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Nanopore sequencing of brain-derived full-length circRNAs reveals circRNA-specific exon usage, intron retention and microexons

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

DOI

Circular RNA (circRNA) is a class of covalently joined non-coding RNAs with functional roles in a wide variety of cellular processes. Their composition shows extensive overlap with exons found in linear mRNAs making it difficult to delineate their composition using short-read RNA sequencing, particularly for long and multi-exonic circRNAs. Here, we use long-read nanopore sequencing of nicked circRNAs (circNick-LRS) and characterize a total of 18,266 and 39,623 circRNAs in human and mouse brain, respectively. We further develop an approach for targeted long-read sequencing of a panel of circRNAs (circPanel-LRS), eliminating the need for prior circRNA enrichment and find >30 circRNA isoforms on average per targeted locus. Our data show that circRNAs exhibit a large number of splicing events such as novel exons, intron retention and microexons that preferentially occur in circRNAs. We propose that altered exon usage in circRNAs may reflect resistance to nonsense-mediated decay in the absence of translation.

OriginalsprogEngelsk
Artikelnummer4825
TidsskriftNature Communications
Vol/bind12
ISSN2041-1723
DOI
StatusUdgivet - aug. 2021

Bibliografisk note

Funding Information:
We acknowledge the support of this project by Danish Council for Independent Research (4181-00446B), the Novo Nordisk Foundation (NNF18OC0032824), and the Villum Foundation (00013393). We are grateful to Anne Færch Nielsen and Thomas Birkballe Hansen for editing and critical reading of the manuscript.

Publisher Copyright:
© 2021, The Author(s).

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