Reverse complementary matches simultaneously promote both back-splicing and exon-skipping

Abstract

Circular RNAs (circRNAs) play diverse roles in different biological and physiological environments and are always expressed in a tissue-specific manner. Tissue-specific circRNA expression profile can help understand how circRNAs are regulated. Here, using large-scale neuron isolation from the first larval stage of Caenorhabditis elegans (C. elegans) followed by whole-transcriptome RNA sequencing, I provide the first neuronal circRNA data in C. elegans. I show that circRNAs are highly expressed in the neurons of C. elegans and are preferably derived from neuronal genes. More importantly, reverse complementary matches in circRNA-flanking introns are not only required for back-splicing but also promote the skipping of exon(s) to be circularized. Interestingly, one pair of RCM in zip-2 is highly conserved across five nematode ortholog genes, which show conserved exon-skipping patterns. Finally, through one-by-one mutagenesis of all the splicing sites and branch points required for exon-skipping and back-splicing in the zip-2 gene, I show that exon-skipping is not absolutely required for back-splicing, neither the other way. Instead, the coupled exon-skipping and back-splicing are happening at the same time.