Characteristics of plant circular RNAs

Qinjie Chu; Panpan Bai; Xintian Zhu; Xingchen Zhang; Lingfeng Mao; Qian-Hao Zhu; Longjiang Fan; Chu-Yu Ye

doi:10.1093/bib/bby111

Characteristics of plant circular RNAs

Brief Bioinform. 2020 Jan 17;21(1):135-143. doi: 10.1093/bib/bby111.

Authors

Qinjie Chu^{1

2}, Panpan Bai¹, Xintian Zhu^{1

2}, Xingchen Zhang¹, Lingfeng Mao^{1

2}, Qian-Hao Zhu³, Longjiang Fan^{1

2}, Chu-Yu Ye¹

Affiliations

¹ Institute of Crop Science, Zhejiang University, Hangzhou, China.
² Institute of Bioinformatics, Zhejiang University, Hangzhou, China.
³ CSIRO Agriculture and Food, Canberra, Australia.

PMID: 30445438
DOI: 10.1093/bib/bby111

Abstract

Circular RNA (circRNA) is a kind of covalently closed single-stranded RNA molecules that have been proved to play important roles in transcriptional regulation of genes in diverse species. With the rapid development of bioinformatics tools, a huge number (95143) of circRNAs have been identified from different plant species, providing an opportunity for uncovering the overall characteristics of plant circRNAs. Here, based on publicly available circRNAs, we comprehensively analyzed characteristics of plant circRNAs with the help of various bioinformatics tools as well as in-house scripts and workflows, including the percentage of coding genes generating circRNAs, the frequency of alternative splicing events of circRNAs, the non-canonical splicing signals of circRNAs and the networks involving circRNAs, miRNAs and mRNAs. All this information has been integrated into an upgraded online database, PlantcircBase 3.0 (http://ibi.zju.edu.cn/plantcircbase/). In this database, we provided browse, search and visualization tools as well as a web-based blast tool, BLASTcirc, for prediction of circRNAs from query sequences based on searching against plant genomes and transcriptomes.

Keywords: BLASTcirc; PlantcircBase; non-canonical splicing signals; plant circRNAs.