A considerable share of hyper-acetylated peaks was located
in super-enhancer regions (~21-25%) (Fig. 3B-D), and
~20% of super-enhancers contained a hyper-acetylated
region after 24 hours of butyrate treatment (Supplementary Fig. 5C).
Yet, only ~0.4% of hyper-acetylated super-enhancers were
linked to transcriptionally upregulated genes, similar to
hyper-acetylated typical enhancers and TSS regions (Supplementary Fig.
5D). Instead, weak hyper-acetylation (i.e. not passing our thresholds
for differential enrichment) at typical enhancers may better explain why
expression is induced at such genes (Supplementary Fig. 5E, F).
In summary, these data indicate that super-enhancers are an important
target of butyrate-induced HDAC inhibition, most often resulting in a
loss of H3K27Ac and correlating with reduced expression of many
associated key mast cell genes.