title: Quaking and PTB control overlapping splicing regulatory networks during muscle cell differentiation.
abstract: Alternative splicing contributes to muscle development, but a complete set of muscle-splicing factors and their combinatorial interactions are unknown. Previous work identified ACUAA ("STAR" motif) as an enriched intron sequence near muscle-specific alternative exons such as Capzb exon 9. Mass spectrometry of myoblast proteins selected by the Capzb exon 9 intron via RNA affinity chromatography identifies Quaking (QK), a protein known to regulate mRNA function through ACUAA motifs in 3' UTRs. We find that QK promotes inclusion of Capzb exon 9 in opposition to repression by polypyrimidine tract-binding protein (PTB). QK depletion alters inclusion of 406 cassette exons whose adjacent intron sequences are also enriched in ACUAA motifs. During differentiation of myoblasts to myotubes, QK levels increase two- to threefold, suggesting a mechanism for QK-responsive exon regulation. Combined analysis of the PTB- and QK-splicing regulatory networks during myogenesis suggests that 39% of regulated exons are under the control of one or both of these splicing factors. This work provides the first evidence that QK is a global regulator of splicing during muscle development in vertebrates and shows how overlapping splicing regulatory networks contribute to gene expression programs during differentiation.
authors.affiliation: RNA Center, Department of Molecular, Cell, and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California 95064, USA.
authors.forename: Megan P
authors.initials: MP
authors.lastname: Hall
authors.forename: Roland J
authors.initials: RJ
authors.lastname: Nagel
authors.forename: W Samuel
authors.initials: WS
authors.lastname: Fagg
authors.forename: Lily
authors.initials: L
authors.lastname: Shiue
authors.forename: Melissa S
authors.initials: MS
authors.lastname: Cline
authors.forename: Rhonda J
authors.initials: RJ
authors.lastname: Perriman
authors.forename: John Paul
authors.initials: JP
authors.lastname: Donohue
authors.forename: Manuel
authors.initials: M
authors.lastname: Ares
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D001665:Binding Sites; D002454:Cell Differentiation / Q000235:genetics*; D002478:Cells, Cultured; D005091:Exons; D018507:Gene Expression Regulation, Developmental; D053263:Gene Regulatory Networks; D006367:HeLa Cells; D006801:Humans; D007438:Introns; D032342:Muscle Cells / Q000166:cytology / Q000378:metabolism; D024510:Muscle Development / Q000235:genetics; D009928:Organ Specificity; D038941:Polypyrimidine Tract-Binding Protein / Q000235:genetics / Q000378:metabolism; D012326:RNA Splicing / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D020413:3' Untranslated Regions; C490832:QKI protein, human; D016601:RNA-Binding Proteins; D038941:Polypyrimidine Tract-Binding Protein