Methionine overaccumulation reinforces heterochromatic non-CG hypermethylation and transposon silencing in Arabidopsis.

Methionine is a key sulfur-containing amino acid and the precursor of S-adenosylmethionine, the universal methyl donor for DNA and histone methylation. While reduced S-adenosylmethionine availability is known to cause DNA hypomethylation, the effects of elevated methionine/S-adenosylmethionine remain poorly understood. Here, we addressed the effect of elevated methionine using the mto1 mutant of Arabidopsis thaliana, which over-accumulates methionine and S-adenosylmethionine due to a mutation in cystathionine γ-synthase, the first committed enzyme of methionine biosynthesis. Whole-genome bisulfite sequencing analysis revealed widespread hypermethylation in mto1, particularly in non-CG contexts (CHG and CHH), with the strongest changes found in pericentromeric heterochromatin. Hypermethylation was concentrated within transposable elements (TEs), especially from the Gypsy and Copia superfamilies. Transcriptome profiling showed that TE-genes were broadly downregulated, consistent with reinforced TE silencing due to hypermethylation. When the expression level of ONSEN (Copia78) was examined under heat stress, it was found to be significantly lower than in the wild type. In addition, compared to wild type, mto1 showed significantly greater reactive oxygen species accumulation. These findings suggest a link between elevated methionine levels and altered stress responses. Despite the observed epigenetic changes, the expression of core DNA methyltransferases and demethylases genes was essentially unchanged, suggesting that increased S-adenosylmethionine availability enhances enzymatic activity rather than gene expression. Together, these findings demonstrate that an excess of methionine/S-adenosylmethionine reinforces heterochromatic DNA methylation and transposon silencing, providing new insights into the connection between amino acid metabolism and epigenetic regulation in plants.