Abundant mRNA m1A modification in dinoflagellates: a new layer of gene regulation [MeRIP-seq, RNA-seq, Ribo-seq]

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 (m1A) remain controversial due to its limited presence in typical eukaryotic mRNA. This study found that m1A, rather than N6-methyladenosine (m6A), is the most prevalent internal mRNA modification in various dinoflagellate species, with an asymmetrically distribution along mature transcripts. In Amphidinium carterae, we identified 6549 m1A sites characterized by a non-tRNA T-loop-like sequence motif within the transcripts of 3196 genes, many involved in regulating carbon and nitrogen metabolism. With enrichment within 3'UTR, dinoflagellate mRNA m1A exhibits negative correlation with translation efficiency. Notably, nitrogen depletion led to a significant decrease in mRNA m1A. Furthermore, our analysis revealed that distinctive patterns of m1A modification influence the expression of metabolism-related genes through translation control. Thus, this study provides a comprehensive map of m1A in dinoflagellate mRNA, highlighting its crucial role as a post-transcriptional regulatory layer and enhancing the understanding of mRNA m1A modification. Overall design: In order to gain further insight into the roles of m1A, particularly its methylation level, distribution, and how mRNA translation responds to N-depletion stress, we conducted MeRIP-seq, RNA-seq and Ribo-seq under both normal conditions and N-depletion conditions. For the MeRIP-seq, each of the three replicates under normal conditions and N-depletion conditions has an associated input. RNA-seq was also executed to capture the broader transcriptomic landscape, with three replicates for each condition. To delve deeper into the intricacies of mRNA translation in relation to these conditions, Ribo-seq was employed, for which we provide data from two replicates.