Trichostatin A Treatment Has Little Impact on Nuclear compartments in Cells Depleted of H3K9me, H3K27me3, and uH2A [ChIP-Seq]

In the mammalian nucleus, heterochromatin is segregated from transcriptionally active euchromatic regions (A compartments), forming large, condensed, and inactive nuclear compartments (B compartments). However, the mechanisms underlying its spatial organization remain incompletely understood. We previously demonstrated that simultaneous depletion of H3K9 methylation, H3K27me3, and H2A monoubiquitination in immortalized mouse embryonic fibroblasts (iMEFs) leads to heterochromatin weakening and alterations in nuclear compartments. However, the overall pattern of A/B compartments remains largely preserved even under these conditions, suggesting the involvement of unknown factors. Since histone deacetylation is a key factor in transcriptional repression, we investigated the impact of histone deacetylase (HDAC) inhibition on nuclear compartments by treating cells depleted of H3K9 methylation, H3K27me3, and H2A K119 monoubiquitylation (H2AK119ub/uH2A) with the HDAC inhibitor Trichostatin A (TSA). We performed Hi-C analysis to assess the nuclear compartment changes. Our results showed that, although TSA treatment globally increased H3K27ac levels, the difference in H3K27ac enrichment between A/B compartments remained evident, and nuclear compartments were minimally affected. These findings suggest that factors other than HDACs maintain nuclear compartmentalization when repressive chromatin modifications are depleted.