P-values are given in Supplementary Data 3) interactions following 90 min IBET, 24 h AT1, or 7d DOT1Li treatment. Nonsignificantly affected interactions are not plotted. Violin plot shows frequency distribution. Boxplot midline shows median, with upper and lower hinges showing 25th and 75th percentile, respectively. Upper and lower hinges extend to the largest and smallest datapoints within 1.5 times the interquartile range of either hinge. Dots represent individual BRD4 peaks. Source data are provided as a Source Data file. Right: number of BRD4 peaks (10 kb windows) that show statistically significant increased (pink) or decreased (blue) interactions following 90 min IBET, 24 h AT1, or 7d DOT1Li treatment.