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ChIP-seq analysis of changes in H3K27ac by endoplasmic reticulum stress (ERS) in mouse primary hepatocytes.

ABSTRACT: ChIP-seq analysis of changes in H3K27ac by endoplasmic reticulum stress (ERS) in mouse primary hepatocytes.

PROVIDER: PRJNA505776 | ENA |

REPOSITORIES: ENA

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ChIP-seq analysis of changes in H3K27ac by endoplasmic reticulum stress (ERS) in mouse primary hepatocytes.

Project description:Mouse primary hepatocytes (MPH) prepared from C57Bl6 male adult mice were treated with the ERS-drug thapsigargin and ChIP-seq was performed using an H3K27ac antibody (Active Motif ref 39685).

2020-04-29 | GSE122613 | GEO

Transcriptomic analysis of endoplasmic reticulum stress (ERS) regulated genes in mouse primary hepatocytes.

Project description:Transcriptomic analysis of endoplasmic reticulum stress (ERS) regulated genes in mouse primary hepatocytes.

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Transcriptomic analysis of endoplasmic reticulum stress (ERS) regulated genes in mouse primary hepatocytes.

Project description:Mouse primary hepatocytes (MPH) prepared from C57Bl6 male adult mice were treated with the ERS-drug thapsigargin and used to prepare RNA.

2020-04-29 | GSE122507 | GEO

Hepatocytes cyclooxygenase-2 deficiency improves liver injury via inhibition of endoplasmic reticulum stress and epithelial-mesenchymal transition

Project description:The mechanism underlying the loss of normal liver tissues in liver cirrhosis, mainly hepatocytes, is not well-characterized. Endoplasmic reticulum (ER) stress-induced cell death has emerged as a potential mechanism for chronic liver diseases. We have previously demonstrated that cyclooxygenase-2 (COX-2) is closely related to the progress of liver cirrhosis. In this study, we aimed to verify whether hepatocytes COX-2 deficiency could protect liver injury via inducing ER stress in liver cirrhosis.

2024-04-28 | GSE183888 | GEO

Transcriptomic and epigenomic analysis of endoplasmic reticulum stress signaling in mouse primary hepatocytes and liver

Project description:Transcriptomic and epigenomic analysis of endoplasmic reticulum stress signaling in mouse primary hepatocytes and liver

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Transcriptomic analysis of endoplasmic reticulum stress (ERS) regulated genes in mouse gastrocnemius muscle

Project description:Transcriptomic analysis of endoplasmic reticulum stress (ERS) regulated genes in mouse gastrocnemius muscle

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Ribosome footprinting in the cytosol and endoplasmic reticulum

Project description:In eukaryotic cells, the spatial regulation of protein expression is frequently conferred through the coupling of mRNA localization and the local control of translation. mRNA localization to the endoplasmic reticulum (ER) is a prominent example of such regulation and serves a ubiquitous role in segregating the synthesis of secretory and integral membrane proteins to the ER. Recent genomic and biochemical studies have now expanded this view to suggest a role for the ER in global protein synthesis. We have utilized cell fractionation and ribosome profiling to obtain a genomic survey of the subcellular organization of mRNA translation and report that ribosomal loading of mRNAs, a proxy for mRNA translation, is biased to the ER. Notably, ER-associated mRNAs encoding both cytosolic and topogenic signal-encoding proteins display similar ribosome loading densities, suggesting that ER-associated ribosomes serve a global role in mRNA translation. We propose that the partitioning of mRNAs and their translation between the cytosol and ER compartments may represent a novel mechanism for the post-transcriptional regulation of gene expression. HEK293 cells were fractionated between the cytosol and endoplasmic reticulum. Within each fraction, ribosome footprints were generated and sequenced. In parallel, total mRNA was sequenced.

2011-12-20 | E-GEOD-31539 | biostudies-arrayexpress

The SND proteins constitute an alternative targeting route to the endoplasmic reticulum

Project description:In eukaryotes, up to one-third of cellular proteins are targeted to the endoplasmic reticulum, where they undergo folding, processing, sorting and trafficking to subsequent endomembrane compartments. Targeting to the endoplasmic reticulum has been shown to occur co-translationally by the signal recognition particle (SRP) pathway or post-translationally by the mammalian transmembrane recognition complex of 40 kDa (TRC40) and homologous yeast guided entry of tail-anchored proteins (GET) pathways. Despite the range of proteins that can be catered for by these two pathways, many proteins are still known to be independent of both SRP and GET, so there seems to be a critical need for an additional dedicated pathway for endoplasmic reticulum relay. We set out to uncover additional targeting proteins using unbiased high-content screening approaches. To this end, we performed a systematic visual screen using the yeast Saccharomyces cerevisiae, and uncovered three uncharacterized proteins whose loss affected targeting. We suggest that these proteins work together and demonstrate that they function in parallel with SRP and GET to target a broad range of substrates to the endoplasmic reticulum. The three proteins, which we name Snd1, Snd2 and Snd3 (for SRP-independent targeting), can synthetically compensate for the loss of both the SRP and GET pathways, and act as a backup targeting system. This explains why it has previously been difficult to demonstrate complete loss of targeting for some substrates. Our discovery thus puts in place an essential piece of the endoplasmic reticulum targeting puzzle, highlighting how the targeting apparatus of the eukaryotic cell is robust, interlinked and flexible.

2016-11-30 | GSE85686 | GEO

Transcriptomic analysis of endoplasmic reticulum stress (ERS) regulated genes in the liver of NFIL3 KO mice.

Project description:Transcriptomic analysis of endoplasmic reticulum stress (ERS) regulated genes in the liver of NFIL3 KO mice.

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Transcriptional changes associated with endoplasmic reticulum stress in the eye imaginal disc of Drosophila melanogaster

Project description:We obtained transcriptional profiles of third instar eye imaginal disc nuclei with or without endoplasmic reticulum stress using next generation sequencing (NGS). We employed an isolation of nuclei tagged in specific cell type (INTACT) protocol (Ma and Weake, J. of Vis. Exp., 2014) to label nuclear membranes of GMR-GAL4-expressing cells with EGFP. The experimental group also expressed a mutant allele of the membrane visual protein rhodopsin (Rh-1(G69D)), which is known to cause endoplasmic reticulum stress and initiate Unfolded Protein Response (UPR) signaling. The goal of this study was to characterize the transcriptional changes associated with endoplasmic reticulum stress responses in a commonly used platform, the eye imaginal disc.

2021-09-20 | GSE150058 | GEO

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