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

Marina Danilenko, Caroline Dalgliesh, Vittoria Pagliarini, Chiara Naro, Ingrid Ehrmann, Mikael Feracci, Mahsa Kheirollahi-Chadegani, Alison Tyson-Capper, Gavin J. Clowry, Philippe Fort, Cyril Dominguez, Claudio Sette, David J. Elliott

Research output: Contribution to journalArticle

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.

Original languageEnglish
JournalNucleic Acids Research
DOIs
Publication statusE-pub ahead of print - Dec 19 2016

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Exons
Binding Sites
RNA
Proteins
Joints
RNA Precursors
Amino Acids
Brain

Keywords

  • Journal Article

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Binding site density enables paralog-specific activity of SLM2 and Sam68 proteins in Neurexin2 AS4 splicing control. / Danilenko, Marina; Dalgliesh, Caroline; Pagliarini, Vittoria; Naro, Chiara; Ehrmann, Ingrid; Feracci, Mikael; Kheirollahi-Chadegani, Mahsa; Tyson-Capper, Alison; Clowry, Gavin J.; Fort, Philippe; Dominguez, Cyril; Sette, Claudio; Elliott, David J.

In: Nucleic Acids Research, 19.12.2016.

Research output: Contribution to journalArticle

Danilenko, M, Dalgliesh, C, Pagliarini, V, Naro, C, Ehrmann, I, Feracci, M, Kheirollahi-Chadegani, M, Tyson-Capper, A, Clowry, GJ, Fort, P, Dominguez, C, Sette, C & Elliott, DJ 2016, 'Binding site density enables paralog-specific activity of SLM2 and Sam68 proteins in Neurexin2 AS4 splicing control', Nucleic Acids Research. https://doi.org/10.1093/nar/gkw1277
Danilenko, Marina ; Dalgliesh, Caroline ; Pagliarini, Vittoria ; Naro, Chiara ; Ehrmann, Ingrid ; Feracci, Mikael ; Kheirollahi-Chadegani, Mahsa ; Tyson-Capper, Alison ; Clowry, Gavin J. ; Fort, Philippe ; Dominguez, Cyril ; Sette, Claudio ; Elliott, David J. / Binding site density enables paralog-specific activity of SLM2 and Sam68 proteins in Neurexin2 AS4 splicing control. In: Nucleic Acids Research. 2016.
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T1 - Binding site density enables paralog-specific activity of SLM2 and Sam68 proteins in Neurexin2 AS4 splicing control

AU - Danilenko, Marina

AU - Dalgliesh, Caroline

AU - Pagliarini, Vittoria

AU - Naro, Chiara

AU - Ehrmann, Ingrid

AU - Feracci, Mikael

AU - Kheirollahi-Chadegani, Mahsa

AU - Tyson-Capper, Alison

AU - Clowry, Gavin J.

AU - Fort, Philippe

AU - Dominguez, Cyril

AU - Sette, Claudio

AU - Elliott, David J.

N1 - © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

PY - 2016/12/19

Y1 - 2016/12/19

N2 - 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.

AB - 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.

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