Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

95 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MRNA immunoprecipitated with CUGBP1 in C2C12

ABSTRACT: Dramatic changes in gene expression occur in response to extracellular stimuli and during differentiation. Although transcriptional effects are important, alterations in mRNA decay also play a major role in achieving rapid and massive changes in mRNA abundance. Moreover, just as transcription factor activity varies between different cell types, the factors influencing mRNA decay are also cell-type specific.GREs are recognized by CUGBP1, an RNA-binding protein and instability factor whose function is affected in several neuromuscular diseases. To dectect the mRNA associated with CUGBP1, we utilized RNA immunoprecipitation followed by microarray (RIP-Chip) to identify CUGBP1-associated transcripts. To identify the mRNA associated with CUGBP1, we performed the immunoprecipitation followed by microarray (RIP-Chip)

ORGANISM(S): Mus musculus

SUBMITTER: Ju Youn Lee

PROVIDER: E-GEOD-21235 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Systematic analysis of cis-elements in unstable mRNAs demonstrates that CUGBP1 is a key regulator of mRNA decay in muscle cells

Project description:This SuperSeries is composed of the following subset Series: GSE21233: Expression data from C2C12 mouse myoblast with treatment actinomycin D GSE21235: mRNA immunoprecipitated with CUGBP1 in C2C12 Refer to individual Series

2010-07-08 | E-GEOD-21236 | biostudies-arrayexpress

mRNA immunoprecipitated with CUGBP1 in C2C12

Project description:Dramatic changes in gene expression occur in response to extracellular stimuli and during differentiation. Although transcriptional effects are important, alterations in mRNA decay also play a major role in achieving rapid and massive changes in mRNA abundance. Moreover, just as transcription factor activity varies between different cell types, the factors influencing mRNA decay are also cell-type specific.GREs are recognized by CUGBP1, an RNA-binding protein and instability factor whose function is affected in several neuromuscular diseases. To dectect the mRNA associated with CUGBP1, we utilized RNA immunoprecipitation followed by microarray (RIP-Chip) to identify CUGBP1-associated transcripts.

2010-06-21 | GSE21235 | GEO

Exon array analysis in the mouse myoblast cell line, C2C12 cells treated with control-, Cugbp1- or Mbnl1-siRNA

Project description:CUGBP1 and MBNL1 are developmentally regulated RNA-binding proteins that are causally associated with myotonic dystrophy type 1. Using HITS-CLIP anlysis, we found CUGBP1 and MBNL1 preferentially bind to alternatively spliced introns and exons, as well as to the 3' UTRs. To analyze more directly the role of CUGBP1/MBNL1 binding in alternative splicing, we performed exon array analysis in C2C12 cells using expression arrays. We analyzed total RNA of C2C12 cells treated with control-, Cugbp1- or Mbnl1-siRNA. RNA was harvested 48 hrs after transfection.

2012-01-03 | E-GEOD-29990 | biostudies-arrayexpress

Expression profiles of primary cortical neurons after knocking down Cugbp1

Project description:To clarify the functional properties of Cugbp1, we established the differentially expressed alternative exons in Cugbp1-silenced primary cortical neurons by using exon-sensitive microarray technology. We analyzed total RNA of primary motor neuron infected with lentivirus expressing shRNA against mouse Cugbp1 or control. RNA was harvested 11 days after transfection.

2013-04-18 | E-GEOD-46147 | biostudies-arrayexpress

Global characterization of miR-574-5p decoy to CUGBP1 in human lung cancer using a mass spectrometry proteomics approach

Project description:We aimed to characterize decoy to the RNA-binding protein CUG-RNA binding protein 1 (CUGBP1 mechanism in A549 lung cancer cells. We identified several new canonical targets of CUGBP1 but those were not regulated by miR-574-5p via the decoy mechanism. This can be explained by the localization of CUGBP1 and miR-574-5p in the nucleus, where CUGBP1 regulates alternative splicing. Next, we analyzed the 3’UTRs of potential targets and found that the decoy-dependent regulation of mPGES-1 splicing is unique. Therefore, we postulate that in A549 cells mPGES-1 is the only protein regulated by the decoy mechanism of CUGBP1 and miR-574-5p which suggests that the decoy mechanism allows the specific regulation of the expression of distinct targets.

2020-03-02 | PXD016803 | Pride

mRNA decay analysis in the mouse myoblast cell line, C2C12 cells treated with conrtol-, Cugbp1- or Mbnl1-siRNA

Project description:CUGBP1 and MBNL1 are developmentally regulated RNA-binding proteins that are causally associated with myotonic dystrophy type 1. Using HITS-CLIP anlysis, we found CUGBP1 and MBNL1 preferentially bind to alternatively spliced introns and exons, as well as to the 3' UTRs. To analyze more directly the role of CUGBP1/MBNL1 binding to the 3’ UTR, we performed global analysis of mRNA stability in C2C12 cells using expression arrays, and found that CUGBP1 and MBNL1 regulate decay of endogenous mRNAs.

