Base-resolution mapping reveals distinct m¹A methylome in nuclear- and mitochondrial-encoded transcripts

SUMMARY

Gene expression can be post-transcriptionally regulated via dynamic and reversible RNA modifications. N¹-methyladenosine (m¹A) is a recently identified mRNA modification; however, little is known about its precise location, regulation and function. Here, we develop a base-resolution m¹A profiling method, based on m¹A-induced misincorporation during reverse transcription, and report distinct classes of m¹A methylome in the human transcriptome. m¹A in 5’-UTR, particularly those at the first nucleotide of mRNA, associate with increased translation efficiency. A different subset of m¹A exhibit a GUUCRA tRNA-like motif, are evenly distributed in the transcriptome and are dependent on the methyltransferase TRMT6/61A. Additionally, we show for the first time that m¹A is prevalent in the mitochondrial-encoded transcripts. Manipulation of m¹A level via TRMT61B, a mitochondria-localizing m¹A methyltransferase, demonstrates that m¹A in mitochondrial mRNA interferes with translation. Collectively, our approaches reveal distinct classes of m¹A methylome and provide a resource for functional studies of m¹A-mediated epitranscriptomic regulation.