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Mus musculus

ABSTRACT: Knockdown of SR protein family in P19 cells and RNA-seq of cytoplasmic and whole cell polyA+ RNA

OTHER RELATED OMICS DATASETS IN: GSE69734

PROVIDER: PRJNA286282 | ENA |

REPOSITORIES: ENA

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Similar Datasets

Knockdown of SR protein family in P19 cells and RNA-seq of cytoplasmic and whole cell polyA+ RNA

Project description:Our data suggest that all SR proteins contribute to mRNA export via NXF1. To identify endogenous export targets we depleted all seven SR proteins individually from P19 WT cells prepared cytoplasmic fractions. We sequenced the cytoplasmic fraction and as a control whole celll RNA from the identical sample. Knockdown of seven SR Proteins plus control, total RNA and cytoplasmic RNA, polyA+ enriched, 2 biological replicates per condition, 2 technical replicates per condition

2016-03-07 | E-GEOD-69733 | biostudies-arrayexpress

Knockdown of SR protein family in P19 cells and RNA-seq of cytoplasmic and whole cell polyA+ RNA

2016-03-07 | GSE69733 | GEO

RNAi profiling by array of mouse P19 cells to investigate how SR proteins coordinate gene expression programs

Project description:Members of the SR protein family of RNA binding proteins play numerous roles in gene expression, including the regulation of pre-mRNA splicing, mRNA export, and translation. How SR proteins coordinate gene expression programs has been largely unexplored, and comprehensive knowledge of endogenous mRNA targets is lacking. Gene expression changes upon SRp20 or SRp75 RNAi in P19 parental, SRp75-BAC, and SRp20-BAC cells were measured with mouse whole genome microarrays. The knockdown of either SRp20 or SRp75 led to up- or downregulation of specific transcripts. Phenotypic rescue in the SRp75-BAC, and SRp20-BAC cells demonstrated functionality of the GFP-tagged SR proteins, and showed the specificity of the knockdowns.

2010-07-20 | E-MEXP-2640 | biostudies-arrayexpress

RNA-seq analysis of the eight Drosophila SR protein family members

Project description:Using RNA-seq, we characterize the global AS regulation of the eight Drosophila SR protein family members RNA-seq experiments on two replicate samples from 8 individual SR protein knockdown (exptGroup=S), two replicates of simultaneous SR protein knockdown (XL6:B52 & SC35:B52) (exptGroup=D). Each exptGroup includes duplicate of its own non-specific (NS) controls.

2014-11-23 | E-GEOD-63263 | biostudies-arrayexpress

Drosophila melanogaster

Project description:RNA-seq analysis of the eight Drosophila SR protein family members

| PRJNA268196 | ENA

RNA-seq analysis of the eight Drosophila SR protein family members

Project description:Using RNA-seq, we characterize the global AS regulation of the eight Drosophila SR protein family members

2014-11-23 | GSE63263 | GEO

Phosphorylation regulates arginine-rich RNA-binding protein solubility and oligomerization

Project description:Post-translational modifications (PTMs) within splicing factor RNA-binding proteins (RBPs), such as phosphorylation, regulate several critical steps in RNA metabolism including spliceosome assembly, alternative splicing and mRNA export. Notably, the arginine-/serine-rich (RS) domains in SR proteins are densely modified by phosphorylation compared with the remainder of the proteome. Previously, we showed that dephosphorylation of SRSF2 regulated increased interactions with similar arginine-rich RBPs U1-70K and LUC7L3. In this work, we dephosphorylated nuclear extracts using phosphatase in vitro and analyzed equal amounts of detergent-soluble and -insoluble fractions by mass spectrometry-based proteomics. Correlation network analysis resolved 27 distinct modules of differentially soluble nucleoplasm proteins. We found classes of arginine-rich RBPs that decrease in solubility following dephosphorylation and enrich to the insoluble pelleted fraction, including the SR protein family and the SR-like LUC7L RBP family. However, increased insolubility was not observed across broad classes of RBPs. Phosphorylation regulated SRSF2 structure, as dephosphorylated SRSF2 formed high molecular weight oligomeric species in vitro. Reciprocally, phosphorylation of SRSF2 by serine-/arginine protein kinase 2 (SRPK2) in vitro prevented high molecular weight SRSF2 species formation. Furthermore, we pharmacologically inhibited SRPKs in mammalian cells and observed increased cytoplasmic granules as well as the formation of cytoplasmic SRSF2 tubular structures that associate with microtubules by immunocytochemical staining. Collectively, these findings demonstrate that phosphorylation may be a critical modification that prevents arginine-rich RBP insolubility and oligomerization.

2021-11-02 | PXD026894 | Pride

Mus musculus

Project description:Transcriptome-wide mapping of RNA:protein interactions of seven SR proteins and NXF1 in P19 cells by iCLIP

| PRJNA286202 | ENA

PDZ domain-containing adaptor protein GIPC1 interacts with the SR-B1 and modulates its expression and lipid transport function

Project description:PDZ family protein GIPC1 physically interacts with SR-B1 and regulates SR-B1 expression by promoting SR-B1 protein stability.

2021-03-09 | PXD024595 | iProX

HeLa cell response to overexpression of wild type and mutated forms of the P19 splice variant of c-H-ras

Project description:The c-H-ras proto-oncogene undergoes alternative splicing of the exon termed IDX giving rise to a novel protein of the Ras family, p19 (H-RasIDX). The experiment tests the effect on the transcriptome of overexpressing the wild type and W164A mutated forms of p19. Keywords: genetic modification

2009-12-30 | GSE12059 | GEO

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