Trans-splicing facilitated by RNA pairing greatly expands sDscam isoform diversity but not homophilic binding specificity

The Down syndrome cell adhesion molecule 1 (Dscam1) gene can generate tens of thousands of isoforms via alternative splicing, which is essential for nervous and immune functions. Chelicerates generate approximately 50 to 100 shortened Dscam (sDscam) isoforms by alternative promoters, similar to mammalian protocadherins. Here, we reveal that trans-splicing markedly increases the repository of sDscam. isoforms in Tetranychus urticae. Unexpectedly, every variable exon cassette engages in trans-splicing with constant exons from another cluster. Moreover, we provide evidence that competing RNA pairing not only governs alternative cis-splicing but also facilitates trans-splicing. Trans-spliced sDscam isoforms mediate cell adhesion ability but exhibit the same homophilic binding specificity as their cis-spliced counterparts. Thus, we reveal a single sDscam locus that generates diverse adhesion molecules through cis- and trans-splicing coupled with alternative promoters. These findings expand understanding of the mechanism underlying molecular diversity and have implications for the molecular control of neuronal and/or immune specificity.

Automated summary

The Down syndrome cell adhesion molecule 1 (Dscam1) gene generates tens of thousands of isoforms through alternative splicing, and trans-splicing markedly increases the repertoire of shortened Dscam (sDscam) isoforms in Tetranychus urticae. These trans-spliced sDscam isoforms exhibit cell adhesion ability and share the same binding specificity as their cis-spliced counterparts, providing molecular diversity and implications for neuronal and/or immune specificity.