title: αCP binding to a cytosine-rich subset of polypyrimidine tracts drives a novel pathway of cassette exon splicing in the mammalian transcriptome.
abstract: Alternative splicing (AS) is a robust generator of mammalian transcriptome complexity. Splice site specification is controlled by interactions of cis-acting determinants on a transcript with specific RNA binding proteins. These interactions are frequently localized to the intronic U-rich polypyrimidine tracts (PPT) located 5' to the majority of splice acceptor junctions. αCPs (also referred to as polyC-binding proteins (PCBPs) and hnRNPEs) comprise a subset of KH-domain proteins with high affinity and specificity for C-rich polypyrimidine motifs. Here, we demonstrate that αCPs promote the splicing of a defined subset of cassette exons via binding to a C-rich subset of polypyrimidine tracts located 5' to the αCP-enhanced exonic segments. This enhancement of splice acceptor activity is linked to interactions of αCPs with the U2 snRNP complex and may be mediated by cooperative interactions with the canonical polypyrimidine tract binding protein, U2AF65. Analysis of αCP-targeted exons predicts a substantial impact on fundamental cell functions. These findings lead us to conclude that the αCPs play a direct and global role in modulating the splicing activity and inclusion of an array of cassette exons, thus driving a novel pathway of splice site regulation within the mammalian transcriptome.
authors.affiliation: Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA jixinjun@mail.med.upenn.edu.
authors.forename: Xinjun
authors.initials: X
authors.lastname: Ji
authors.affiliation: Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA KBRIN Bioinformatics Core, University of Louisville, Louisville, KY 40202, USA.
authors.forename: Juw Won
authors.initials: JW
authors.lastname: Park
authors.affiliation: Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Emad
authors.initials: E
authors.lastname: Bahrami-Samani
authors.affiliation: Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Lan
authors.initials: L
authors.lastname: Lin
authors.affiliation: Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Duncan-Lewis
authors.affiliation: Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Gordon
authors.initials: G
authors.lastname: Pherribo
authors.affiliation: Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA yxing@ucla.edu.
authors.forename: Yi
authors.initials: Y
authors.lastname: Xing
authors.affiliation: Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA liebhabe@mail.med.upenn.edu.
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Liebhaber
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics / Q000378:metabolism; D017398:Alternative Splicing; D001483:Base Sequence; D001665:Binding Sites; D051357:Cyclin-Dependent Kinase 2 / Q000235:genetics / Q000378:metabolism; D003596:Cytosine / Q000378:metabolism; D004268:DNA-Binding Proteins; D005091:Exons; D005786:Gene Expression Regulation; D034441:Heterogeneous-Nuclear Ribonucleoproteins / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D007438:Introns; D020014:K562 Cells; D008969:Molecular Sequence Data; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism*; D011108:Polymers / Q000378:metabolism; D011485:Protein Binding; D011743:Pyrimidines / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D017413:Ribonucleoprotein, U2 Small Nuclear / Q000235:genetics / Q000378:metabolism*; D012261:Ribonucleoproteins / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D000072668:Splicing Factor U2AF; D059467:Transcriptome
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D004268:DNA-Binding Proteins; D034441:Heterogeneous-Nuclear Ribonucleoproteins; D009687:Nuclear Proteins; C094604:PCBP1 protein, human; C501903:PCBP2 protein, human; D011108:Polymers; D011743:Pyrimidines; D016601:RNA-Binding Proteins; D017413:Ribonucleoprotein, U2 Small Nuclear; D012261:Ribonucleoproteins; C518910:SH2B1 protein, human; D000072668:Splicing Factor U2AF; C000607494:U2AF2 protein, human; D003596:Cytosine; C495894:CDK2 protein, human; D051357:Cyclin-Dependent Kinase 2