Both canonical and back-splicing occur frequently in the mammalian brain, and events from both processes have been show to play essential roles during neural development. The biogenesis of circRNA through back-splicing employs at least partial of the splicing machinery required for canonical splicing. How is the regulation of these two splicing processes coordinated to confer them functional but distinct roles in the brain? To address this question, we employed a combination of nascent and steady-state RNA-seq data from brain derived cells. We stratified brain circRNAs based on the nature of their splice sites in the context of alternative back-splicing and canonical splicing. We also performed co-expression analysis to identify “in-sync exons” that co-vary with circRNAs in their transcript inclusion level. Finally, we compared the cis-element profile of in-sync exons versus that of their partner circRNAs.
We found that alternative back-splicing employs splice sites that often engage in alternative linear splicing. For splice sites that engage in back-splicing but with no competitive or alternative back-splice sites, they are more frequently constitutively spliced than alternatively spliced in linear transcripts. We also found that genes that harbour circRNAs with in-sync exons are enriched in diverse GO-defined biological processes and functions. Overall, our observations support the hypothesis of coordinated regulation of back-splicing and linear splicing in the brain.