Nuclear total RNA sequencing reveals primary sequence context of recursive splicing in long genes

Background Recursive splicing (RS) is a mechanism to excise long introns from messenger RNA precursors. We focused on nuclear RNA, which is enriched for RS splicing intermediates and nascent transcripts, to investigate RS in the mouse brain.

Results We identified novel RS sites and discovered that RS is constitutive between excitatory and inhibitory neurons and between sexes in the mouse cerebral cortex. We found that the primary sequence context, including the U1 snRNA binding site, the polypyrimidine tract, and a strong 3’ splice site, distinguishes the RS AGGT site from hundreds of non-RS AGGT sites in the same intron. Moreover, we uncovered a new type of exon-like RS events termed exonicRS.

Conclusions We demonstrate that nuclear total RNA sequencing is an efficient approach to identify RS events. We find the importance of the primary sequence context in the definition of RS AGGT sites. The exonicRS may represent an intermediate stage of RS sites evolving into annotated exons. Overall, our findings provide novel insights into the mechanisms of RS in long genes.