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Nucleo-cytoplasmic RNA distribution responsible for maintaining neuroinflammatory microenvironment.

ABSTRACT: Nucleo-cytoplasmic RNA distribution responsible for maintaining neuroinflammatory microenvironment.

PROVIDER: PRJNA674859 | ENA |

REPOSITORIES: ENA

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Nucleo-cytoplasmic RNA distribution responsible for maintaining neuroinflammatory microenvironment.

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

Cytoplasmic cleavage of IMPA1 3’UTR is necessary for maintaining axon integrity.

Project description:Cytoplasmic cleavage of IMPA1 3’UTR is necessary for maintaining axon integrity.

| PRJNA671669 | ENA

Nucleo-cytoplasmic mRNA distribution

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. Keywords: other

2004-05-01 | GSE1344 | GEO

bioadapt2011_cytopheno-CYTOPHENO: Nucleo-cytoplasmic co-adaptation and adaptive plant phenotypes

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

EXPORTIN 1A Prevents Transgene Silencing in Arabidopsis through Modulating the Nucleo-cytoplasmic Partitioning of HDA6

Project description:In eukaryotic cells, nucleo-cytoplasmic trafficking of macromolecules across the nuclear envelope is an essential process that ensures a rapid exchange of different cellular components, including proteins and RNAs, between the nucleus and cytoplasm. The significance of the nucleo-cytoplasmic trafficking of chromatin regulators in regulating DNA methylation and gene silencing is not well understood. Here, using a genetic screen, we identified XPO1A, one of the nuclear export receptors in Arabidopsis, as an anti-silencing factor that protects transgenes from transcriptional silencing. Loss-of-function of XPO1A leads to locus-specific DNA hypermethylation at transgene promoters and some endogenous loci. We found that XPO1A directly interacts with histone deacetylase HDA6 in vivo and the xpo1a mutation causes increased nuclear retention of HDA6 protein, resulting in reduced histone acetylation and enhanced transgene silencing. Our results revealed a new mechanism of epigenetic regulation through the modulation of XPO1A-dependent nucleo-cytoplasm partitioning of a chromatin regulator.

2019-01-12 | GSE119098 | GEO

bioadapt2011_cytopheno-CYTOPHENO: Nucleo-cytoplasmic co-adaptation and adaptive plant phenotypes

Project description:bioadapt2011_cytopheno-CYTOPHENO: Nucleo-cytoplasmic co-adaptation and adaptive plant phenotypes

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Drosophila melanogaster

Project description:Nucleo-cytoplasmic mRNA distribution

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Nucleo-cytoplasmic partitioning of ARF proteins controls auxin responses in Arabidopsis thaliana

Project description:Nucleo-cytoplasmic partitioning of ARF proteins controls auxin responses in Arabidopsis thaliana

| PRJNA412513 | ENA

Changes in nuclear and cytoplasmic microRNA distribution following hypoxic stress

Project description:Purpose: MicroRNAs have well characterized roles in cytoplasmic gene regulation by binding mRNA and inhibiting translation. However, besides this post-transcriptional gene silencing, miRNAs have also been implicated in transcriptional gene regulation and alternative splicing, events that are restricted to the cell nucleus. The nuclear functions of miRNAs are currently not understood, and there is a paucity of systematic studies of miRNA nuclear-cytoplasmic distribution and fewer still which have investigated this in the context of physiological conditions. Methods: Here we performed nuclear-cytoplasmic fractionation in a mouse endothelial cell line in hypoxia and characterized the localization of miRNAs using small RNA sequencing. Results: We show here that there is a broad population of mature miRNAs in the cell nucleus and that it is also altered upon exposure to hypoxia. Conclusions: Our results strongly imply that miRNAs have extensive regulatory functions in the nucleus and expand potential therapeutic use of small RNA molecules.

2019-07-17 | GSE125390 | GEO

Nucleo-cytoplasmic partitioning of ARF proteins controls auxin responses in Arabidopsis thaliana

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

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