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bioRxiv · 10.1101/2021.05.06.442990

NERD-seq: A novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs

Saville, L.·Cheng, Y.·Gollen, B.·Mitchell, L.·Stuart-Edwards, M.·Haight, T.·Mohajerani, M.·Zovoilis, A.
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Abstract

The new next-generation sequencing platforms by Oxford Nanopore Technologies for direct RNA sequencing (direct RNA-seq) allow for an in-depth and comprehensive study of the epitranscriptome by enabling direct base calling of RNA modifications. Non-coding RNAs constitute the most frequently documented targets for RNA modifications. However, the current standard direct RNA-seq approach is unable to detect many of these RNAs. 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. Using total RNA from a tissue with high known transcriptional and non-coding RNA activity in mouse, the brain hippocampus, we show that, in addition to detecting polyadenylated coding and non-coding transcripts as the standard approach does, NERD-seq is able to significantly expand the representation for other classes of RNAs such as snoRNAs, snRNAs, scRNAs, srpRNAs, tRNAs, rRFs and non-coding RNAs originating from LINE L1 elements. Thus, NERD-seq presents a new comprehensive direct RNA-seq approach for the study of epitranscriptomes in brain tissues and beyond.

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Saville, L., Cheng, Y., Gollen, B., Mitchell, L., Stuart-Edwards, M., Haight, T., Mohajerani, M., Zovoilis, A.. 2021-05-07. NERD-seq: A novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs. https://doi.org/10.1101/2021.05.06.442990

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