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Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing

ABSTRACT: Global analyses of two prototypical SR proteins (SRFS1 and SFRS2 using splicing-sensitive arrays and CLIP-seq on mouse embryo fibroblasts carrying tet-repressible versions of the two genes.

ORGANISM(S): Mus musculus

PROVIDER: GSE44583 | GEO | 2013/03/01

SECONDARY ACCESSION(S): PRJNA190106

REPOSITORIES: GEO

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Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing

Project description:Global analyses of two prototypical SR proteins (SRFS1 and SFRS2 using splicing-sensitive arrays and CLIP-seq on mouse embryo fibroblasts carrying tet-repressible versions of the two genes. 4 biological replicate sets of SFRS1 or SFRS2 tet-repressible MEFs were grown for 5 days -/+ docycline. Total RNA was isolated and labeled targets hybridized to Affymetrix mouse splicing arrays. This is the gene expression component of the study only.

2013-03-01 | E-GEOD-44583 | biostudies-arrayexpress

Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing

Project description:SR proteins are well-characterized RNA binding proteins that promote exon inclusion by binding to exonic splicing enhancers (ESEs). However, it has been unclear whether regulatory rules deduced on model genes apply generally to activities of SR proteins in the cell. Here, we report global analyses of two prototypical SR proteins SRSF1 (SF2/ASF) and SRSF2 (SC35) using splicing-sensitive arrays and CLIP-seq on mouse embryo fibroblasts (MEFs). Unexpectedly, we find that these SR proteins promote both inclusion and skipping of exons in vivo, but their binding patterns do not explain such opposite responses. Further analyses reveal that loss of one SR protein is accompanied by coordinated loss or compensatory gain in the interaction of other SR proteins at the affected exons. Therefore, specific effects on regulated splicing by one SR protein actually depend on a complex set of relationships with multiple other SR proteins in mammalian genomes. SRSF1 and SRSF2 CLIP-seq

2013-04-05 | E-GEOD-44591 | biostudies-arrayexpress

Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing

2013-04-05 | GSE44591 | GEO

iCLIP seq reveals distribution of genome-wide SR protein-RNA binding

Project description:We identified the precise genome-wide binding sites for all SR proteins, using iCLIP-seq SR proteins were encoded on stable transgenes, transfected in S2 cells, FLAG-tag immunopurified, and the bound RNA purified and subjected to RNA-seq. The resulting reads (CLIP tags) were aligned to the Drosophila genome and generated 38,695-5,900,000 unique CLIP tags for each SR-protein replicate.

2014-11-23 | E-GEOD-63262 | biostudies-arrayexpress

Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing.

Project description: Not available

| S-EPMC3640356 | biostudies-literature

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

Expression data from RH30 vector and RH30 IκBα SR cells

Project description:Classical NF-κB activity can be inhibited by overexpression of the IκBα super repressor (SR). To determine the role of NF-κB in rhabdomyosarcoma cells, we overexpressed the IκBα SR in RH30 rhabdomyosarcoma cells. IκBα SR was overexpressed in RH30 cells. RH30 vector cells were used as control group.

2018-03-30 | GSE112119 | GEO

Competition-cooperation relationship networks characterize the competition and cooperation between proteins.

Project description: Not available

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Transcriptomic profiling of E9.5 mouse embryos lacking the lipoprotein receptor SR-B1

Project description:The high-density lipoprotein receptor SR-B1 mediates cellular uptake of several lipid species, including cholesterol and vitamin E. During early development, SR-B1 is located in the maternal-fetal interface, where it facilitates vitamin E transport towards the embryo. Consequently, embryos lacking SR-B1 are vitamin E-deficient, and around half of them fail to close the neural tube and show neural tube defects (NTD). Here, we studied the transcriptomic profile of mouse embryos lacking SR-B1 to identify the molecular determinants of this phenotypic difference. We used RNA-Seq to analyze the expression of mRNA globally in E9.5 wild-type embryos and embryos lacking SR-B1 with or without NTD, in order to compare expression profiles in those groups and to identify putative genes driving phenotypic differences.

2018-09-21 | GSE115091 | GEO

Expression data of human melanoma cell lines treated with siRNA targeting SR-BI or with the pharmacologic inhibitor BLT-1

Project description:Melanoma patients with high mRNA levels of the HDL receptor SR-BI (SCARB1) reveal poor survival outcome. The aim of the study was to evaluate the role of SR-BI in cancer progression. Therefore, SR-BI was targeted either by siRNA or by using the SR-BI specific lipid transfer inhibitor BLT-1. The SR-BI knockdown specifically revealed reduced protein glycosylation, STAT5 target gene expression and EMT pathway activation. Thus, SR-BI target genes reflect the metastatic phenotype in melanoma cells. We used the transcriptome analysis to compare SR-BI depletion to BLT-1 treatment (which specifically blocks SR-BI mediated lipid transfer) in human melanoma cells.

2018-01-02 | GSE96743 | GEO

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