Advances in circular RNA detection

CIRI-full is a new method for full-length and isoform-level quantification of circular RNAs

Reconstruction of full-length circular RNAs enables isoform-level quantification

Yi Zheng†,
Peifeng Ji†,
Shuai Chen,
Lingling Hou and
Fangqing ZhaoEmail author View ORCID ID profile

†Contributed equally

Genome Medicine201911:2

https://doi.org/10.1186/s13073-019-0614-1

Received: 3 July 2018
Accepted: 10 January 2019
Published: 19 January 2019

Abstract

Currently, circRNA studies are shifting from the identification of circular transcripts to understanding their biological functions. However, such endeavors have been limited by large-scale determination of their full-length sequences and also by the inability of accurate quantification at the isoform level. Here, we propose a new feature, reverse overlap (RO), for circRNA detection, which outperforms back-splice junction (BSJ)-based methods in identifying low-abundance circRNAs. By combining RO and BSJ features, we present a novel approach for effective reconstruction of full-length circRNAs and isoform-level quantification from the transcriptome. We systematically compared the difference between the BSJ-level and isoform-level differential expression analyses using human liver tumor and normal tissues and highlight the necessity of deepening circRNA studies to the isoform-level resolution. The CIRI-full software can be accessed at https://sourceforge.net/projects/ciri.