Base-Resolution Mapping Reveals Distinct m1 A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts

Gene expression can be post-transcriptionally regulated via dynamic and reversible RNA modifications. N-1-methyladenosine (m(1) A) is a recently identified mRNA modification; however, little is known about its precise location and biogenesis. Here, we develop a base-resolution m(1) A profiling method, based on m(1) A-induced misincorporation during reverse transcription, and report distinct classes of m(1) A methylome in the human transcriptome. m(1) A in 50 UTR, particularly those at the mRNA cap, associate with increased translation efficiency. A different, small subset of m1 A exhibit a GUUCRA tRNA-like motif, are evenly distributed in the transcriptome, and are dependent on the methyltransferase TRMT6/61A. Additionally, we show that m(1) A is prevalent in the mitochondrial-encoded transcripts. Manipulation of m(1) A level via TRMT61B, a mitochondria-localizing m(1) A methyltransferase, demonstrates that m(1) A in mitochondrial mRNA interferes with translation. Collectively, our approaches reveal distinct classes of m(1) A methylome and provide a resource for functional studies of m(1) A-mediated epitranscriptomic regulation.