Nanopore long-read sequencing of circRNAs

TY - JOUR

T1 - Nanopore long-read sequencing of circRNAs

AU - Rahimi, Karim

AU - Færch Nielsen, Anne

AU - Venø, Morten T.

AU - Kjems, Jørgen

N1 - Publisher Copyright: © 2021 The Authors

PY - 2021/12

Y1 - 2021/12

N2 - 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.

AB - 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.

KW - Alternative splicing

KW - Back splice junction

KW - CircRNA

KW - Long-read

KW - Nanopore sequencing

UR - http://www.scopus.com/inward/record.url?scp=85116461125&partnerID=8YFLogxK

U2 - 10.1016/j.ymeth.2021.09.010

DO - 10.1016/j.ymeth.2021.09.010

M3 - Journal article

C2 - 34571139

AN - SCOPUS:85116461125

SN - 1046-2023

VL - 196

SP - 23

EP - 29

JO - Methods

JF - Methods

ER -