Base-Resolution Mapping Reveals Distinct mA Methylome in Nuclear- and Mitochondrial-Encoded Transcripts.

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