Nucleo-cytoplasmic mRNA distribution
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE1344 | GEO | 2004/05/01
SECONDARY ACCESSION(S): PRJNA90091
REPOSITORIES: GEO
Similar Datasets
Project description:Nuclear and cytoplasmic RNA were extracted by hypotonic cell lysis from D.-mel2 cell knock down by RNAi against dU2AF50 or with non-specific dsRNA.
2007-07-05 | E-GEOD-1344 | biostudies-arrayexpress
Project description:Characteristics of subcellular localization of RNAs are closely associated with their transcriptional outputs and, therefore, involved in the physiological process of many cases of central nervous system diseases, such as hemorrhagic stroke, which threatens millions of people and causes of death and long-term disability world-wide. Using whole-transcriptome sequencing (RNA-seq), here we report a subcellular gene profiling during hemorrhagic damage. Differentially expressed genes owing to spatial distribution of oxyhemoglobin (oxy-hb) treated-microglial nuclear and cytoplasmic fractions were enriched in biological processes in RNA metabolism and RNA splicing regardless of the duration of stimulation; while hemorrhage-induced differentially expressed genes played roles in inflammation regardless of the duration of stimulation. Interestingly, nuclear-retained intron of microglial nucleocytoplasmic transport genes may result in their down-regulation in 24 hours of oxy-Hb stimulation. This transcriptome study advances our understanding of the contributor of subcellular components, revealing new insights into cytoplasmic non-coding RNAs in response to hemorrhage and provide a resource for investigating comparable diseases.
2021-02-26 | GSE160934 | GEO
Project description:Nucleo-cytoplasmic RNA distribution responsible for maintaining neuroinflammatory microenvironment.
| PRJNA674859 | ENA
Project description:This project aimed to identify novel endosomal proteins and therefore cellular fractionation experiments were performed. Adherent mouse embryonic fibroblast were scraped on ice into hypotonic lysis buffer (10 mM HEPES-KOH pH 7.2, 0.25 M sucrose, 1 mM EDTA, 1 mM MgOAc and protease & phosphatase inhibitors (PhosSTOP and Complete mini tablets from Roche). Cell membranes were fragmented with French Press and nuclei removed with 10 min 1000 x g centrifugation. Plasma membrane fraction was collected with 10 min 10 000 x g centrifugation and endosomal/cytoplasmic fractions with 1h 100,000 x g centrifugation. Membrane fractions were washed at least once with lysis buffer and cytoplasmic fractions were centrifuged twice. All fractionation steps were performed at +4°C or on ice. All fractions were dissolved in sample buffer for immunoblotting
2015-10-14 | PXD001870 | Pride
Project description:The cytopheno project studies cytoplasmic-nucleus interactions by characterizing cytolines (same nucleus but different cytoplasm, and conversely) at several levels (growth, germination, transcriptomic, proteomic, metabolomic) notably in response to nitrogen deficiency. For this project, there are 48 hybridizations performed as following, on leaf samples from hydroponically grown plants. bioadapt2011_cytopheno - bioadapt2011_cytopheno - Evaluation of the impact of nucleo-cytoplasmic co-adaptation disruptions on nuclear genome expression in Arabidopsis - Obtaining samples by hydroponic culture.
2020-06-17 | GSE144597 | GEO
Project description:The dynamic shuttling of proteins between the nucleus and cytoplasm orchestrates vital functions in eukaryotes. Here, we unveil multifaceted functions of Arabidopsis Sin3-associated protein 18 kDa (SAP18) in regulating development and stress tolerance. As a crucial component of the Apoptosis- and Splicing-Associated Protein (ASAP) complex in the nucleus, SAP18 plays an integral role in the precise splicing of genes associated with leaf development, decoding its significance in post-transcriptional regulatory networks. Under heat shock conditions, SAP18 relocates to cytoplasmic stress granules and processing bodies, suggesting a novel thermoprotective role. This dual localization highlights SAP18 versatility in coordinating cellular responses, encompassing both nuclear splicing regulation and cytoplasmic stress granule dynamics. Our findings significantly expand the understanding of the intricate involvement of SAP18 in plant growth, and pave the way for future exploration of its diverse functions in thermotolerance mechanisms.