2012-01-03 | GSE27583 | GEO

RNA CLIP-seq for Cugbp1, Mbnl1 and Ptbp1 in mouse C2C12 myoblasts

Project description:CUG-binding protein 1 (CUGBP1) and muscleblind-like 1 (MBNL1) are developmentally regulated RNA-binding proteins that are causally associated with myotonic dystrophy type 1. We extensively determined RNA-binding sites of CUGBP1 and MBNL1 to investigate their roles in RNA processing. We also analyzed polypyrimidine tract-binding protein (PTB) as a control. CUGBP1 and MBNL1 preferentially bind to alternatively spliced introns and exons, respectively, and regulate alternative splicing events. Moreover, CUGBP1 and MBNL1 are preferentially bound to the 3' untranslated regions (UTRs), in particular of genes for RNA-binding proteins, and facilitate decay of the bound mRNAs. In addition, CUGBP1 and MBNL1 mutually destabilize mRNA. Precise temporal regulation of CUGBP1 and MBNL1 are likely to be essential for accurate control of destabilization of a broad spectrum of genes as well as of alternative splicing events in cell differentiation and tissue development.

2012-01-04 | E-MTAB-414 | biostudies-arrayexpress

mRNA decay analysis in the mouse myoblast cell line, C2C12 cells treated with conrtol-, Cugbp1- or Mbnl1-siRNA

Project description:CUGBP1 and MBNL1 are developmentally regulated RNA-binding proteins that are causally associated with myotonic dystrophy type 1. Using HITS-CLIP anlysis, we found CUGBP1 and MBNL1 preferentially bind to alternatively spliced introns and exons, as well as to the 3' UTRs. To analyze more directly the role of CUGBP1/MBNL1 binding to the 3’ UTR, we performed global analysis of mRNA stability in C2C12 cells using expression arrays, and found that CUGBP1 and MBNL1 regulate decay of endogenous mRNAs. We analyzed total RNA of C2C12 cells treated with control-, Cugbp1- or Mbnl1-siRNA. We analyzed 3 time points after addition of actionmycin D (0, 2.5, 5 hours).

2012-01-03 | E-GEOD-27583 | biostudies-arrayexpress

Hepatic transcriptome in CUGBP1 S302A knock-in mice highlights CUGBP1 degradation by Gankyrin through diethylnitrosamine (DEN) activation, leading to fatty liver and liver cancer

Project description:Purpose: CUGBP1 is an important regulator of liver homeostasis, through splicing regulation, stability, and mRNA translation. To aim to characterize the transcriptome of DEN-mediated liver cancer in CUGBP1 knock-in mice with Ser302 mutated to Ala (which mimics unphosphorylated CUGBP1 isoform) through RNA sequencing. Specifically, we compared gene expression levels to identify the impact of DEN-driven activation in both wildtype and CUGBP1 Ser302-to-Ala knock-in mice, focusing on downstream CUGBP1 targets and tumor activating pathways. Methods: Hepatic mRNA profiles were obtained through RNA sequencing of flash-frozen samples obtained at time of sacrifice. Results: We observe an augmentation of up- and downregulated cancer-related genes and pathways in CUGBP1 s302a knock-in mice compared to WT mice. We observe not only changes in expression related to oncogenesis, but also in splicing. Reduction of CUGBP1 protein due to the s302a variant leads to higher sensitivity to the development of liver cancer as a result of alterations in expression of down-stream mRNAs at both the splicing and expression levels. Conclusion: CUGBP1 is a strong tumor suppressor in the liver, and reduction of the CUGBP1 protein accelerates the development of liver cancer.

2017-06-12 | GSE83240 | GEO

Impact of Cugbp1 knockout on skeletal muscle and brain trancsriptome in neonatal mice

Project description:To elucidate the role of Cugbp1 knockout on the structure and function of skeletal muscle and brain, we have performed a microarray of mRNA obtained from skeletal muscle and brain samples obtained from neonatal WT and Cugbp1 KO mice. Between-genotype differences were assessed using a Student's T-test, with a p-value cutoff of 0.05 and fold change cutoff of 1.5. 929 genes were identified as differentially regulated; ontological enrichments within this geneset indicated Cugbp1 may regulate differentiation, extracellulat matrix and other muscle functions during myogenesis.

2018-08-08 | GSE85396 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data