Fig. 2: SEs control the expression of cancer stemness genes and pro-invasive genes.

a JQ1 inhibited MED1 occupancies on genome by ChIP-seq. b JQ1 disrupted SEs in SCC cells based on MED1 enrichments. c GO analysis of 608 SE-associated genes in SCC cells. d Genes associated with SEs display higher expression than genes associated with total pool of all enhancers (ALL) and typical enhancers (TE) in SCC1 cells. Statistical analysis was performed using two-tailed unpaired Student’s t-test. Boxplot: middle line of box indicates median and the bounds indicate quartile 1 and quartile 3. e Boxplots showing log2 fold changes for downregulated transcripts associated with total pool of ALL, TEs, and SEs after JQ1 treatment in SCC1 cells. Statistical analysis was performed using two-tailed unpaired Student’s t-test. Boxplot: middle line of box indicates median and the bounds indicate quartile 1 and quartile 3. f JQ1 disrupted SEs in SCC cells based on BRD4 enrichments. g JQ1 strongly inhibited BRD4 binding in SEs compared with genome-wide regions. h JQ1 displaced p65 occupancies in both genome-wide and SE regions. i BRD4 selectively colocalized with MED1 and p65 to form SEs in SCC cells.