Regulation of Dscam exon 17 alternative splicing by steric hindrance in combination with RNA secondary structures

Abstract

The gene Down syndrome cell adhesion molecule (Dscam) potentially encodes 38 016 distinct isoforms in Drosophila melanogaster via mutually exclusive splicing. Here we reveal a combinatorial mechanism of regulation of Dscam exon 17 mutually exclusive splicing through steric hindrance in combination with RNA secondary structure. This mutually exclusive behavior is enforced by steric hindrance, due to the close proximity of the exon 17.2 branch point to exon 17.1 in Diptera, and the interval size constraint in non-Dipteran species. Moreover, intron-exon RNA structures are evolutionarily conserved in 36 non-Drosophila species of six distantly related orders (Diptera, Lepidoptera, Coleoptera, Hymenoptera, Hemiptera, and Phthiraptera), which regulates the selection of exon 17 variants via masking the splice site. By contrast, a previously uncharacterized RNA structure specifically activated exon 17.1 by bringing splice sites closer together in Drosophila, while the other moderately suppressed exon 17.1 selection by hindering the accessibility of polypyrimidine sequences. Taken together, these data suggest a phylogeny of increased complexity in regulating alternative splicing of Dscam exon 17 spanning more than 300 million years of insect evolution. These results also provide models of the regulation of alternative splicing through steric hindrance in combination with dynamic structural codes.

Keywords: :

• mutually exclusive splicing
• steric hindrance
• RNA secondary structures
• Dscam exon 17
• evolution

10.4161/rna.27176

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

Acknowledgments

This work was partly supported by research grants from the National Natural Science Foundation of China (31125011, 31071148, 31270844), the Natural Science Foundation of Zhejiang Province (No. R3090177), the National Science and Technology Project (2012ZX09102301-009), and the Doctoral Foundation of Ministry of Education (20110101130012).

Accession Numbers

The insect Dscam gene sequences were deposited into GenBank with accession numbers KC733353-KC733360.

Supplemental Materials

Supplemental materials may be found here: www.landesbioscience.com/journals/rnabiology/article/27176/