Precise identification of an RNA methyltransferase's substrate modification site.

Here we report a simple and nonradioactive biochemical assay which is capable of accurately determining the substrate methylation sites of human RNA N6-methyladenosine methyltransferases METTL3/METTL14 and METTL16. This method employs enzyme-assisted chemical labelling of a specific base in an RNA substrate with the assistance of an allyl-substituted methyltransferase cofactor, and enables precise identification of the labelling site by a mutation signal from standard nucleic acid sequencing. Our method provides a platform to investigate the enzymatic methylations of long and structurally complex RNA substrates, and facilitates the discovery of new methyltransferases.