Influence of Histone Acetylation on Chromatin 3D Organization in Drosophila S2 Cells

Alterations in histone acetylation are frequently detected in various cancers and neurological diseases. Histone acetylation is known to disrupt both intra- and inter-nucleosomal interactions, but its influence on higher-order chromatin organization has been studied to a lesser extent. In this study, we changed global levels of histone acetylation in Drosophila S2 cells by treatment with trichostatin A (TSA; an inhibitor of histone deacetylases) or with curcumin (an inhibitor of histone acetyltransferases and histone deacetylases). We also performed a knockdown of the main histone deacetylase HDAC1/Rpd3 in S2 cells. According to ChIP-seq analysis, histone H4 pan-acetylation was mostly increased in the active chromatin regions and decreased in the inactive regions after TSA treatment, whereas after curcumin treatment, it changed in the opposite direction. Changes in the level of histone acetylation affect the packaging density of topologically associating domains (TADs), which are the units of higher-order chromatin organization. Importantly, increased histone acetylation leads to decreased packaging density of TADs and vice versa. Moreover, the increased histone acetylation within active TADs enhances their spatial segregation from the inactive ones. Our findings highlight the key role of histone acetylation in determining the 3D organization of chromatin domains, supporting the idea that the separation of active and inactive TADs in Drosophila, at least in part, is mediated by histone acetylation. These results may help to understand how agents such as histone deacetylase inhibitors exert their therapeutic effects in certain cancers and other human diseases.