Engineering circular RNA expression systems to minimize contaminating linear RNA byproducts
Year: 2026
Type: preprint
Abstract: ABSTRACT Circular RNAs (circRNAs) are generated by backsplicing of eukaryotic protein-coding transcripts and can regulate microRNAs and RNA binding proteins, or serve as translation templates. Their covalently closed structure confers resistance to exonuclease-mediated degradation, extending their half-life and supporting their development as RNA therapeutics. However, existing overexpression methods often yield substantial contaminating linear RNAs, limiting their utility. Here, we systematically benchmarked plasmid-based circRNA overexpression strategies in human cells, comparing spliceosome- and ribozyme-based mechanisms across constructs incorporating widely used flanking sequences. The ribozyme-based Tornado system produced the highest circRNA yield but introduced extraneous “molecular scars” into the mature product. By contrast, spliceosome-mediated circularization using introns from the Drosophila Laccase2 gene, which contain imperfect complementary repeats, produced scarless circRNA with substantially lower linear RNA contamination. Linear RNA was further reduced by engineering the primary transcript to terminate in a non-polyadenylated end, increasing its susceptibility to exonucleases. Building on this optimized system, we developed a dual-output platform co-expressing a linear fluorescent reporter alongside a circRNA from a single promoter (CIRCUS, circ RNA and u pstream linear s ystem), enabling efficient screening of circRNA-driven cellular phenotypes, including site-specific A-to-I editing of target mRNAs. Together, this toolkit provides high-purity circRNA production suitable for mechanistic studies and circRNA-based therapeutic development.
Institutions: Baylor College of Medicine, Flinders University
Language: English
Topic: Circular RNAs in diseases
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Awards: G1064628705, Circular RNAs as genome destabilisers in human disease, CyTOF XT with Hyperion XTi platform, G5750893613, G6039749861, Advanced Multiparameter Cytometry and Cell Sorting Core, G699606022, Recruitment of Rising Stars, G7837447426, G9000240210, Regulatory roles for the Integrator complex and circular RNAs, Baylor College of Medicine Cancer Center - Cancer Center Support Grant, BD FACSDiscover S8 Spectral and Imaging Cell Sorter
OpenAlex ID: W7212273570