Antibody-free enzyme-assisted chemical labeling for detection of transcriptome-wide N6-methyladenosine

The inert chemical property of RNA modification N6-methyladenosine (m6A) makes it very challenging to detect, and all of the transcriptome-wide m6A detection methods rely on m6A-antibody immunoprecipitation. However, their results are dependent on the quality and specificity of antibodies. Although the endoribonuclease-based single-base m6A sequencing is antibody-free, it maps only 16~25% sites. Here, we present an antibody-free, FTO-assisted chemical labeling method termed m6A-SEAL for m6A detection. We applied m6A-SEAL to profile m6A landscapes in human and plant, which had good overlaps with antibody-based results and displayed the known m6A distribution features in transcriptome. Comparison with all available m6A sequencing methods and specific m6A sites validation by SELECT, we demonstrated that m6A-SEAL has good sensitivity, specificity, and reliability for transcriptome-wide detection of m6A. Given its tagging ability and FTO oxidation property, m6A-SEAL enables many applications like enrichment, imaging, and sequencing techniques to drive future functional studies of m6A and other modifications.