Short-term methionine starvation reshapes diurnal hepatic m6A RNA methylation.

Abstract

Dietary methionine restriction improves metabolic health and has therapeutic potential in multiple disease contexts. Methionine metabolism regulates transmethylation reactions, including N6-methyladenosine (m6A) RNA methylation, by modulating availability of S-adenosyl methionine (SAM). Both m6A methylation and methionine metabolism have separately been linked to circadian regulation, but whether dietary methionine influences circadian rhythms through m6A remains unknown. Here we show that short-term methionine deprivation induces diurnal variation in serum methionine and SAM and reprograms diurnal expression of m6A writers, erasers, and readers in mouse liver. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) at two timepoints (ZT9, ZT21) revealed that a methionine-deficient (MD) diet was associated with a roughly 10-fold increase in differentially methylated m6A peaks between timepoints relative to control, despite no change in methylation at core clock transcripts. These diet-induced oscillations arose at sites already methylated under the control diet, indicating that methionine restriction alters the rhythmicity of existing m6A marks rather than inducing new methylation, and were enriched in transcripts involved in RNA processing, translation, ubiquitination, and mTORC1 signaling. Integrating RNA-seq and proteomics, we found that a subset of these m6A changes co-occurred with altered mRNA and/or protein abundance, indicating gene-specific rather than global effects. Notably, reduced m6A methylation of Mat2a and Cbs, encoding enzymes central to methionine homeostasis, was associated with increased MAT2A and decreased CBS protein levels, respectively. These findings identify diet-induced, diurnally rhythmic m6A methylation as a candidate mechanism linking methionine metabolism to circadian biology and nominate specific m6A sites and pathways for future investigation.