title: Differential connectivity of splicing activators and repressors to the human spliceosome.
abstract: BACKGROUND
  During spliceosome assembly, protein-protein interactions (PPI) are sequentially formed and disrupted to accommodate the spatial requirements of pre-mRNA substrate recognition and catalysis. Splicing activators and repressors, such as SR proteins and hnRNPs, modulate spliceosome assembly and regulate alternative splicing. However, it remains unclear how they differentially interact with the core spliceosome to perform their functions.
  
  
  RESULTS
  Here, we investigate the protein connectivity of SR and hnRNP proteins to the core spliceosome using probabilistic network reconstruction based on the integration of interactome and gene expression data. We validate our model by immunoprecipitation and mass spectrometry of the prototypical splicing factors SRSF1 and hnRNPA1. Network analysis reveals that a factor's properties as an activator or repressor can be predicted from its overall connectivity to the rest of the spliceosome. In addition, we discover and experimentally validate PPIs between the oncoprotein SRSF1 and members of the anti-tumor drug target SF3 complex. Our findings suggest that activators promote the formation of PPIs between spliceosomal sub-complexes, whereas repressors mostly operate through protein-RNA interactions.
  
  
  CONCLUSIONS
  This study demonstrates that combining in-silico modeling with biochemistry can significantly advance the understanding of structure and function relationships in the human spliceosome.
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.|Present address: Envisagenics, Inc, 315 Main St., 2nd floor, Huntington, NY, 11743, USA.
authors.forename: Martin
authors.initials: M
authors.lastname: Akerman
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.|Watson School of Biological Sciences, Cold Spring Harbor, NY, 11724, USA.|Present address: Fred Hutchinson Cancer Research Center, Division of Human Biology, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
authors.forename: Oliver I
authors.initials: OI
authors.lastname: Fregoso
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
authors.forename: Shipra
authors.initials: S
authors.lastname: Das
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.|Present address: New England Biolabs, 240 County Road, Ipswich, MA, 01938, UK.
authors.forename: Cristian
authors.initials: C
authors.lastname: Ruse
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.|Present address: Santaris Pharma A/S, Horsholm, Denmark.
authors.forename: Mads A
authors.initials: MA
authors.lastname: Jensen
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
authors.forename: Darryl J
authors.initials: DJ
authors.lastname: Pappin
authors.affiliation: Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, 75080, USA.|Bioinformatics Division, TNLIST, Tsinghua University, Beijing, 100084, China.
authors.forename: Michael Q
authors.initials: MQ
authors.lastname: Zhang
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. krainer@cshl.edu.
authors.forename: Adrian R
authors.initials: AR
authors.lastname: Krainer
mesh_terms: D017398:Alternative Splicing; D003198:Computer Simulation; D000076245:Heterogeneous Nuclear Ribonucleoprotein A1; D034481:Heterogeneous-Nuclear Ribonucleoprotein Group A-B / Q000378:metabolism*; D006801:Humans; D015233:Models, Statistical; D025941:Protein Interaction Mapping; D000068103:Serine-Arginine Splicing Factors / Q000378:metabolism*; D017381:Spliceosomes / Q000378:metabolism*
chemical_list: D000076245:Heterogeneous Nuclear Ribonucleoprotein A1; D034481:Heterogeneous-Nuclear Ribonucleoprotein Group A-B; C000595779:SRSF1 protein, human; C000619656:hnRNPA1 protein, human; D000068103:Serine-Arginine Splicing Factors