Ontology highlight
ABSTRACT:
PROVIDER: PRJNA825129 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18697000_1.fastq.gz | Fastqsanger.gz | |||
| SRR18697000_2.fastq.gz | Fastqsanger.gz | |||
| SRR18697001_1.fastq.gz | Fastqsanger.gz | |||
| SRR18697001_2.fastq.gz | Fastqsanger.gz | |||
| SRR18697002_1.fastq.gz | Fastqsanger.gz |
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Project description:Embryonic stem cells (ESCs) are self-renewing and pluripotent. In recent years, factors controlling pluripotency, mostly nuclear, have been identified. To reveal non-nuclear regulators of ESCs, we screened an endogenously-labelled fluorescent fusion-protein library in mouse ESCs. One of the more compelling hits was the cell cycle-associated protein, CAPRIN1. CAPRIN1, a Stress Granule (SG) component, exhibited a strikingly cyclical localization pattern in sync with mitosis, and localized to SGs, in response to stress. CAPRIN1 knockout had little effect in ESCs, but dramatically skewed differentiation and gene expression programs. RIP-seq and SLAM-seq revealed that CAPRIN1 associates with, and promotes the degradation of, thousands of RNA transcripts. CAPRIN1 interactome identified XRN2 as the likely ribonuclease. Upon early differentiation or stress, XRN2 colocalizes with CAPRIN1 inside SGs in a CAPRIN1-dependent manner. We propose that CAPRIN1 regulates an RNA degradation pathway operating during early ESC differentiation, eliminating undesired spuriously transcribed transcripts in ESCs.
2022-11-18 | GSE179002 | GEO
Project description:Stress granules (SGs) assembly in response to various stress, has been demonstrated in the regulation of anti-viral immune response and tumor progression. However, lack of evidence to illustrate the relation between SGs formation and allergic diseases. Applied G3BP1-RIP-seq in RAW264.7 cells, G3BP1 binding mRNAs are defined.
2024-05-01 | GSE264137 | GEO
Project description:Cells limit energy-consuming mRNA translation during stress to maintain metabolic homeostasis. Sequestration of mRNAs by RNA binding proteins (RBPs) into stress granules (SGs) reduces translation, but it remains unclear whether SGs also function in partitioning of specific transcripts to polysomes (PSs) to guide selective translation and stress-adaptation in cancer. Transcripts enriched in PSs, defined by polysome fractionation and RNAseq, were compared with mRNAs complexed with the SG-nucleator protein, G3BP1, defined by spatially-restricted enzymatic tagging. Short-term oxidative stress profoundly altered mRNA translation by promoting selective enrichment of transcripts within SGs or PSs. G3BP1 participates in this compartmentalisation by sequestering transcripts in SGs. Under stress, G3BP1-bound transcripts are PS-depleted and encode proteins involved in mRNA translation, pro-apoptosis, and mitochondrial function. In contrast, specific PS-enriched transcripts disassociate from G3BP1 under stress to encode proteins involved in diverse cellular cytoprotective pathways. Therefore, G3BP1 partitioning guides selective translation to support stress adaptation and cell survival.
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Project description:Stress granules are small RNA-protein granules that modify the translational landscape during cellular stress to promote survival. The RhoGTPase RhoA is implicated in the formation of RNA stress granules. Our data demonstrate that the cytokinetic proteins ECT2 and AurkB are localized to stress granules in human astrocytoma cells. AurkB and its downstream target histone-3 are phosphorylated during arsenite-induced stress. Chemical (AZD1152-HQPA) and siRNA inhibition of AurkB results in fewer and smaller stress granules when analyzed utilizing high throughput fluorescent based cellomics assays. RNA immunoprecipitation with the known stress granule aggregates TIAR and G3BP1 was performed on astrocytoma cells and subsequent analysis revealed that astrocytoma stress granules harbour unique mRNAs for various cellular pathways including cellular migration, metabolism, translation and transcriptional regulation. Human astrocytoma cell stress granules contain mRNA that are known to be involved in glioma signaling and the mTOR pathway. These data provide evidence that RNA stress granules are a novel form of epigenetic regulation in astrocytoma cells, which may be targetable by chemical inhibitors and enhance astrocytoma susceptiblity to conventional therapy such as radiation and chemotherapy. Astrocytoma cells were either untreated or treated with arsenite to induce stress granule formation and RNA immunoprecipitates were analyzed by exon array analysis. RNA species that were enriched in TIAR RIPs and G3BP1 RIPS, respectively were compared to compared to TIAR and G3BP1 RIPs from untreated cells and input controls. Ingenuity pathway analysis was performed on the stress granule enriched mRNAs from the TIAR and G3BP1 RIPs to identify significant functional biology networks.
