期刊
GENOME MEDICINE
卷 11, 期 -, 页码 -出版社
BMC
DOI: 10.1186/s13073-019-0614-1
关键词
Alternative splicing; Circular RNA (circRNA); Transcript reconstruction; Isoform quantification
资金
- NSFC [31722031, 91640117, 91531306, 31701148]
- National Key RD Program [2018YFC0910400]
- Beijing Natural Science Foundation [JQ18020]
- Strategic Priority Research Program of the Chinese Academy of Sciences [XDB13000000]
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.
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