RUNX3 acetylation-mediated enhancer activation increases immune function-related gene expression via long-range chromatin interactions. (A) Activated RUNX3 target genes identified by integrated analysis of RUNX3 ChIP-seq, H3K27ac ChIP-seq, and H3K27ac HiChIP. (B) RNA-seq MA plot for the activated RUNX3 target genes. The number of genes exhibiting > 1.3-fold increases in control (orange) or Vorinostat (purple) with an FDR < 0.05 are indicated. (C) Enrichment of biological process gene ontology terms on the activated RUNX3 target genes whose RNA expression was upregulated in Vorinostat. (D, E) Snapshots (left panels) showing RUNX3 and H3K27ac ChIP-seq signal tracks and significant H3K27ac HiChIP loops at the typical activated RUNX3 target genes, including NFKBIZ (D) MXI1 (E). Arcs showing significant interactions with −Log10(Q) ≥ 5. Gray and blue vertical bars highlight the location of promoters of activated RUNX3 target genes and enhancers bound by activated RUNX3, respectively. Only activated RUNX3-mediated loops interacting with the viewpoint are displayed. Expression of RUNX3 target genes was measured by qRT-PCR (right panels). (F) Scheme showing the action mechanism of Vorinostat where RUNX3 acetylation-mediated enhancer activation increases immune function-related gene expression via long-range chromatin interactions.
