Fig. 5

The loss of ARID1A leads to a loss of enhancer activity. Six thousand seven hundred forty-one genes associated with ARID1A-bound enhancers were determined. Three hundred seventeen genes were also downregulated by the knockout of ARID1A. Among these were the EREG, F3, and JAG1 genes (a). The three MEK/ERK pathway target genes identified were downregulated by the deletion of ARID1A in both KRAS-mutated cell lines (HCT116 and DLD1) (b). At the genomic loci for these genes, we identified potential enhancers which are occupied by ARID1A, JUND, and H3K27ac within the same topologically associated domains (TAD). Vertical dotted lines represent TAD boundaries. The potential enhancers are also accessible as assessed by ATAC-seq and are transcriptionally active as assessed by PRO-seq (c). There is a significant reduction of H3K27ac at these enhancers upon the deletion of ARID1A (c, d). qRT-PCRs for gene expression and ChIP were run in biological triplicates and technical duplicates. The dotted lines represent the average ChIP-qPCR signal for the negative control IgG. Error bars represent the standard deviation between three biological replicates. Significance was calculated using unpaired t test, *p < 0.05, **p < 0.01, ***p < 0.001