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

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 .

SUBMITTER: Zheng Y

PROVIDER: S-EPMC6339429 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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

Zheng Yi Y Ji Peifeng P Chen Shuai S Hou Lingling L Zhao Fangqing F

Genome medicine 20190119 1

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 ...[more]

PMID: 30660194

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