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The Glycogen Synthase Kinase-3 Phosphoproteome: GSK-3 Phosphorylates Multiple Splicing Factors and Regulates Alternative Splicing

ABSTRACT: Glycogen Synthase Kinase-3 (GSK-3) is a constitutively active, ubiquitously expressed protein kinase that regulates multiple signaling pathways. Over 100 putative GSK-3 substrates have been reported in diverse cell types based on in vitro kinase assays or genetic and pharmacological manipulation of GSK-3. Many more have been predicted based on a recurrent GSK-3 consensus motif, but this prediction has not been tested by analyzing the GSK-3 phosphoproteome. We used stable isotope labeling of amino acids in culture (SILAC) and mass spectrometry to analyze the repertoire of GSK-3 dependent substrates in mouse embryonic stem cells (ESCs). A comparison of wild-type and Gsk3a;Gsk3b knockout (DKO) ESCs revealed prominent GSK-3-dependent phosphorylation of multiple splicing factors and regulators of RNA biosynthesis, as well as proteins that regulate transcription, translation, and cell division. We demonstrate direct, GSK-3-dependent phosphorylation of the splicing factors RBM8A and PSF as well as the nucleolar protein NPM1. RNA sequencing to compare the transcriptomes of wild-type and Gsk3 DKO ESCs identified more than 210 genes that are alternatively spliced in a GSK-3-dependent manner, supporting a broad role for GSK-3 in regulating alternative splicing. Overall, this study provides the first unbiased analysis of the GSK-3 phosphoproteome and strong evidence for GSK-3 as a regulator of alternative splicing.

ORGANISM(S): Mus musculus

PROVIDER: GSE90921 | GEO | 2017/08/24

SECONDARY ACCESSION(S): PRJNA356332

REPOSITORIES: GEO

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Project description:Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia-Absent Radius (TAR) Syndrome is a rare congenital disease presenting with reduced blood platelets (megakaryocytic thrombocytopenia) and forelimb anomalies, concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing, transport, and nonsense-mediated decay. How perturbing a general mRNA-processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here, we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity (PCP) signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function, we find a significant reduction of cd41-positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a-mutant zebrafish embryos already after gastrulation accumulate mRNAs with erroneously included introns, a hallmark of defective nonsense-mediated decay. Affected mRNAs include transcripts encoding components of the non-canonical Wnt pathway involved in PCP signaling, and rbm8a mutant-embryos show hallmarks of Wnt/PCP-dependent, early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b, wnt11f2, fzd7a, and vangl2. Following axis formation, rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm (LPM) that forms the hematopoietic, cardiovascular, kidney, and forelimb skeleton progenitors. Subsequently, rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a, kdrl, sox7, and the megakaryocyte regulator gfi1aa. Lastly, we document similar hematopoietic defects upon loss of vangl2. Together, our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.

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The Glycogen Synthase Kinase-3 Phosphoproteome: GSK-3 Phosphorylates Multiple Splicing Factors and Regulates Alternative Splicing

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