Elevated methionine induces DNA hypermethylation of transposable elements in Arabidopsis

Methionine (Met) is a key sulfur-containing amino acid and the precursor of S-adenosylmethionine (SAM), the universal methyl donor for DNA and histone methylation. While reduced SAM availability is known to cause DNA hypomethylation, the effects of elevated Met/SAM remain poorly understood. Here, we examined the Arabidopsis thaliana mto1 mutant, which accumulates Met and SAM due to a mutation in cystathionine γ-synthase, the first committed enzyme of Met biosynthesis. Whole-genome bisulfite sequencing (WGBS) analysis revealed widespread hypermethylation in mto1, particularly in non-CG contexts (CHG and CHH), with the strongest changes in pericentromeric heterochromatin. Hypermethylation was concentrated in transposable elements (TEs), especially retrotransposon families such as Gypsy and Copia. Transcriptome profiling showed that TE-genes (TEGs) were broadly downregulated, consistent with reinforced TE silencing due to the hypermethylation. Despite these epigenetic changes, expression of core DNA methyltransferases and demethylases was largely unchanged, suggesting that increased SAM availability enhances enzymatic activity rather than gene expression. In addition, ~25% of protein-coding genes were differentially expressed in mto1, though most changes were not directly linked to promoter- or gene-body methylation. Instead, the strong bias toward hypermethylation of TEs and repression of TEGs suggests that elevated Met/SAM primarily affects gene expression indirectly. Together, these findings demonstrate that an excess of Met/SAM reinforces heterochromatic DNA methylation and transposon silencing, providing new insights into the connection between amino acid metabolism and epigenetic regulation in plants.