circRIP: an accurate tool for identifying circRNA–RBP interactions

• Published in: Briefings in bioinformatics 2022-07, Vol.23 (4)
• Main Authors: Dong, Xin, Chen, Ke, Chen, Wenbo, Wang, Jun, Chang, Liuping, Deng, Jin, Wei, Lei, Han, Leng, Huang, Chunhua, He, Chunjiang
• Format: Article
• Language: English
• Subjects: Algorithms; Binding; Cell lines; Crosslinking; Gene sequencing; Genomes; Immunoprecipitation; Ribonucleic acid; RNA; RNA-binding protein; Sensitivity analysis
• ISSN: 1467-5463; 1477-4054
• DOI: 10.1093/bib/bbac186

Abstract Circular ribonucleic acids (RNAs) (circRNAs) are formed by covalently linking the downstream splice donor and the upstream splice acceptor. One of the most important functions of circRNAs is mainly exerted through binding RNA-binding proteins (RBPs). However, there is no efficient algorithm for identifying genome-wide circRNA–RBP interactions. Here, we developed a unique algorithm, circRIP, for identifying circRNA–RBP interactions from RNA immunoprecipitation sequencing (RIP-Seq) data. A simulation test demonstrated the sensitivity and specificity of circRIP. By applying circRIP, we identified 95 IGF2BP3-binding circRNAs based on the IGF2BP3 RIP-Seq dataset. We further identified 2823 and 1333 circRNAs binding to >100 RBPs in K562 and HepG2 cell lines, respectively, based on enhanced cross-linking immunoprecipitation (eCLIP) data, demonstrating the significance to survey the potential interactions between circRNAs and RBPs. In this study, we provide an accurate and sensitive tool, circRIP (https://github.com/bioinfolabwhu/circRIP), to systematically identify RBP and circRNA interactions from RIP-Seq and eCLIP data, which can significantly benefit the research community for the functional exploration of circRNAs.