Antibody-free enzyme-assisted chemical approach for detection of N6-methyladenosine

The inert chemical property of RNA modification N-6-methyladenosine (m(6)A) makes it very challenging to detect. Most m(6)A sequencing methods rely on m(6)A-antibody immunoprecipitation and cannot distinguish m(6)A and N-6,2 '-O-dimethyladenosine modification at the cap +1 position (cap m(6)A(m)). Although the two antibody-free methods (m(6)A-REF-seq/MAZTER-seq and DART-seq) have been developed recently, they are dependent on m(6)A sequence or cellular transfection. Here, we present an antibody-free, FTO-assisted chemical labeling method termed m(6)A-SEAL for specific m(6)A detection. We applied m(6)A-SEAL to profile m(6)A landscapes in humans and plants, which displayed the known m(6)A distribution features in transcriptome. By doing a comparison with all available m(6)A sequencing methods and specific m(6)A sites validation by SELECT, we demonstrated that m(6)A-SEAL has good sensitivity, specificity and reliability for transcriptome-wide detection of m(6)A. Given its tagging ability and FTO's oxidation property, m(6)A-SEAL enables many applications such as enrichment, imaging and sequencing to drive future functional studies of m(6)A and other modifications.