Mapping N6-Methyladenosine (m6A) in RNA: Established Methods, Remaining Challenges, and Emerging Approaches

N-6-Methyladenosine (m(6)A) is the most abundant internal modification in eukaryotic mRNA. Specific m(6)A reader and eraser proteins link this modification to many aspects of mRNA metabolism and regulate its levels in a dynamic way. Precise localization and quantification in varying biological samples is, therefore, relevant to understand the functional role of m(6)A and mechanisms governing its regulation. In this Minireview, we summarize established and emerging concepts for m(6)A mapping. Starting with the seminal m(6)A-sequencing techniques based on immunoprecipitation, we will highlight technical improvements by photo-cross-linking and remaining challenges. As an alternative, antibody-free approaches will be presented. These include wild-type or engineered m(6)A-sensitive enzymes and chemical biology approaches combining substrate analogues, chemical derivatization, and enzymatic steps to trace m(6)A. Finally, single-molecule sequencing as a new avenue for direct detection of mRNA modifications will be discussed.