Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: We used GFP-tagged SR proteins expressed at endogenous levels and iCLIP to identify and compare endogenous RNA targets of individual SR proteins, map the preferential sites of binding, compare binding pattern and binding motifs between family members and to NXF1 and quantify binding of SR proteins and NXF1 to spliced versus unspliced RNAs to study the role of SR proteins in mRNA export via NXF1.

ORGANISM(S): Mus musculus

PROVIDER: GSE69689 | GEO | 2016/03/07

SECONDARY ACCESSION(S): PRJNA286202

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

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

Transcriptome-wide mapping of RNA:protein interactions of three SR proteins in HeLa cells by iCLIP

Project description:We used GFP-tagged SR proteins expressed at endogenous levels and iCLIP to compare the extent and pattern of SR protein binding to expression-matched lincRNAs and protein-coding RNAs

2018-10-31 | GSE113813 | 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

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

The Nuclear-retained non-coding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation

Project description:Alternative splicing (AS) of pre-mRNA is utilized by higher eukaryotes to achieve increased transcriptome and proteomic complexity. The serine/arginine (SR) splicing factors regulate tissue- or cell type-specific AS in a concentration and phosphorylation dependent manner. However, the mechanisms that modulate the cellular levels of active SR proteins remain to be elucidated. In the present study, we provide evidence for a role for the long nuclear-retained regulatory RNA (nrRNA), MALAT1 in AS regulation. MALAT1 interacts with SR proteins and influences the distribution of these and other splicing factors in nuclear speckle domains. Depletion of MALAT1 changes AS of endogenous pre-mRNAs, similar to what was observed upon overexpression of SR proteins. Furthermore, MALAT1 regulates cellular levels of phosphorylated forms of SR proteins. Taken together, our results suggest that MALAT1 regulates AS by modulating the levels of active SR proteins. Our results further highlight a novel role for a nrRNA in the regulation of gene expression. Malat1 Antisense and control knockdowns evaluated on a microarray platform to profile alternative splicing levels for 5782 cassette-type alternative exons.

2010-09-01 | E-GEOD-22963 | biostudies-arrayexpress

The Nuclear-retained non-coding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation

2010-09-01 | GSE22963 | 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

2014-11-23 | GSE63262 | GEO