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RNA-seq of ER-targeted and cytosolic mRNAs with control or CNOT1-targeting siRNA treatment in HEK293 cells

ABSTRACT: RNA-seq of ER-targeted and cytosolic mRNAs with control or CNOT1-targeting siRNA treatment in HEK293 cells

PROVIDER: PRJNA759272 | ENA |

REPOSITORIES: ENA

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RNA-seq of ER-targeted and cytosolic mRNAs with control or CNOT1-targeting siRNA treatment in HEK293 cells

Project description:Determination of mRNA localisation in HEK293 cells with and without the depletion of CNOT1

2021-09-07 | GSE183148 | GEO

mRNA stability experiments with control or CNOT1-targeting siRNA treatment in HEK293 cells

Project description:Determination of mRNA half-life in HEK293 cells with and without the depletion of CNOT1.

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Ribosome Profiling with CNOT1 depletion

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mRNA stability experiments with control or CNOT1-targeting siRNA treatment in HEK293 cells

Project description:mRNA stability experiments with control or CNOT1-targeting siRNA treatment in HEK293 cells

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Ribosome Profiling with CNOT1 depletion

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CNOT1 and Transcriptomic Landscape of a HeLa Cell Line

Project description:Purpose: The goals of this study are to compare NGS-derived total transcriptome profiling (RNA-seq) of CNOT1-depleted cells (using siRNA) with control HeLa cells before and after DNA damage to examine quantitative gene expression.

2019-12-05 | GSE141496 | GEO

Knockout of CNOT1 and CNOT10 in primary CD4+ T-cells causes a type-1 interferon response

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ChIP-seq of livers in control and Cnot1 tamoxifen-inducible liver-specific knockout mice

Project description:Gene expression is balanced by transcription and mRNA degradation. Shortening of polyadenosine (poly(A)) tails (deadenylation) is the initial step in the decay of most mRNAs. However, the mechanism by which deadenylation controls mRNA expression is not fully understood. This experiment aimed to determine changes in transcriptional activity in livers of control and Cnot1 tamoxifen-inducible liver-specific knockout mice. Control and Cnot1 tamoxifen-inducible liver-specific knockout mice placed on tamoxifen-containing food at 6 weeks of age for 2 weeks. Lysates from livers were subjected to ChIP assay with Histone H3 (tri methyl K4) (H3K4me3) antibody (ab8580; abcam) using SimpleChIP Enzyatic Chromatin IP Kit (#9003; Cell Signaling Technology). Libraries for DNA sequence were prepared from DNA isolated by ChIP assays with a KAPA Hyper Prep Kit (Illumina). 109 base-pair pair-end read DNA-seq was performed with Hiseq PE Rapid Cluster Kit v2-HS and Hiseq Rapid SBS Kit v2-HS (200 Cycle) on Illumina Hiseq2500.

2020-03-30 | E-MTAB-5887 | biostudies-arrayexpress

RNA-seq of livers in control and Cnot1 tamoxifen-inducible liver-specific knockout mice

Project description:Gene expression is balanced by transcription and mRNA degradation. Shortening of polyadenosine (poly(A)) tails (deadenylation) is the initial step in the decay of most mRNAs. However, the mechanism by which deadenylation controls mRNA expression is not fully understood. This experiment aimed to determine changes in gene expression and mRNA stability in livers of control and Cnot1 tamoxifen-inducible liver-specific knockout mice. For comprehensive mRNA half-life profiling, we injected control and Cnot1 tamoxifen-inducible liver-specific knockout mice, which were placed on a tamoxifen-containing diet at 6 weeks of age for 2 weeks, intraperitoneally with 2 mg actinomycin D per g body weight for 4 and 8 hr. 1 g of total RNA was used for RNA-seq library preparation with Illumina TruSeq Stranded mRNA LT Sample Prep Kit. 109 base-pair pair-end read RNA-seq was performed with Hiseq PE Rapid Cluster Kit v2-HS and Hiseq Rapid SBS Kit v2-HS (200 Cycle) on Illumina Hiseq2500.

2020-03-30 | E-MTAB-5901 | biostudies-arrayexpress

The Mammalian Cytosolic Thioredoxin Reductase Pathway Acts via a Membrane Protein to Reduce ER-localised Proteins

Project description:Folding of proteins entering the mammalian secretory pathway requires the insertion of the correct disulfide bonds. Disulfide formation involves both an oxidative pathway for their insertion and a reductive pathway to remove incorrectly formed disulfides. Reduction of these disulfides is critical for correct folding and degradation of misfolded proteins. Previously, we showed that the reductive pathway is driven by NADPH generated in the cytosol. Here, by reconstituting the pathway using purified proteins and ER microsomal membranes, we demonstrate that the thioredoxin reductase system provides the minimal cytosolic components required for reducing proteins within the ER lumen. In particular, saturation of the pathway and its protease sensitivity demonstrates the requirement for a membrane protein to shuttle electrons from the cytosol to the ER lumen. These results provide compelling evidence for the critical role of the cytosol in regulating ER redox homeostasis to ensure correct protein folding and to facilitate the degradation of misfolded ER proteins.

2020-04-09 | PXD017923 | Pride

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