Epigenetic synergies between methyl donors and biotin in gene repression are mediated by holocarboxylase synthetase (HLCS)

Abstract

HLCS catalyzes the binding of biotin to proteins in humans. Previously, we have shown (1) that HLCS interacts physically with the methyl transferase EHMT‐1, which creates histone H3 K9 methylation (H3K9me) gene repression marks, (2) that biotinylation of EHMT‐1 strengthens interactions with HLCS, (3) that biotin depletion and HLCS knockdown cause a loss of H3K9me marks leading to de‐repression of long terminal repeats (LTRs) and to chromosomal abnormalities, and (4) that erasure of DNA methylation impairs HLCS‐dependent biotinylation events. Here, we tested the novel hypothesis that methyl donors and biotin synergize in mediating gene repression through epigenetic marks, and that HLCS contributes toward mediating these synergies. Co‐immunoprecipitation (Co‐IP) and limited proteolysis assays (LPA) confirmed that HLCS interacts physically with the DNA methyl transferase DNMT1 and methyl CpG binding protein MeCP2. Overexpression of HLCS in HEK293 cells caused a 200% increase of H3K9me marks in LTRs (Kruskal‐Wallis, P<0.001), judged by ChIP, and an 84% decrease in LTR mRNA (t‐test, P<0.05), judged by qRT‐PCR, compared with controls; erasure of DNA methylation by azacytidine abrogated effects of HLCS. We conclude that interactions between HLCS and chromatin proteins create epigenetic synergies between biotin and methyl donors in gene repression, thereby maintaining genome stability.Grant Funding Source: ARD Hatch, NIFA, NIH