To gain a more quantitative picture of H3K27Ac dynamics
upon butyrate treatment, we performed differential enrichment analyses
with DESeq2 on reproducible peaks, which showed that most regions
acetylated at baseline (>68%) were not significantly (fold
change > 2 and adjusted P value < 0.05) affected
by 3-24 h butyrate treatment (Supplementary Fig. 3). After 3 h exposure,
butyrate mostly triggered hyper-acetylation (6.3% hyper-acetylated vs.
2.2% hypo-acetylated peaks), whereas 12 h butyrate exposure showed
similar proportions of hyper- and hypo-acetylation at baseline H3K27Ac+
regions (13.3% vs. 12.8%). Finally, 24 h of treatment mostly induced
hypo-acetylation of existing peaks (13.1% vs. 18.6%, Supplementary
Fig. 3).
To better annotate at which regulatory sites
butyrate-induced histone acetylation dynamics occur, we intersected
regions of dynamic acetylation with TSS locations and putative typical
enhancer or super-enhancer regions as defined by the ROSE
algorithm 28,35. At untreated
conditions (indicated as 0 h), histone acetylation was primarily located
distant from TSS regions, with the bulk of H3K27Ac+ sites located 50-500
kb away from the TSS (Fig. 3A, bar graph). Furthermore,
~52% and ~19% of acetylated peaks were
associated with typical enhancers and super-enhancers, respectively,
whereas 17% of acetylated peaks were associated with TSS regions (Fig.
3A, donut graph).