Translatome of NIH3T3 cells: control vs. stress treatment
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE36206 | GEO | 2012/03/02
SECONDARY ACCESSION(S): PRJNA152879
REPOSITORIES: GEO
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Project description:Translation efficiencies of mouse mRNAs in control and in cells treated with thapsigargin 10microM for 3h. Two-conditions experiments. Biological replicates: 1 from three pooled control experiments, 1 from three pooled stress experiments
2012-03-02 | E-GEOD-36206 | biostudies-arrayexpress
Project description:Translation efficiencies of Jurkat mRNAs in control and in cells treated with thapsigargin 10microM for 1h and 3h.
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Project description:Translation efficiencies of Jurkat mRNAs in control and in cells treated with thapsigargin 10microM for 1h and 3h. Three-conditions experiments. Biological replicates: 1 from three pooled control experiments, 1 from three pooled 1h stress experiment, 1 from three pooled 3h stress experiment.
2012-03-02 | E-GEOD-36207 | biostudies-arrayexpress
Project description:Disruption of protein folding in the endoplasmic reticulum triggers the Unfolded Protein Response (UPR), a transcriptional and translational control network designed to restore protein homeostasis. Central to the UPR is PERK phosphorylation of the alpha subunit of eIF2 (eIF2~P), which represses global translation coincident with preferential translation of mRNAs, such as ATF4 and CHOP, that serve to implement the UPR transcriptional regulation. In this study, we used sucrose gradient ultracentrifugation and a genome-wide microarray approach to measure changes in mRNA translation during ER stress. Our analysis suggests that translational efficiencies vary across a broad range during ER stress, with the majority of transcripts being either repressed or resistant to eIF2~P, while a notable cohort of key regulators are subject to preferential translation. From this latter group, we identify IBTKa as being subject to both translation and transcriptional induction during eIF2~P in both cell lines and a mouse model of ER stress. Translational regulation of IBTKalpha mRNA involves the stress-induced relief of two inhibitory uORFs in the 5'-leader of the transcript. Depletion of IBTKalpha by shRNA reduced viability of cultured cells coincident with increased caspase 3/7 cleavage, suggesting that IBTKalpha is a key regulator in determining cell fate during the UPR. We used a genome-wide microarray approach to determine how individual mRNAs were differentially translated during endoplasmic reticulum stress. A microarray analysis from our laboratory identified gene transcripts suggested to be under translation control in mouse embryonic fibroblast (MEF) cells following a 6 hour treatment with thapsigargin, a potent inducer of ER stress, or no stress. The mRNAs were separated by sucrose gradient analyses to yield three fractions, those transcripts associated with large polysomes (?4 ribosomes per mRNA), those associated with monosome, disomes, or trisomes, and those fractionated at the top of the gradient with free ribosomes. RNA was extracted from sucrose gradients corresponding to these fractions and hybridized on Affymetrix microarrays. In parallel, we also measured total levels for each gene transcript in the presence or absence of thapsigargin treatment to address transcription regulation coincident with translational control. Please note that the treatment plus fractionation based on association with different numbers of ribosomes did yield different populations of mRNAs, which resulted in considerable variation in normalized data across the samples.
2014-06-02 | E-GEOD-54581 | biostudies-arrayexpress
Project description:Heat stress is one of the most prominent and deleterious environmental threads affecting plant growth and development. Upon high temperatures, plants launch specialized gene expression programs that promote stress protection and survival. These programs involve global and specific changes at the transcriptional and translational levels. However the coordination of these processes and their specific role in the establishment of the heat stress response is not fully elucidated. In this report, we have carried out a genome-wide analysis to simultaneously monitor the individual changes in the transcriptional and translational mRNA levels of Arabidopsis thaliana seedlings after the exposure to a heat shock stress. Our results demonstrated that, superimposed to transcription, translation exerts a wide but dual regulation of gene expression. For the majority of mRNAs, translation is severely repressed, causing a decreased of 50% of the association of the bulk of mRNAs to polysomes. However, some relevant mRNAs involved in different aspects of homeostasis maintenance follow a differential pattern of translation. Analysis of the sequence of the differentially translated mRNAs unravels that some features, like the 5M-BM-4UTR G+C content and the cDNA length, may take part in the discrimination mechanisms for mRNA polysome loading. Among the differential translated genes stand out master regulators of the stress response, highlighting the main role of translation in the early establishment of physiological response of plants to elevated temperatures. In total 8 ATH1 Affymetrix GeneChips were hybridized with all combinations of two factors: total mRNA/polysome-bound-RNA; 22M-BM-:C/38M-BM-:C. Two biological replicates per sample type were performed.
