Identification of potential proteins translated from circular RNA splice variants

• Published in: European journal of cell biology 2023-03, Vol.102 (1), p.151286-151286, Article 151286
• Main Authors: Das, Aniruddha, Sinha, Tanvi, Mishra, Smruti Sambhav, Das, Debojyoti, Panda, Amaresh C.
• Format: Article
• Language: English
• Subjects: Alternative splicing; Alternative Splicing - genetics; Backsplicing; Cap-independent translation; Circular RNA; HeLa Cells; Humans; MicroRNAs - genetics; Protein Biosynthesis; Protein Isoforms - genetics; Protein Isoforms - metabolism; RNA, Circular - genetics; RNA, Circular - metabolism; Splice variants
• ISSN: 0171-9335; 1618-1298
• DOI: 10.1016/j.ejcb.2023.151286

Circular RNAs (circRNAs) are covalently closed RNA molecules generated from precursor RNAs by the head-to-tail backsplicing of exons. Hundreds of studies demonstrated that circRNAs are ubiquitously expressed and regulate cellular events by modulating microRNA (miRNA) and RNA-binding protein (RBP) activities. A few circRNAs are also known to translate into functional polypeptides regulating cellular physiology. All these functions primarily depend on the full-length sequence of the circRNAs. CircRNA backsplice junction sequence is the key to identifying circRNAs and their full-length mature sequence. However, some multi-exonic circRNAs exist in different isoforms sharing identical backsplice junction sequences and are termed circRNA splice variants. Here, we analyzed the previously published HeLa cell RNA-seq datasets to identify circRNA splice variants using the de novo module of the CIRCexplorer2 circRNA annotation pipeline. A subset of circRNAs with splice variants was validated by the circRNA-rolling circle amplification (circRNA-RCA) method. Interestingly, several validated circRNAs were predicted to translate into proteins by the riboCIRC database. Furthermore, polyribosome fractionation followed by quantitative PCR confirmed the association of a subset of circRNAs with polyribosome supporting their protein-coding potential. Finally, bioinformatics analysis of proteins derived from splice variants of circCORO1C and circASPH suggested altered protein sequences and structures that could affect their physiological functions. Together, our study identified novel circRNA splice variants and their potential translation into protein isoforms which may regulate various physiological processes. •More than 30,000 unique backsplice junctions were identified in HeLa cells.•Over 11,000 backsplice junctions generate two or more splice variants with different sequences.•More than 700 circRNAs in HeLa cells were predicted to translate into proteins.•Novel polypeptides could be translated from circRNA splice variants.