Mitotic H3K9ac is controlled by phase-specific activity of HDAC2, HDAC3 and SIRT1

Abstract

Mitosis comprises multiple changes, including chromatin condensation and transcription reduction. Intriguingly, while histone acetylation levels are reduced during mitosis, the mechanism of this reduction is unclear. We studied the mitotic regulation of H3K9ac by using inhibitors of histone deacetylases. We evaluated the involvement of the targeted enzymes in regulating H3K9ac during mitotic stages and cytokinesis by immunofluorescence and immunoblots. We identified HDAC2, HDAC3 and SIRT1 as modulators of the mitotic levels of H3K9ac. HDAC2 inhibition increased H3K9ac levels in prophase, whereas HDAC3 or SIRT1 inhibition, increased H3K9ac levels in metaphase. Next, we performed ChIP-seq in mitotic cells following targeted inhibition of these histone deacetylases. While the genomic areas impacted by HDAC2 and HDAC3 were mostly concordant, a subset of loci were unique to each enzyme. Interestingly, HDAC3-specific targets were enriched for genes involved in mitosis regulation. Our results support a model in which H3K9 deacetylation is a stepwise process - at prophase HDAC2 modulates most transcription-associated H3K9ac-marked loci and at metaphase HDAC3 maintains the reduced acetylation, whereas SIRT1 potentially regulates H3K9ac by impacting HAT activity.

Dynamics and regulation of mitotic chromatin accessibility bookmarking at single-cell resolution

“…We observed that chromatin accessibility gradually decreased after prophase and began to increase after reaching its nadir in metaphase (Fig. 1H), which is consistent with our scATAC-seq analysis and recent studies on the dynamics of active histone modifications of H3K27ac and H3K9ac during mitosis ( 19 , 20 ). Similar dynamic trends of mitotic chromatin accessibility were also observed in the other two cell lines (HepG2 and HUH7) by ATAC-see (fig.…”

“…Mitotic bookmarking is influenced by chromosome condensation, which is highly dynamic at different stages of mitosis ( 18 ). In addition, several studies have shown that some epigenetic signatures previously considered as bookmarking factors ( 7 ) were not consistently retained on chromatin throughout mitosis ( 19 , 20 ). Thus, it is limiting to study the bookmarking using drug-synchronized mitotic cells.…”

Mycobacterium tuberculosis Phosphoribosyltransferase Promotes Bacterial Survival in Macrophages by Inducing Histone Hypermethylation in Autophagy-Related Genes

“…Histone deacetylation is catalysed by various histone deacetylases (HDAC) such as HDAC1, HDAC2 and HDAC3 (Seto and Yoshida, 2014). Specifically, H3K9 and H3K27 deacetylation is induced by HDAC1, HDAC2 and HDAC3 (Vecěrǎ et al, 2018;Praestholm et al, 2020;Gandhi et al, 2021).We observed that the level of HDAC3 was higher in Mtb Prt -infected macrophages than in control cells (Figure 2H), whereas HDAC1 and HDAC2 expression levels did not change (Figure S2). These data show that Mtb PRT-induced HDAC3 expression mediates H3K9 and H3K27 deacetylation.…”