Nm-REP-seq Reveals 2'-O-Methylation Landscape at the 3'-end of Noncoding RNAs with Single-base Resolution

Many non-coding RNAs (ncRNAs), such as piRNAs, miRNAs and siRNAs, contain Nm at the 3'-end nucleotides, protecting the 3'-ends form terminal nucleotide addition or exonucleolytic degradation, but whether other kinds of RNAs contain a 3'-terminal Nm remain unknown. Here, we developed Nm-REP-seq to globally profile the 3'end-Nm sites and we revealed several novel classes of Nm-containing ncRNAs in mice and drosophila. Importantly, we discovered that Nm distribute at the end of miRNA, snoRNA, snRNA, tRNA as well as fragments derived from them. Collectively, our approach precisely redefines the genome-wide distribution of Nm and provides new technologies for functional studies of Nm-mediated gene regulation. Method: We developed Nm-REP-seq to globally profile the 3'-end Nm sites. Results: We discovered that Nm distribute at the end of miRNA, snoRNA, snRNA, tRNA as well as fragments derived from them. Conclusion:Collectively, our approach precisely redefines the genome-wide distribution of Nm and provides new technologies for functional studies of Nm-mediated gene regulation. Overall design: Total RNA was extracted from mouse testis as well as drosophila Kc167 cell and subjected to modified Nm-REP-seq library construction protocol, in three biological repeats (rep1, rep2 and rep3).