Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Proteome and Transcriptome of Stress Granules and P-Bodies during Human T Lymphocytes Activation

ABSTRACT: Stress granules (SGs) and processing bodies (PBs) are membraneless cytoplasmic assemblies regulating mRNAs under environmental stress such as viral infections, neurological disorders, or cancer. Upon antigen stimulation, T lymphocytes mediate their immune functions under regulatory mechanisms involving SGs and PBs. However, the impact of T cell activation on such complexes, in term of formation, constitution and relationship remains unknown. Here, by combining proteomic, transcriptomic and immunofluorescence approaches, we simultaneously characterized the SGs and PBs from primary human T lymphocytes pre- and post-stimulation. The proteomes and transcriptomes of SGs and PBs were identified, unveiling an unanticipated molecular and functional complementarity. Notwithstanding, these granules keep distinct spatial organizations and abilities to interact with mRNAs. This comprehensive characterization of the RNP granule proteomic and transcriptomic landscapes provides a unique resource for future investigations on SGs and PBs in T lymphocytes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE197001 | GEO | 2023/03/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

The Proteome and Transcriptome of Stress Granules and P-Bodies during Human T Lymphocytes Activation

Project description:Stress granules (SGs) and processing bodies (PBs) are membraneless cytoplasmic assemblies regulating mRNAs under environmental stress such as viral infections, neurological disorders, or cancer. Upon antigen stimulation, T lymphocytes mediate their immune functions under regulatory mechanisms involving SGs and PBs. However, the impact of T cell activation on such complexes, in term of formation, constitution and relationship remains unknown. Here, by combining proteomic, transcriptomic and immunofluorescence approaches, we simultaneously characterized the SGs and PBs from primary human T lymphocytes pre- and post-stimulation. The proteomes and transcriptomes of SGs and PBs were identified, unveiling an unanticipated molecular and functional complementarity. Notwithstanding, these granules keep distinct spatial organizations and abilities to interact with mRNAs. This comprehensive characterization of the RNP granule proteomic and transcriptomic landscapes provides a unique resource for future investigations on SGs and PBs in T lymphocytes.

2023-03-10 | PXD031639 | Pride

Integrated multi-omics reveals common properties underlying stress granule and P-body formation

Project description:Non-membrane-bound compartments such as mRNA processing bodies (PBs) and stress granules (SGs) play important roles in the regulation of gene expression following environmental stresses. We have systematically determined the protein and mRNA composition of PBs and SGs formed in response to a common stress condition imposed by glucose depletion. We find that high molecular weight (HMW) complexes exist prior to glucose depletion that may act as seeds for the further condensation of proteins forming mature PBs and SGs. Both before and after glucose depletion, these HMW complexes are enriched for proteins containing low complexity and RNA binding domains. The mRNA content of these HMW complexes is enriched for long, structured mRNAs that become more poorly translated following glucose depletion. Many proteins and mRNAs are shared between PBs and SGs, suggesting a complex pattern of functional protein and mRNA pools exist in different condensates. Even where the precise identity of mRNAs and proteins localizing to PBs and SGs is distinct, the mRNAs and proteins share common biophysical and chemical features that likely trigger their phase separation.

2021-11-03 | PXD018762 | Pride

Analysis of P-body (Dcp1) and Stress Granule (Pbp1) RNA content

Project description:Non-membrane-bound compartments such as mRNA processing bodies (PBs) and stress granules (SGs) play important roles in the regulation of gene expression following environmental stresses. Here we perform RIP-seq to determine the RNA interactors of Dcp1 (PB marker) and Pbp1 (SG marker) before and after an appropriate glucose stress.