2024-11-04 | PXD050985 | Pride
Project description:RNA interference (RNAi) is a potent mechanism for down-regulating gene expression. Conserved RNAi pathway components are found in animals, plants, fungi and other eukaryotes. In C. elegans, the RNAi response is greatly amplified by the synthesis of abundant secondary siRNAs. Exogenous double stranded RNA is processed by Dicer and RDE-1/Argonaute into primary siRNA that guides target mRNA recognition. The RDE-10/RDE-11 complex and the RNA dependent RNA polymerase RRF-1 then engage the target mRNA for secondary siRNA synthesis. However, the molecular link between primary siRNA production and secondary siRNA synthesis remains largely unknown. Furthermore, it is unclear if the sub-cellular sites for target mRNA recognition and degradation coincide with sites where siRNA synthesis and amplification occur. In the C. elegans germline, cytoplasmic P granules at the nuclear pores and perinuclear Mutator foci contribute to target mRNA surveillance and siRNA amplification, respectively. We report that RDE-12, a conserved FG domain containing DEAD-box helicase, localizes in P-granules and cytoplasmic foci that are enriched in RSD-6 but are excluded from the Mutator foci. Our results suggest that RDE-12 promotes secondary siRNA synthesis by orchestrating the recruitment of RDE-10 and RRF-1 to primary siRNA targeted mRNA in distinct cytoplasmic compartments. Examination of exogenous dsRNA trigger derived siRNA in wildtype and rde-12 mutant animals
2014-03-27 | E-GEOD-53830 | biostudies-arrayexpress
Project description:The metazoan protein BCL2-associated athanogene cochaperone 6 (Bag6) forms a hetero-trimeric complex with ubiquitin-like 4A and transmembrane domain recognition complex 35 (TRC35). This Bag6 complex is involved in tail-anchored protein targeting and various protein quality-control pathways in the cytosol as well as regulating transcription and histone methylation in the nucleus. Here we present a crystal structure of Bag6 and its cytoplasmic retention factor TRC35, revealing that TRC35 is remarkably conserved throughout the opisthokont lineage except at the C-terminal Bag6-binding groove, which evolved to accommodate Bag6, a unique metazoan factor. While TRC35 and its fungal homolog, guided entry of tail-anchored protein 4 (Get4), utilize a conserved hydrophobic patch to bind their respective partners, Bag6 wraps around TRC35 on the opposite face relative to the Get4-5 interface. We further demonstrate that TRC35 binding is critical not only for occluding the Bag6 nuclear localization sequence from karyopherin ? to retain Bag6 in the cytosol but also for preventing TRC35 from succumbing to RNF126-mediated ubiquitylation and degradation. The results provide a mechanism for regulation of Bag6 nuclear localization and the functional integrity of the Bag6 complex in the cytosol.
| S-EPMC5676875 | biostudies-literature
Project description:BackgroundThe transcription factor NFAT5 is a major inducer of osmoprotective genes and is required to maintain the proliferative capacity of cells exposed to hypertonic stress. In response to hypertonicity, NFAT5 translocates to the nucleus, binds to regulatory regions of osmoprotective genes and activates their transcription. Besides stimulus-specific regulatory mechanisms, the activity of transcription factors in cycling cells is also regulated by the passage through mitosis, when most transcriptional processes are downregulated. It was not known whether mitosis could be a point of control for NFAT5.Methodology/principal findingsUsing confocal microscopy we observed that NFAT5 was excluded from chromatin during mitosis in both isotonic and hypertonic conditions. Analysis of NFAT5 deletions showed that exclusion was mediated by the carboxy-terminal domain (CTD). NFAT5 mutants lacking this domain showed constitutive binding to mitotic chromatin independent of tonicity, which caused them to localize in the nucleus and remain bound to chromatin in the subsequent interphase without hypertonic stimulation. We analyzed the contribution of the CTD, DNA binding, and nuclear import and export signals to the subcellular localization of this factor. Our results indicated that cytoplasmic localization of NFAT5 in isotonic conditions required both the exclusion from mitotic DNA and active nuclear export in interphase. Finally, we identified several regions within the CTD of NFAT5, some of them overlapping with transactivation domains, which were separately capable of causing its exclusion from mitotic chromatin.Conclusions/significanceOur results reveal a multipart mechanism regulating the subcellular localization of NFAT5. The transactivating module of NFAT5 switches its function from an stimulus-specific activator of transcription in interphase to an stimulus-independent repressor of binding to DNA in mitosis. This mechanism, together with export signals acting in interphase, resets the cytoplasmic localization of NFAT5 and prevents its nuclear accumulation and association with DNA in the absence of hypertonic stress.
| S-EPMC2737149 | biostudies-literature
Project description:The phytohormone auxin plays crucial roles in nearly every aspect of plant growth and development. The AUXIN RESPONSE FACTOR (ARF) family of transcription factors regulates auxin-responsive gene expression and exhibit nuclear localization in regions of high auxin responsiveness. Here we show that activating ARF7 and ARF19 proteins accumulate in micron-sized assemblies within the cytoplasm of tissues with attenuated auxin responsiveness. The intrinsically disordered middle region and the folded PB1 interaction domain of ARFs drive protein assembly formation. Mutation of a single lysine within the PB1 domain abrogates cytoplasmic assemblies, promotes ARF nuclear localization, and results in an altered transcriptome and morphological defects. Our data suggest a model in which ARF nucleo-cytoplasmic partitioning regulates auxin responsiveness, thus providing a mechanism for cellular competence for auxin signaling.
2019-07-24 | GSE104385 | GEO