Analysis of circular RNAs by the Oxford Nanopore long-read sequencing platform
Circular RNAs (circRNAs) are a class of ring-link regulatory RNAs that are important for the regulation of how genes are expressed in a cell. This has important implications in different diseases, such as cancer. The expression of a circRNA can be analyzed on the global level of a cell by using high-throughput sequencing, such as the Illumina platform. The problem is that those techniques produce only short fragments and allow not to reveal the full sequence of a circRNA. However, that is important to study its function. The recently emerged long-read sequencing techniques, such as Oxford Nanopore bear great potential to obtain this missing information. We adapted a protocol to sequence circRNAs by Oxford Nanopore and tested this on 4 different anaplastic large-cell lymphoma cell lines. By this means we identified 1000s of different circRNAs, of which >99% are discovered in full-length and further validated candidates in vitro. Taken together, this protocol enables reliable full-length analysis of circRNAs, a noncoding RNA type involved in a growing number of physiologic and pathologic conditions.
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PLoS One. 2022 Sep 7;17(9):e0273253.doi: 10.1371/journal.pone.0273253. eCollection 2022.
Generation of full-length circular RNA libraries for Oxford Nanopore long-read sequencing
Steffen Fuchs, Loélia Babin, Elissa Andraos, Chloé Bessiere, Semjon Willier, Johannes H Schulte, Christine Gaspin, Fabienne Meggetto
Collaborations and acknowledgements
INRAE Toulouse, Dr. Christine Gaspin
- Association Eva pour la Vie,
- Grandir Sans Cancer,
- La ligue contre le cancer (Equipes Labeliseé 2017-2021),
- TOUCAN/Laboratory of Excellence Toulouse Cancer
Toulouse Cancer Research Center (Oncopole)
Toulouse – FR
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