A metabolic labeling method detects mA transcriptome-wide at single base resolution.

Transcriptome-wide mapping of N-methyladenosine (mA) at base resolution remains an issue, impeding our understanding of mA roles at the nucleotide level. Here, we report a metabolic labeling method to detect mRNA mA transcriptome-wide at base resolution, called 'mA-label-seq'. Human and mouse cells could be fed with a methionine analog, Se-allyl-L-selenohomocysteine, which substitutes the methyl group on the enzyme cofactor SAM with the allyl. Cellular RNAs could therefore be metabolically modified with N-allyladenosine (aA) at supposed mA-generating adenosine sites. We pinpointed the mRNA aA locations based on iodination-induced misincorporation at the opposite site in complementary DNA during reverse transcription. We identified a few thousand mRNA mA sites in human HeLa, HEK293T and mouse H2.35 cells, carried out a parallel comparison of mA-label-seq with available mA sequencing methods, and validated selected sites by an orthogonal method. This method offers advantages in detecting clustered mA sites and holds promise to locate nuclear nascent RNA mA modifications.