AlkAniline‐Seq: Profiling of m7G and m3C RNA Modifications at Single Nucleotide Resolution

Abstract RNA modifications play essential roles in gene expression regulation. Only seven out of >150 known RNA modifications are detectable transcriptome‐wide by deep sequencing. Here we describe a new principle of RNAseq library preparation, which relies on a chemistry based positive enrichment of reads in the resulting libraries, and therefore leads to unprecedented signal‐to‐noise ratios. The proposed approach eschews conventional RNA sequencing chemistry and rather exploits the generation of abasic sites and subsequent aniline cleavage. The newly generated 5′‐phosphates are used as unique entry for ligation of an adapter in library preparation. This positive selection, embodied in the AlkAniline‐Seq, enables a deep sequencing‐based technology for the simultaneous detection of 7‐methylguanosine (m 7 G) and 3‐methylcytidine (m 3 C) in RNA at single nucleotide resolution. As a proof‐of‐concept, we used AlkAniline‐Seq to comprehensively validate known m 7 G and m 3 C sites in bacterial, yeast, and human cytoplasmic and mitochondrial tRNAs and rRNAs, as well as for identifying previously unmapped positions.