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Project description:Cells limit energy-consuming mRNA translation during stress to maintain metabolic homeostasis. Sequestration of mRNAs by RNA binding proteins (RBPs) into stress granules (SGs) reduces translation, but it remains unclear whether SGs also function in partitioning of specific transcripts to polysomes (PSs) to guide selective translation and stress-adaptation in cancer. Transcripts enriched in PSs, defined by polysome fractionation and RNAseq, were compared with mRNAs complexed with the SG-nucleator protein, G3BP1, defined by spatially-restricted enzymatic tagging. Short-term oxidative stress profoundly altered mRNA translation by promoting selective enrichment of transcripts within SGs or PSs. G3BP1 participates in this compartmentalisation by sequestering transcripts in SGs. Under stress, G3BP1-bound transcripts are PS-depleted and encode proteins involved in mRNA translation, pro-apoptosis, and mitochondrial function. In contrast, specific PS-enriched transcripts disassociate from G3BP1 under stress to encode proteins involved in diverse cellular cytoprotective pathways. Therefore, G3BP1 partitioning guides selective translation to support stress adaptation and cell survival.
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Project description:Time-resolved proteomic profiling of SGs from cultured human U2OS cells over a prolonged heat-shock (HS) and a successive recovery period, sampling at the 6 time points of HS exposure (10, 20, 30, 60, 120, 180 min), as well as 2 time points of recovery (5, 10 min). From the sampled cells, we prepared SG samples using a differential centrifugation plus endogenous G3BP1 immunoprecipitation protocol. Peptides were subsequently TMT-labeled and analyzed by quantitative LC-MS/MS. In G3BP1 dataset, rep1-rep3, HS-10, 20, 30, 60, 120, 180, re5, re10, SG-ls, G3BP1-IP samples were labeled with TMT-126, 127N, 127C, 128N, 128C,129N, 129C, 130N, 130C, 131 label Reagents, respectively; G3BP1_HS0 was a dataset created to integrate a non-heat shock control (HS-0) into the G3BP1 dataset, contains HS0, HS10, and HS60, and the results was integrated into the G3BP1 dataset using the ComBat processing, HS-0_rep1, HS-0_rep2, HS-0_rep3, HS-10_rep1, HS-10_rep2, HS-10_rep3, HS-60_rep1, HS-60_rep2, HS-60_rep3 samples were labeled with TMT-126, 127N, 127C, 128N, 128C,129N, 129C, 130N, 130C label Reagents, respectively. In CAPRIN1 dataset, rep1-rep3, HS-0, 10, 20, 30, 60, 120, 180, re5, re10 samples were labeled with TMT-126, 127N, 127C, 128N, 128C,129N, 129C, 130N, 130C label Reagents, respectively.
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Project description:Mitochondrial calcium signaling plays a critical role in mitochondrial homeostasis during non-alcoholic steatohepatitis (NASH) progression. Here, we report Ras‐GTPase activating protein SH3 domain‐binding protein 1 (G3BP1), a core protein of stress granule (SG), significantly upregulated in NAFLD/NASH patients, mouse models and palmitic acid-stimulated hepatocytes. Hepatocyte-specific G3BP1 deficiency attenuates NASH in two dietary mouse models. SG and the mitochondrial import protein TOM70 collaboratively mediate the translocation of G3BP1 to the mitochondria. G3BP1 interacts and stabilizes mitochondrial calcium uptake 1 (MICU1) via inhibiting YME1L1-mediated degradation of MICU1, and also impedes MCU complex activity and assembly, leading to mitochondrial calcium overload. Moreover, metabolic stress suppresses TRIM25-mediated K63-ubiquitination of G3BP1 and subsequent SG disassembly. Pharmacological inhibition of G3BP1 impairs the G3BP1-MICU1 interaction and prevents mitochondrial homeostasis imbalance and NASH progression. Collectively, we uncover the significant role of mitochondrial G3BP1 in mitochondrial homeostasis and NASH progression, which provides a potential target for therapeutic interventions.
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Project description:Mitochondrial calcium signaling plays a critical role in mitochondrial homeostasis during non-alcoholic steatohepatitis (NASH) progression. Here, we report Ras‐GTPase activating protein SH3 domain‐binding protein 1 (G3BP1), a core protein of stress granule (SG), significantly upregulated in NAFLD/NASH patients, mouse models and palmitic acid-stimulated hepatocytes. Hepatocyte-specific G3BP1 deficiency attenuates NASH in two dietary mouse models. SG and the mitochondrial import protein TOM70 collaboratively mediate the translocation of G3BP1 to the mitochondria. G3BP1 interacts and stabilizes mitochondrial calcium uptake 1 (MICU1) via inhibiting YME1L1-mediated degradation of MICU1, and also impedes MCU complex activity and assembly, leading to mitochondrial calcium overload. Moreover, metabolic stress suppresses TRIM25-mediated K63-ubiquitination of G3BP1 and subsequent SG disassembly. Pharmacological inhibition of G3BP1 impairs the G3BP1-MICU1 interaction and prevents mitochondrial homeostasis imbalance and NASH progression. Collectively, we uncover the significant role of mitochondrial G3BP1 in mitochondrial homeostasis and NASH progression, which provides a potential target for therapeutic interventions.
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