m1A modification of nuclear- and mitochondria-encoded mRNA: Rare, dynamic and potent
Modifications on mRNA offer the potential of regulating mRNA fate post-transcriptionally, in an analogous manner to post-translational modifications on proteins. Recent studies have suggested the widespread presence of N1-methyladenosine (m1A), a modification disrupting Watson-Crick basepairing, at internal sites of mRNAs. These studies lacked the resolution of identifying individual modified bases, and did not identify specific sequence motifs undergoing the modification or an enzymatic machinery catalyzing them. We developed an approach allowing the semi-quantitative mapping of m1A at single nucleotide resolution and in a transcriptome-wide manner. Surprisingly, we found that within the cytosol, m1A is present in a low number of mRNAs, typically at low stoichiometries, and that its presence represses translation, likely via a mechanism involving ribosomal scanning/translation. In contrast, we find a single m1A site in the mitochondrial ND5 mRNA, catalyzed by TRMT10C, with methylation levels that are highly tissue specific and tightly developmentally controlled. In particular, we find that this modification is present at close to stoichiometric levels in early development up to the 8 cell stage, whereupon they dramatically decrease. This shift coincides with a metabolic shift from glycolysis to oxidative phosphorylation occurring at the same developmental stage. Our findings suggest that m1A on mRNA, likely due to its disruptive impact on base pairing, leads to translational repression, and is generally avoided by cells, while revealing one case in mitochondria where tight spatiotemporal control over m1A levels was adopted as a potential means of post-transcriptional regulation, potentially acting as a metabolic switch.