Abundant mRNA m1A modification in dinoflagellates: a new layer of gene regulation

Abstract Dinoflagellates, a class of unicellular eukaryotic phytoplankton, exhibit minimal transcriptional regulation, representing a unique model for exploring gene expression. The biosynthesis, distribution, regulation, and function of mRNA N1-methyladenosine (m 1 A) remain controversial due to its limited presence in typical eukaryotic mRNA. This study provides a comprehensive map of m 1 A in dinoflagellate mRNA and shows that m 1 A, rather than N6-methyladenosine (m 6 A), is the most prevalent internal mRNA modification in various dinoflagellate species, with an asymmetric distribution along mature transcripts. In Amphidinium carterae , we identify 6549 m 1 A sites characterized by a non-tRNA T-loop-like sequence motif within the transcripts of 3196 genes, many of which are involved in regulating carbon and nitrogen metabolism. Enriched within 3′UTRs, dinoflagellate mRNA m 1 A levels negatively correlate with translation efficiency. Nitrogen depletion further decreases mRNA m 1 A levels. Our data suggest that distinctive patterns of m 1 A modification might influence the expression of metabolism-related genes through translational control.