title: Binding site density enables paralog-specific activity of SLM2 and Sam68 proteins in Neurexin2 AS4 splicing control.
abstract: 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.
authors.affiliation: Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK.
authors.forename: Marina
authors.initials: M
authors.lastname: Danilenko
authors.affiliation: Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK.
authors.forename: Caroline
authors.initials: C
authors.lastname: Dalgliesh
authors.affiliation: Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy.|Laboratory of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy.
authors.forename: Vittoria
authors.initials: V
authors.lastname: Pagliarini
authors.affiliation: Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy.|Laboratory of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Naro
authors.affiliation: Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK.
authors.forename: Ingrid
authors.initials: I
authors.lastname: Ehrmann
authors.affiliation: Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK.
authors.forename: Mikael
authors.initials: M
authors.lastname: Feracci
authors.affiliation: Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK.
authors.forename: Mahsa
authors.initials: M
authors.lastname: Kheirollahi-Chadegani
authors.affiliation: Institute for Cellular Medicine, Newcastle University, Framlington Place, Newcastle NE2 4HH, UK.
authors.forename: Alison
authors.initials: A
authors.lastname: Tyson-Capper
authors.affiliation: Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle, UK.
authors.forename: Gavin J
authors.initials: GJ
authors.lastname: Clowry
authors.affiliation: Université Montpellier, UMR 5237, Centre de Recherche de Biologie cellulaire de Montpellier, CNRS, 34293 Montpellier, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Fort
authors.affiliation: Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK.
authors.forename: Cyril
authors.initials: C
authors.lastname: Dominguez
authors.affiliation: Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy.|Laboratory of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Sette
authors.affiliation: Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK.
authors.forename: David J
authors.initials: DJ
authors.lastname: Elliott
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics / Q000378:metabolism*; D017398:Alternative Splicing; D000818:Animals; D001665:Binding Sites; D005091:Exons; D007438:Introns; D051379:Mice; D018345:Mice, Knockout; D009419:Nerve Tissue Proteins / Q000235:genetics* / Q000378:metabolism; D000072417:Protein Domains; D012322:RNA Precursors / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D048868:Adaptor Proteins, Signal Transducing; C513253:Khdrbs1 protein, mouse; C486528:Khdrbs3 protein, mouse; D009419:Nerve Tissue Proteins; D012322:RNA Precursors; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; C093175:neurexin II