Fig 2: BRD4 recruits MED1 and p65 to form SEs.a The knockdown of BRD4 impaired both p65 and MED1 recruitments to SEs in TP63 (n = 3 per group). b The knockdown of BRD4 impaired both p65 and MED1 recruitments to SEs in MET (n = 3 per group). c JQ1 treatment or p65 knockdown significantly inhibited the recruitment of both CDK9 and CCNT1 to SEs in TP63 (n = 3 per group). d JQ1 treatment or p65 knockdown significantly inhibited the recruitment of both CDK9 and CCNT1 to SEs in MET (n = 3 per group). e RT-qPCR showed that knockdown of p65 and MED1 significantly inhibited the expression of TP63, MET, BIRC3, and MMP3 (n = 3 per group). f Increased enrichments of both p65 and BRD4 on SEs of TP63 in CSC-like cell (n = 3 per group). g Increased enrichments of both p65 and BRD4 on SEs of MET in CSC-like cells (n = 3 per group). h CSCs had significantly higher TP63 and MET expression levels (n = 3 per group). Data are presented as mean values ± SD in a–m. Statistical analysis was performed using two-tailed unpaired Student’s t-test. The data in a–m are representative of three experiments with similar results. Source data are provided as a Source data file.

Fig 3: Redistribution of MED1 genomic occupancy upon rosi treatment. (A) Number of eRNAs up-regulated or down-regulated at each time point. (B) Work flow for identification of MED1-binding sites with regulated eRNAs. (C) Scatter plot comparing MED1-binding strength in reads per million (RPM) with and without 1 h of rosi treatment, with sites containing an up-regulated eRNA highlighted in red. (D) Scatter plot comparing MED1-binding strength with and without 1 h of rosi treatment, with sites containing a down-regulated eRNA highlighted in blue. (E) MED1 ChIP-qPCR at sites with up-regulated or down-regulated eRNAs. N = 5. Error bars indicate SEM. (*) P < 0.05; (**) P < 0.01; (***) P < 0.005 by paired t-test. (F) Box plot showing average change in MED1 genome-wide occupancy upon rosi treatment at sites of regulated eRNAs. (**) P < 10−15.

Fig 4: FOXA and master transcription factors are essential to recruit Mediator and Cohesin.Depletion of either the master transcription factor ERa or the pioneer transcription factor FOXA1 in MCF7 cells decreases MED1 and SMC1 recruitment at regulatory elements of the TFF1 and GREB1 genes in MCF7. Amplified enhancer (E1 and E2) and TSS regions are indicated by boxes. Enrichment fold were calculated relative to control regions without MED1 or SMC1 signal. The bar graphs display the enrichment fold of a representative experiment. Error bars show the standard error of the mean for technical qPCR triplicates.

Fig 5: Ino80 occupies genomic regions near melanoma-related genes. (A) Ino80 peak distribution in the genome. (B,C) Heat maps showing Ino80, Med1, H3K27ac, and H3K4me1 occupancy in the BRAF mutant A375 cells (B) or NRAS mutant SK-MEL-147 cells (C). Genes were sorted based on the Ino80 signal around the Ino80 peak center. (D) Genome browser showing Ino80, Med1, and H3K27ac occupancy near representative SE genes in A375 and SK-MEL-147 melanoma cells and in primary melanocytes. (E–H) Dependency of Ino80 occupancy on MITF and Sox9. MITF or Sox9 was silenced by lentiviral shRNAs in A375 cells (E,G), and the Ino80 occupancy at selected genes was determined by ChIP-qPCR (F,H).