2-Hydroxyglutarate modulates histone methylation at specific loci and alters gene expression via Rph1 inhibition.

Abstract

2-Hydroxyglutarate (2-HG) is an oncometabolite that accumulates in certain cancers. Gain-of-function mutations in isocitrate dehydrogenase lead to 2-HG accumulation at the expense of alpha-ketoglutarate. Elevated 2-HG levels inhibit histone and DNA demethylases, causing chromatin structure and gene regulation changes with tumorigenic consequences. We investigated the effects of elevated 2-HG levels in Saccharomyces cerevisiae, a yeast devoid of DNA methylation and heterochromatin-associated histone methylation. Our results demonstrate genetic background-dependent gene expression changes and altered H3K4 and H3K36 methylation at specific loci. Analysis of histone demethylase deletion strains indicated that 2-HG inhibits Rph1 sufficiently to induce extensive gene expression changes. Rph1 is the yeast homolog of human KDM4 demethylases and, among the yeast histone demethylases, was the most sensitive to the inhibitory effect of 2-HG in vitro. Interestingly, Rph1 deficiency favors gene repression and leads to further down-regulation of already silenced genes marked by low H3K4 and H3K36 trimethylation, but abundant in H3K36 dimethylation. Our results provide novel insights into the genome-wide effects of 2-HG and highlight Rph1 as its preferential demethylase target.

• Authors: Marios Gavriil, Marco Proietto, Nicole Paczia, Aurelien Ginolhac, Rashi Halder, Elena Valceschini, Thomas Sauter, Carole L Linster, Lasse Sinkkonen
• Journal: Life science alliance (Life Sci Alliance) Vol. 7 Issue 2 (Feb 2024) ISSN: 2575-1077 [Electronic] United States
• PMID: 38011998 (Publication Type: Journal Article)
• Copyright: © 2023 Gavriil et al.

Chemical References

• alpha-hydroxyglutarate
• Histone Demethylases
• Histones
• Saccharomyces cerevisiae Proteins
• RPH1 protein, S cerevisiae

Topics

• Gene Expression
• Histone Demethylases (genetics, metabolism)
• Histones (metabolism)
• Methylation
• Saccharomyces cerevisiae (genetics, metabolism)
• Saccharomyces cerevisiae Proteins (genetics, metabolism)