NERD-seq - A novel approach of Nanopore direct RNA sequencing - mouse
Non-coding RNAs constitute the most frequently documented targets of RNA modification machinery. Oxford Nanopore Technologies' pore-based sequencing technology enables the direct sequencing of RNA molecules and as such, the direct detection of modified bases. Ordinarily, direct RNA sequencing uses polyadenylation selection, enabling the study of primarily mRNA gene expression. Here we present NERD-seq, a sequencing approach which enables the detection of multiple classes of non-coding RNAs excluded by the current standard approach, alongside natively polyadenylated transcripts. Using neural tissues as a proof of principle, we show that NERD-seq substantially expands the representation of multiple classes of non-coding RNAs, that are frequent targets for RNA modifications, such as snoRNAs, snRNAs, scRNAs, srpRNAs, tRNAs, rRFs and non-coding RNAs originating from LINE L1 elements. Therefore, NERD-seq presents a new comprehensive direct RNA-seq approach for the simultaneous study of epitranscriptomes in brain tissues for both mRNAs and the above classes of non-coding RNAs. The current submission includes the mouse samples of this project. A separate submission is available for the human samples.