circRNA Biogenesis Competes with Pre-mRNA Splicing

Circular RNAs (circRNAs) are widely expressed noncoding RNAs. However, their biogenesis and possible functions are poorly understood. Here, by studying circRNAs that we identified in neuronal tissues, we provide evidence that animal circRNAs are generated cotranscriptionally and that their production rate is mainly determined by intronic sequences. We demonstrate that circularization and splicing compete against each other. These mechanisms are tissue specific and conserved in animals. Interestingly, we observed that the second exon of the splicing factor muscleblind (MBL/MBNL1) is circularized in flies and humans. This circRNA (circMbl) and its flanking introns contain conserved muscleblind binding sites, which are strongly and specifically bound by MBL. Modulation of MBL levels strongly affects circMbl biosynthesis, and this effect is dependent on the MBL binding sites. Together, our data suggest that circRNAs can function in gene regulation by competing with linear splicing. Furthermore, we identified muscleblind as a factor involved in circRNA biogenesis. [Display omitted] •circRNAs are generated cotranscriptionally•circRNA production rate is mainly mediated by intronic sequences•circRNA production competes with canonical pre-mRNA splicing•muscleblind interacts with flanking introns to promote exon circularization Ashwal-Fluss et al. provide evidence that circRNA production competes with linear mRNA splicing. They demonstrate that intronic sequences largely determine the production rate of circRNAs and identify a splice factor (muscleblind) that can promote circularization.