2021-09-30 | E-MTAB-9096 | biostudies-arrayexpress

Intracellular Energy Controls Dynamics of Stress-induced Ribonucleoprotein Granules Implicated in ALS/FTD

Project description:Energy metabolism and membraneless organelles have been implicated in human diseases including neurodegeneration. How energy deficiency regulates ribonucleoprotein particles such as stress granules (SGs) is still unclear. Here we identified a unique type of granules formed under energy deficiency and uncovered the mechanisms by which the dynamics of diverse stressinduced granules are regulated. Severe energy deficiency induced the rapid formation of energy deficiency-induced stress granule (eSGs), whereas moderate energy deficiency delayed the clearance of conventional SGs. The formation of eSGs or the clearance of SGs was regulated by the mTOR-4EBP1-eIF4E pathway or eIF4A1, involving eIF4F complex assembly or RNA condensation, respectively. In ALS patients’ neurons or cortical organoids, the eSG formation was enhanced, and conventional SG clearance was impaired. These results reveal a critical role for intracellular energy in the regulation of diverse granules and suggest that disruptions in energycontrolled granule dynamics may contribute to the pathogenesis of relevant diseases.

2022-10-15 | PXD035747 | Pride

Stress granule assembly impairs macrophage efferocytosis [RIP-seq]

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

Tudor Staphylococcal Nuclease (TSN) proteome isolation

Project description:Stress granules (SGs) are transient membraneless organelles protecting yeast and mammalian cells from stress-induced damage, whereas plant SGs remain poorly understood. Recently, we identified Tudor Staphylococcal Nuclease (TSN) as a stable component of Arabidopsis SGs. As a first step to investigate the role of TSN in stress granule formation, we characterised its proteome by using an alternative tandem affinity purification (TAPa).

2021-06-11 | PXD018095 | JPOST Repository

A novel paracrine induction of RNA Granules by Feline Calicivirus

Project description:We are here presenting a new paracrine induction of RNA granules by viruses. Infection by viruses imposes major stress on the host cell. In response to this stress, infected cells can induce several defence mechanisms, which include the activation of stress response pathways and the innate immune response. These often result in an inhibition of translation culminating in the assembly of cytoplasmic granules called stress granules (SGs). SGs assembly follows from liquid phase separation of aggregation-prone proteins such G3BP1 and TIA-1, leading to the sequestration of mRNAs. Because this threatens viral gene expression, viruses need to evade these stress response pathways to propagate. Using feline calicivirus (FCV), surrogate for norovirus, the main virus responsible for gastroenteritis outbreaks worldwide, we previously showed that FCV impairs SGs assembly by cleaving the scaffold protein G3BP1. Interestingly, we observed that uninfected bystander cells assembled G3BP1 granules, suggesting a paracrine response trigged by the infection. We now present evidence that virus-free supernatant generated from infected cells can induce the formation of RNA granules. We have characterised the dynamic of the granules assembly via confocal microscopy. Moreover, we provide an understanding of paracrine granules function and specificity through their affinity purification followed by proteomics and RNAseq analysis of their proteins and mRNAs content. This helps to define rules of assembly and novel functions for paracrine granules highlighting fundamental differences with canonical stress granules.

2022-03-14 | PXD021881 | Pride

Protein and metabolite composition of the Arabidopsis stress granules.

Project description:Stress granules are evolutionary conserved aggregates of proteins and untranslated mRNAs formed in response to stress. Herein, we report protein composition of the Arabidopsis SGs supporting their role in plant response to stress. Moreover, and to our knowledge for the first time, we provide evidence for not only mRNAs and proteins, but also phospholipids and amino-acids accumulation in the SGs. A quarter of the identified proteins constituted known or predicted SGs components, supporting evolutionary conserved mechanism of SGs assembly and dynamics. Intriguingly, remaining proteins were enriched in key enzymes and regulators mediating plant response to stress, such as cyclin dependent kinase A (CDKA), pointing to the important role of SGs in moderating plant response to stress by selective storage and temporary inactivation of the proteins. We hypothesize that phospholipid sequestration into SGs may serve partly analogous role providing protection from the phospholipase mediated degradation occurring upon combination of heat and dark stress.

2022-03-27 | PXD010455 | Pride

G3BP1-linked mRNA partitioning supports selective protein synthesis in response to oxidative stress

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.

2019-11-01 | GSE138058 | GEO

G3BP1-linked mRNA partitioning supports selective protein synthesis in response to oxidative stress

2020-04-30 | PXD015491 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data