2014-01-22 | E-GEOD-44053 | biostudies-arrayexpress
Project description:Heat stress is one of the most prominent and deleterious environmental threads affecting plant growth and development. Upon high temperatures, plants launch specialized gene expression programs that promote stress protection and survival. These programs involve global and specific changes at the transcriptional and translational levels. However the coordination of these processes and their specific role in the establishment of the heat stress response is not fully elucidated. In this report, we have carried out a genome-wide analysis to simultaneously monitor the individual changes in the transcriptional and translational mRNA levels of Arabidopsis thaliana seedlings after the exposure to a heat shock stress. Our results demonstrated that, superimposed to transcription, translation exerts a wide but dual regulation of gene expression. For the majority of mRNAs, translation is severely repressed, causing a decreased of 50% of the association of the bulk of mRNAs to polysomes. However, some relevant mRNAs involved in different aspects of homeostasis maintenance follow a differential pattern of translation. Analysis of the sequence of the differentially translated mRNAs unravels that some features, like the 5´UTR G+C content and the cDNA length, may take part in the discrimination mechanisms for mRNA polysome loading. Among the differential translated genes stand out master regulators of the stress response, highlighting the main role of translation in the early establishment of physiological response of plants to elevated temperatures.
2014-01-22 | GSE44053 | GEO
Project description:Rcm1 methylates ribosomal RNA at C2278 and a knockout of this gene induces structural alterations of rRNA and decreased translational fidelity. To test the influence of rcm1 knockout on the specific translation of mRNAs, we analysed the mRNA recruitment pattern into polysomes versus total cellular mRNAs under different oxidative stress conditions by microarrays. In order to estimate the efficiency of translation of individual mRNAs, we calculated the translational efficiency (TE) as ratio between signal intensity in the polysome fraction (‘translatome’) versus signal intensity in the total yeast cell lysate (‘transcriptome’) for each probeset on the array. Genes with at least 2-fold up- or downregulation at p < 0.05 were defined to be significantly translationally up- or downregulated.
2014-11-07 | GSE63030 | GEO
Project description:cea03-02_translatome-cd - translatome-cd - Is there a change in the translation in Cadmium stress condition ? - Comparison between translated RNA (polysomes) and total RNA or non translated RNA (monosomes) in cadmium stress conditions. Keywords: transcribed vs translated,treated vs untreated comparison
2007-06-20 | GSE8061 | GEO
Project description:immortalized patient derived kidney epithelial cell were compared to cells exposed to ER stress (thapsigargin) in the absence or present of BRD4780 treatment
2019-04-18 | GSE129942 | GEO
Project description:The unfolded protein response (UPR) couples cellular translation rates and gene expression to the protein folding status of the endoplasmic reticulum (ER). Upon activation, the UPR machinery elicits a general suppression of protein synthesis and activation of stress gene expression, which act coordinately to restore protein folding homeostasis. We report here that UPR activation promotes the release of signal sequence-encoding mRNAs from the ER to the cytosol as a mechanism to decrease protein influx into the ER. This release of mRNA begins rapidly, then gradually recovers with ongoing stress. Upon release into the cytosol, these mRNAs have divergent fates: some synthesize full-length proteins, while others are translationally inactive and retain nascent protein chains. Together, these findings identify the dynamic subcellular localization of mRNAs and translation as a regulatory feature of the cellular response to protein folding stress. Cells were treated with a timecourse of Thapsigargin or DTT, then fractionated and analyzed by mRNA-seq or ribosome profiling
2014-08-28 | E-GEOD-53743 | biostudies-arrayexpress