javascript:void(0)Most super-enhancers (~84%) overlapped with non-TSS regions that were hypoacetylated (fold change > 2 and adjusted P value < 0.05) after 24 hours of butyrate treatment (Fig. 5C,D). Pathway enrichment analyses of the 502 genes associated with hypo-acetylated super-enhancer revealed that they are particularly associated with regulation of cell activation, FCERI mediated Ca+2 mobilization and mast cell mediated immunity (Fig. 5E). Of note, ~19% of hypo-acetylated super-enhancers were linked to transcriptionally downregulated genes (Fig. 5F), as compared to only 6-8% for hypo-acetylated typical enhancers and TSS regions. For genes expressed prior to butyrate treatment (RPKM>1), hypo-acetylation of super-enhancers represented the strongest predictor of transcriptional downregulation (24%), followed by hypo-acetylation of typical enhancers (13.0%) and TSS regions (7.7%) (Supplementary Fig. 5A).
Genes that displayed downregulated expression and super-enhancer hypo-acetylation (n=95, 18.9% of 502 genes) were strongly associated with (mast cell) activation and exocytosis (Fig. 5G). By contrast, downregulated genes linked to hypo-acetylated typical enhancer regions associated with more general immune functions (Supplementary Fig. 5B). Together, these findings provide a plausible epigenetic explanation for the transcriptional deregulation of many downregulated genes, i.e., via loss of histone acetylation of their TSSs, super-enhancers, or both (Fig. 5H ). Of note, out of the 864 downregulated genes, 112 genes were associated with super-enhancers, a majority (85%) of which displayed hypo-acetylation after 24 hours of butyrate.