DART-seq: an antibody-free method for global m(6)A detection

m(6)A is a widespread RNA modification which influences nearly every aspect of the mRNA life cycle. Our understanding of m(6)A has been facilitated by the development of global m(6)A mapping methods, which use antibodies to immunoprecipitate methylated RNA. However, these methods have several limitations, including high input RNA requirements and cross-reactivity to other RNA modifications. Here, we present DART-Seq (deamination adjacent to RNA modification targets), an antibody-free method for detecting m(6)A sites. In DART-Seq, the cytidine deaminase APOBEC1 is fused to the m(6)A-binding YTH domain. APOBEC1-YTH expression in cells induces C to U deamination at sites adjacent to m(6)A residues, which are detected using standard RNA-Seq. DART-Seq identifies thousands of m(6)A sites in cells from as little as 10 nanograms of total RNA and can detect m(6)A accumulation in cells over time. Additionally, we use long-read DART-Seq to gain new insights into m(6)A distribution along the length of individual transcripts.