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

Luke Saville; Li Wu; Jemaneh Habtewold; Yubo Cheng; Babita Gollen; Liam Mitchell; Matthew Stuart-Edwards; Travis Haight; Majid Mohajerani; Athanasios Zovoilis

doi:10.1186/s13059-024-03375-8

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

Genome Biol. 2024 Aug 28;25(1):233. doi: 10.1186/s13059-024-03375-8.

Authors

Luke Saville^{1

2

3

4}, Li Wu^{1

2}, Jemaneh Habtewold^{1

2}, Yubo Cheng^{3

4}, Babita Gollen^{3

4}, Liam Mitchell^{1

2

3

4}, Matthew Stuart-Edwards^{1

2

3

4}, Travis Haight^{1

2

3

4}, Majid Mohajerani⁴, Athanasios Zovoilis^{5

6

7

8}

Affiliations

¹ Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E3N4, Canada.
² Paul Albrechtsen Research Institute, CCMB, Winnipeg, MB, R3E3N4, Canada.
³ Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada.
⁴ Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada.
⁵ Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, R3E3N4, Canada. [email protected].
⁶ Paul Albrechtsen Research Institute, CCMB, Winnipeg, MB, R3E3N4, Canada. [email protected].
⁷ Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada. [email protected].
⁸ Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada. [email protected].

Abstract

Non-coding RNAs (ncRNAs) are frequently documented RNA modification substrates. Nanopore Technologies enables the direct sequencing of RNAs and the detection of modified nucleobases. Ordinarily, direct RNA sequencing uses polyadenylation selection, studying primarily mRNA gene expression. Here, we present NERD-seq, which enables detection of multiple non-coding RNAs, excluded by the standard approach, alongside natively polyadenylated transcripts. Using neural tissues as a proof of principle, we show that NERD-seq expands representation of frequently modified non-coding RNAs, such as snoRNAs, snRNAs, scRNAs, srpRNAs, tRNAs, and rRFs. NERD-seq represents an RNA-seq approach to simultaneously study mRNA and ncRNA epitranscriptomes in brain tissues and beyond.

MeSH terms

Animals
Brain / metabolism
Humans
Mice
Nanopore Sequencing* / methods
RNA, Messenger / genetics
RNA, Untranslated* / genetics
Sequence Analysis, RNA* / methods

Substances

RNA, Untranslated
RNA, Messenger