The Proteome and Transcriptome of Stress Granules and P-Bodies during Human T Lymphocytes Activation
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ABSTRACT:
PROVIDER: PRJNA808315 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18071720_1.fastq.gz | Fastqsanger.gz | |||
| SRR18071720_2.fastq.gz | Fastqsanger.gz | |||
| SRR18071721_1.fastq.gz | Fastqsanger.gz | |||
| SRR18071721_2.fastq.gz | Fastqsanger.gz | |||
| SRR18071722_1.fastq.gz | Fastqsanger.gz |
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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.
2023-03-09 | GSE197001 | GEO
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
Project description:The eukaryotic cytosol contains multiple RNP granules including P-bodies and stress granules. Three different methods have been used to describe the transcriptome of stress granules or P-bodies, but how these methods compare, and how RNA partitioning occurs between P-bodies and stress granules has not been addressed. Herein, we compare the analysis of the stress granule transcriptome based on differential centrifugation, with and without subsequent stress granule immunopurification. We find that while differential centrifugation alone gives a first approximation of the stress granule transcriptome, this methodology contains non-specific transcripts that play a confounding role in the interpretation of results. We also immunopurify and compare the RNAs in stress granules and P-bodies under arsenite stress and compare those results to the P-body transcriptome described under non-stress conditions. We find that the P-body transcriptome is dominated by poorly translated mRNAs under non-stress conditions, but during arsenite stress, when translation is globally repressed, the P-body transcriptome is very similar to the stress granule transcriptome. This suggests that translation is a dominant factor in targeting mRNAs into both P-bodies and stress granules, and during stress, when most mRNAs are untranslated, the composition of P- bodies reflects this broader translation repression.
2019-10-17 | GSE138988 | GEO
Project description:To identify RNAs accumulating in P-bodies (cytoslic RNP granules), P-bodies were purified from HEK293 cell extracts using a Flow Activated Particle Sorting (FAPS) method. Sorted P-bodies were compared to the pre-sorted fraction to identify RNA enriched in P-bodies.
2017-09-01 | E-MTAB-5477 | biostudies-arrayexpress
Project description:Analysis of stress granules in HeLa cells, after exposure to different stimuli. Granules were collected by a newly devised enrichment method, described in manuscript. Proteomics sample preparation of granules was carried out using the Single-pot, solid phase-enhanced sample preparation, SP3 method (Hughes CS et al. Nat Protoc 14, 68 85 (2019)). Desalting, clean-up and loading to the MS was done using an Evosep one EV1000 instrument, following manufacturers protocol, but loading of sample to Evotips was done a pre-existing volume of A Buffer. Samples were measured on a Thermo Exploris 480 mass spectrometer, using data-independent acquisition (DIA) (30 SPD, 44 LC min gradient (Evosep), MS1: 120000 res, 350-1400 m/z, inj. time 50 ms, MS2: 14 m/z isolation windows, 1 /mz overlap, precursor mass range. 350-1020 m/z, stepped collision energy 25,27.5,30, 22 ms inj. time.
RAW files were analyzed using Spectronaut v16, using directDIA mode with default settings, using as database the Homo Sapiens EBI Reference proteome, downloaded on 03/2021 and including an in-house curated contaminants list based on the MaxQuant's contaminants list. Protein summarisation was done with MSstats, using default settings.
2022-11-02 | MSV000090634 | MassIVE
Project description:mRNA processing bodies (P-bodies) are cytoplasmic granules that form in eukaryotic cells in response to numerous stresses to serve as sites of degradation and storage of mRNAs. Functional P-bodies are critical for the DNA replication stress response in yeast, yet the repertoire of P-body targets and the mechanisms by which P-bodies promote replication stress resistance are unknown. In this study, we identify the complete complement of mRNA targets of P-bodies during replication stress induced by hydroxyurea treatment. The key P-body protein Lsm1 controls the abundance of HHT1, ACF4, ARL3, TMA16, RRS1 and YOX1 mRNAs to prevent their toxic accumulation during replication stress. Accumulation of YOX1 mRNA causes aberrant down-regulation of a network of genes critical for DNA replication stress resistance. Among these genes we identify ALD6, whose de-repression is critical to prevent accumulation of acetaldehyde, a strongly toxic molecule during DNA replication stress. This SuperSeries is composed of the SubSeries listed below.
2017-06-26 | GSE83515 | GEO
Project description:Cytotoxic T lymphocytes (CTL) kill malignant and infected cells via cytotoxic proteins such as granzyme B (GzmB) that are released into the immunological synapse in the form of ~110 nm supramolecular attack particles (SMAPs). However, it is not known where SMAPs are stored in the cell and how they are released. To address this, we utilized knock-in mice to label fusogenic cytotoxic granules with synaptobrevin2-mRFP. We identified two classes of fusion-competent granules, single core granules (SCG) and multi core granules (MCG), with different diameter, morphology, and protein composition. Functional analyses demonstrate that both classes of granules fuse with the plasma membrane at the IS. SCG fusion resulted in rapid dispersal of GzmB. MCG labelled with the SMAP marker thrombospondin-1 and their fusion events resulted in deposition of SMAPs. The CTL attack strategy thus includes SCG fusion to disperse immediately active cytotoxic proteins and parallel MCG fusion to deposit concentrated latent SMAPs onto the target.
2022-04-04 | PXD025055 | Pride
Project description:Stress granules are mRNA-protein assemblies formed on nontranslating mRNAs. Stress granules are important in the stress response, related to neuronal mRNP granules, and aberrant stress granules contribute to some degenerative diseases. By RNA-Seq and single molecule FISH, we describe the stress granule transcriptome in both yeast and mammalian cells. This reveals that while essentially every mRNA, and some ncRNAs, can be targeted to stress granules, the efficiency of targeting can vary from <1% to 73%. mRNA accumulation in stress granules is increased by longer coding regions, poor translatability, and correlates with some RNA binding proteins. Standardizing the RNA-Seq analysis by single molecule FISH allows a quantitative description of the general and stress granule transcriptome. Approximately 15% of the bulk mRNA molecules accumulate in stress granules suggesting their effect will be limited primarily to subsets of mRNAs highly accumulating in stress granules
2017-11-10 | GSE99304 | GEO
Project description:RNA localization to stress granules
| PRJNA875210 | ENA
Project description:In response to stress, cells must quickly reprogram gene expression to adapt and survive. This is achieved in part by altering levels of mRNAs and their translation into proteins. Recently, the formation of two stress-induced messenger ribonucleoprotein (mRNP) assemblies named stress granules and processing bodies has been postulated to directly impact gene expression during stress. These assemblies sequester and concentrate specific proteins and RNAs away from the larger cytoplasm during stress, thereby providing a layer of posttranscriptional gene regulation with the potential to directly impact mRNA levels, protein translation, and cell survival. The function of these granules has generally been ascribed either by the protein components concentrated into them or, more broadly, by global changes that occur during stress. Recent proteome- and transcriptome-wide studies have provided a more complete view of stress-induced mRNP granule composition in varied cell types and stress conditions. However, direct measurements of the phenotypic and functional consequences of stress granule and processing body formation are lacking. This leaves our understanding of their roles during stress incomplete. Continued study into the function of these granules will be an important part in elucidating how cells respond to and survive stressful environmental changes. This article is categorized under: Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Export and Localization > RNA Localization.
| S-EPMC6500494 | biostudies-literature