Binding site density enables paralog-specific activity of SLM2 and Sam68 proteins in Neurexin2 AS4 splicing control

Marina Danilenko (1) , Caroline Dalgliesh (1) , Vittoria Pagliarini (2) , Chiara Naro (3) , Ingrid Ehrmann (1) , Mikael Feracci (4) , Mahsa Kheirollahi-Chadegani (1) , Alison Tyson-Capper (5) , Gavin Clowry , Philippe Fort (6) , Cyril Dominguez (7) , Claudio Sette (2) , David Elliott (8)

1 NEWCASTLE UNIVERSITY - Institute of Human Genetics
2 Department of Biomedicine and Prevention
3 Fondazione Santa Lucia [IRCCS]
4 Univ Leicester, Dept Mol & Cell Biol, Henry Wellcome Bldg,Lancaster Rd, Leicester LE1 7RH, Leics, England
5 Newcastle University [Newcastle]
6 CRBM - Centre de recherche en Biologie cellulaire de Montpellier
7 University of Leicester
8 Institute of Genetic Medicine [Newcastle, U.K.]

SLM2 and Sam68 are splicing regulator paralogs that usually overlap in function, yet only SLM2 and not Sam68 controls the Neurexin2 AS4 exon important for brain function. Herein we find that SLM2 and Sam68 similarly bind to Neurexin2 pre-mRNA, both within the mouse cortex and in vitro. Protein domain-swap experiments identify a region including the STAR domain that differentiates SLM2 and Sam68 activity in splicing target selection, and confirm that this is not established via the variant amino acids involved in RNA contact. However, far fewer SLM2 and Sam68 RNA binding sites flank the Neurexin2 AS4 exon, compared with those flanking the Neurexin1 and Neurexin3 AS4 exons under joint control by both Sam68 and SLM2. Doubling binding site numbers switched paralog sensitivity, by placing the Neurexin2 AS4 exon under joint splicing control by both Sam68 and SLM2. Our data support a model where the density of shared RNA binding sites around a target exon, rather than different paralog-specific protein-RNA binding sites, controls functional target specificity between SLM2 and Sam68 on the Neurexin2 AS4 exon. Similar models might explain differential control by other splicing regulators within families of paralogs with indistinguishable RNA binding sites.

Domaines: Embryologie et organogenèse; Cancer; Systématique, phylogénie et taxonomie; Organisation et fonctions cellulaires [q-bio.SC]

Marina Danilenko, Caroline Dalgliesh, Vittoria Pagliarini, Chiara Naro, Ingrid Ehrmann, et al.. Binding site density enables paralog-specific activity of SLM2 and Sam68 proteins in Neurexin2 AS4 splicing control. Nucleic Acids Research, 2017, 45, pp.gkw1277. ⟨10.1093/nar/gkw1277⟩. ⟨hal-02267219⟩