Cellular response to unfolded proteins in cytosol and nucleus
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE65504 | GEO | 2015/09/04
SECONDARY ACCESSION(S): PRJNA274294
REPOSITORIES: GEO
Similar Datasets
Project description:Analysis of the coordinated transcriptional response to unfolded proteins in cytosol and nucleus utilizing mRNA-seq mRNA profiles of NIH3T3 cells which stably expressing DD-sfGFP were generated by deep sequencing using Illumina HiSeq2000. The samples were collected from indicated timepoints after Shield-1 removal.
2015-09-04 | E-GEOD-65504 | biostudies-arrayexpress
Project description:Cellular response to unfolded proteins in cytosol and nucleus
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Project description:Virus infection and over expression of protein in cytosol induce a subset of HSP70s. We named this response the Cytosolic Protein Response (CPR) and have been investigating it in the context of a parallel mechanism in the soluble cytosol with the UPR, and as a subcomponent of the larger HS response. This experiment was carried out to study the transcriptional aspect of CPR. In this analysis, we have triggered CPR by infiltrating proline analogue, L-azetidine-2-carboxylic acid (AZC) into Arabidopsis mature leaves. Since AZC trigger unfolded protein response(UPR) in ER as well as CPR, we have included tunicamycin treatment, which is a specific inducer of UPR to subtract the effect of UPR from the AZC response. Heat shocked samples were included to identify CPR as a subcomponent of larger HS response. We used microarray data to identify the genes upregurated by CPR. These genes were commonly upregulated by AZC and HS but not by tunicamycin treatment. Keywords: stress response
2008-12-11 | GSE11758 | 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
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Project description:Mutated SOD1 immunoprecipitation samples in the nucleus and cytoplasm from the ALS model mouse-derived cell line DF7.
2024-01-27 | PXD039696 | JPOST Repository
Project description:The cytoplasm is an essential part of the cell involved in protein synthesis, energy generation, nutrient processing, transport, metabolism, and homeostasis, but its structure and function are not entirely understood. Almost five decades ago, dynamic nano-compartments of the cytoplasm were observed by high voltage electron microscopy in every living cell. However, the validity of these constructs, have been questioned and counterclaimed as artifacts of histo-techniques. We developed a new method to separate and characterize two different cytoplasmic compartments that we named cytomatrix and cytosol (or cytomedia). Using two compositional different solvents we were able sequentially extract the cytosol (cyto-solution) first then separate the cytomatrix from the nucleus. Our method allows fractionate the cell into three fractions: the cytosol, cytomatrix, and the nucleus.
2023-03-11 | PXD031043 | Pride
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.
2014-08-28 | GSE53743 | GEO
Project description:The RNA seq of cytomatrix and cytosol
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Project description:The vast majority of the mitochondrial proteome originates from nuclear genes and is transported into the organelle after synthesis in the cytosol. Complex machineries, which maintain the specificity of protein import and sorting, include the TIM23 translocase responsible for the transfer of precursor proteins into the matrix and the MIA machinery required for the biogenesis of intermembrane space proteins. Dysfunctions of mitochondrial protein sorting pathways result in diminishing specific substrate proteins, followed by systemic pathology of the organelle and organismal death1-4. Cellular responses that are caused by accumulation of mitochondrial precursor proteins in the cytosol are largely unknown. Here we show a comprehensive picture of the changes in the cellular transcriptome and proteome in response to the stress associated with protein import dysfunction. We identify pathways that protect the cell against mitochondrial biogenesis defects by inhibiting protein synthesis and by activation of the proteasome, a major machine for cellular protein clearance. The proteasomal activity is modulated in proportion to the quantity of mislocalized mitochondrial precursor proteins in the cytosol. We propose that this type of unfolded protein response activated by mistargeting of proteins (UPRam) is beneficial for the cells. UPRam provides a means for buffering the consequences of physiological slowdown in mitochondrial protein import and for counteracting pathologies that are caused or contributed by mitochondrial dysfunction.
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Project description:PolyA+ RNA from cytosol of HeLa and GM06990 cells using Affymetrix ENCODE tiling chip with NCBI build 35 annotation. PolyA+ RNA from cytosol of HeLa and GM06990 cells.
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