meCLICK-Seq - substrate-hijacking and RNA degradation strategy for the study of RNA methylation

The method hijacks RNA methyltransferase activity to introduce an alkyne, instead of a methyl, moiety on RNA. Subsequent copper(I)-catalyzed azide–alkyne cycloaddition (CuAAC) with an imidazole-degrader leads to RNA cleavage and degradation, exploiting a mechanism used by endogenous ribonucleases. Focusing on N6-methyladenosine (m6A), we compare Slick-Seq to current state-of-the-art methods used to study of this modification, and show that the platform identifies methylated transcripts, determines RNA methylase specificity, and reliably maps modification sites in intronic and intergenic regions. Importantly, we discovered that METTL16 deposits m6A to intronic polyadenylation (IPA) sites, which suggests a potential role of METTL16 in IPA and, in turn, splicing. Unlike previously reported methods, Slick-Seq allows a comprehensive and dynamic study of RNA modifications throughout the transcriptome, including regions of low abundance. We have developed Slick-Seq (Surrogate-Click-Degradation-Sequencing), a small-molecule-based method for the study RNA methylation, the most abundant RNA modification.