m6A-Label-seq directly reports m6A methylome at base resolution

Here we report a metabolic labeling method to map mRNA N6-methyladenosine (m6A) modification transcriptome-wide at base resolution, termed m6A-label-seq. The cells were fed with Se-allyl-L-selenohomocysteine, an analog of methoine, which serves as the precursor of methylation enzyme cofactor, so that cellular RNAs were continuously deposited with N6-allyladenosine (a6A) at supposed m6A sites. We enriched a6A-containing mRNAs and sequenced their a6A sites which are identical to m6A sites, based on iodination-induced misincorporation during reverse transcription. Overall design: We profiled m6A sites at base resolution in human HeLa and HEK293T cells and mouse H2.35 cells by metabolically incorporation of Se-derived methionine analog. We assessed the potential stress response in HeLa cells by an RNA-seq experiment.