Histone succinylation directly inhibits Jumonji domain demethylases and stabilizes repressive chromatin states [RNA-Seq]

We investigate the relationship between histone succinylation and Jumonji C (JmjC) domain-containing histone demethylases, a class of enzymes that catalyzes the removal of histone methylation. By using quantitative proteomics and peptide pull-down assays, we identified Jumonji demethylases as candidate interactors of succinylated histone peptides. Biochemical assays demonstrate that succinylated histone peptides bind and inhibit the demethylase activity of KDM4D and KDM6B in a dose-dependent manner. Notably, these two demethylases are responsible for the removal of the silencing marks H3K9me2/3 and H3K27me2/3. We increased histone succinylation in a HepG2/C3A cell model by providing supraphysiological sodium succinate and demonstrated that H3K9me2/3 and H3K27me2/3 increased in relative abundance as well. CUT&Tag and ChIP–mass spectrometry revealed co-occurrence of succinylation with repressive methylation marks, together with reduced levels of transcribed RNA. Altogether, these findings support a model in which histone succinylation contributes to maintaining the silencing marks H3K9me2/3 and H3K27me2/3 on chromatin by locally inhibiting Jumonji domain demethylases. This work establishes a mechanistic link between metabolic state and chromatin regulation and suggests a role for histone succinylation in the maintenance of heterochromatin.