Fig. 4. Dissolution of phase condensate structures with 1,6-hexanediol does not perturb enhancer–promoter interactions.

a Metaplot of reference-normalized mean BRD4 and MED1 levels at BRD4 peaks in untreated SEM cells (light color) or cells treated with 1.5% 1,6-hexanediol for 30 min (dark color). b Boxplot showing the log₂ fold-change (logFC) in reference-normalized levels of BRD4 and MED1 and nascent RNA at super-enhancers (SE; olive), or typical enhancers (TE; green) following treatment with 1.5% 1,6-hexanediol for 30 min. Nascent RNA (eRNA) was measured over 1 kb windows centered on intergenic ATAC-seq peaks overlapping with SEs and TEs. p values indicate the statistical significance of the difference in logFC between SEs and TEs (Wilcoxon rank sum test; for BRD4, p < 2.2 × 10⁻¹⁶; MED1, p = 1.5 × 10⁻⁹; eRNA, p = 3.4 × 10⁻¹⁰). 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; outliers are plotted as dots. Analysis of one experiment (BRD4 and MED1 ChIP-seq) or three independent experiments (eRNA). c MA plot of changes in nascent RNA levels following 30 min treatment with 1.5% 1,6-hexanediol. Mean of three biological replicates. Statistically significant differences (red: increased; orange: decreased; gray: unchanged) from three biological replicates, FDR < 0.05. d Quantification of MYC and BCL2 nascent RNA-seq levels in untreated SEM cells or cells treated with 1.5% 1,6-hexanediol for 30 min. Mean of three biological replicates, normalized to expression in untreated cells; error bars show SEM. Source data are provided as a Source Data file. e Capture-C from the MYC promoter from untreated SEM cells (purple) or following 30 min treatment with 1.5% 1,6-hexanediol (green), mean of three biological replicates. Differential tracks show the change in profile in hexanediol-treated samples: pink bars show increases; blue bars show decreases. Reference-normalized BRD4 and MED1 ChIP-seq from untreated SEM cells and cells treated with 1,6-hexanediol for 30 min. Only the enhancer region is shown. f Capture-C from the BCL2 promoter and reference-normalized ChIP-seq, as in e. g Capture-C traces at genes that are transcriptionally downregulated (orange), upregulated (red) or unaffected (gray) by 30 min 1,6-hexanediol treatment. Purple line shows the profile in untreated cells; green line is from hexanediol-treated cells; 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 hexanediol 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 bar shows 100 kb.