Nanopore long-read sequencing of circRNAs

Karim Rahimi*, Anne Færch Nielsen, Morten T. Venø, Jørgen Kjems

*Corresponding author for this work

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

1 Citation (Scopus)
80 Downloads (Pure)

Abstract

Circular RNA (circRNA) is a group of highly stable RNA molecules with suggested roles in development and disease. They derive from linear pre-mRNAs when a 5′-splice site splices back to an upstream 3′-splice site in a process termed back-splicing. Most circRNAs are multi-exonic and may contain several thousand nucleotides. The extensive sequence overlap between the linear and circular forms of an RNA means that circRNA identification depends on the detection of back-splice-junction sequence reads that are unique to the circRNA. However, the short-read length obtained using standard next-generation sequencing techniques means that the internal sequence, exon composition and alternative splicing of circRNAs are unknown in many cases. Recently, several labs, including ours, have reported protocols for sequencing of circRNAs using long-read nanopore sequencing and thereby expanded our understanding of circRNA size distribution and internal splicing patterns. Here, we review these protocols and discuss the different approaches taken to study the full length composition of circRNAs.

Original languageEnglish
JournalMethods
Volume196
Pages (from-to)23-29
Number of pages7
ISSN1046-2023
DOIs
Publication statusPublished - Dec 2021

Keywords

  • Alternative splicing
  • Back splice junction
  • CircRNA
  • Long-read
  • Nanopore sequencing

Fingerprint

Dive into the research topics of 'Nanopore long-read sequencing of circRNAs'. Together they form a unique fingerprint.

Cite this