Journal
BRIEFINGS IN BIOINFORMATICS
Volume 20, Issue 1, Pages 58-65Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbx089
Keywords
circular RNA; tissue-specific; Arabidopsis; super circular RNA region; RNA-Seq
Funding
- National Natural Science Foundation of China [31571306]
- Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (the second phase)
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Circular RNAs are widely existing in eukaryotes. However, there is as yet no tissue-specific Arabidopsis circular RNA database, which hinders the study of circular RNA in plants. Here, we used 622 Arabidopsis RNA sequencing data sets from 87 independent studies hosted at NCBI SRA and developed AtCircDB to systematically identify, store and retrieve circular RNAs. By analyzing back-splicing sites, we characterized 84 685 circular RNAs, 30 648 tissue-specific circular RNAs and 3486 microRNA-circular RNA interactions. In addition, we used a metric (detection score) to measure the detection ability of the circular RNAs using a big-data approach. By experimental validation, we demonstrate that this metric improves the accuracy of the detection algorithm. We also defined the regions hosting enriched circular RNAs as super circular RNA regions. The results suggest that these regions are highly related to alternative splicing and chloroplast. Finally, we developed a comprehensive tissue-specific database (AtCircDB) to help the community store, retrieve, visualize and download Arabidopsis circular RNAs. This database will greatly expand our understanding of circular RNAs and their related regulatory networks.
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