Differential connectivity of splicing activators and repressors to the human spliceosome

Akerman, M., Fregoso, O. I., Das, S., Ruse, C., Jensen, M. A., Pappin, D. J., Zhang, M. Q., Krainer, A. R. (June 2015) Differential connectivity of splicing activators and repressors to the human spliceosome. Genome Biol, 16 (1). p. 119. ISSN 1465-6914 (Electronic)1465-6906 (Linking)

URL: http://www.ncbi.nlm.nih.gov/pubmed/26047612
DOI: 10.1186/s13059-015-0682-5

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.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > spliceosome complex
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > splicing factor
CSHL Authors:
Communities: CSHL Cancer Center Program > Gene Regulation and Cell Proliferation
CSHL Cancer Center Program > Signal Transduction
CSHL Cancer Center Shared Resources > Antibody and Phage Display Service
CSHL labs > Krainer lab
CSHL labs > Pappin lab
Watson School > Publications
CSHL Cancer Center Shared Resources > Mass Spectrometry Service
CSHL Cancer Center Shared Resources > Proteomics Service
Depositing User: Matt Covey
Date: 6 June 2015
Date Deposited: 09 Jun 2015 17:00
Last Modified: 30 Oct 2015 14:31
URI: http://repository.cshl.edu/id/eprint/31567

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