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

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 (mA) remain controversial due to its limited presence in typical eukaryotic mRNA. This study provides a comprehensive map of mA in dinoflagellate mRNA and shows that mA, rather than N6-methyladenosine (mA), is the most prevalent internal mRNA modification in various dinoflagellate species, with an asymmetric distribution along mature transcripts. In Amphidinium carterae, we identify 6549 mA 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 mA levels negatively correlate with translation efficiency. Nitrogen depletion further decreases mRNA mA levels. Our data suggest that distinctive patterns of mA modification might influence the expression of metabolism-related genes through translational control.