Gene expression analysis of U87 cells with nuclear and non nuclear IGF1R localization
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PROVIDER: PRJNA802569 | ENA |
REPOSITORIES: ENA
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Project description:Transcriptional profiling of U87WT 5 in comparison to U87Mut 5 cells. Three different cultured conditions were tested for 24 h: Serum free media, 50nM IGF1 and 50nM IGF1+ 0.5uM 0SI906
2022-02-02 | GSE195896 | GEO
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Project description:IGF1 and IGF1 receptors (IGF1R) are present in the adult heart and have been shown to be essential for myocardial performance. Insulin-like growth factor 1 (IGF1) is produced in numerous tissues particularly by the liver in response to growth hormone stimulation and is an important factor in the regulation of post-natal growth and development. We have generated and characterized transgenic mice over-expressing the IGF1R. We crossed IGF1R transgenic mice with dominant negative (dn)PI3K (p110) and with constitutively active (ca)PI3K(p110) transgenic mice. Expression profiling was performed on the ventricles of IGF1R, IGF1R-caPI3K, IGF1R-dnPI3K, caPI3K, dnPI3K transgenic female mice at 3 months of age. Non-transgenic littermates were used as controls.
2007-09-29 | E-GEOD-1143 | biostudies-arrayexpress
Project description:The Caenorhabditis elegans oxidative stress response transcription factor, SKN-1, is essential for the maintenance of redox homeostasis and is a functional ortholog of the Nrf family of transcription factors. The numerous levels of regulation that govern these transcription factors underscore their importance. Here, we add a thioredoxin, encoded by trx-1, to the expansive list of SKN-1 regulators. We report that loss of trx-1 promotes nuclear localization of intestinal SKN-1 in a redox-independent, cell non-autonomous fashion from the ASJ neurons. Furthermore, this regulation is not general to the thioredoxin family, as two other C. elegans thioredoxins TRX-2 and TRX-3 do not play a role in this process. Moreover, TRX-1-dependent regulation requires signaling from the p38 MAPK signaling pathway. However, while TRX-1 regulates SKN-1 nuclear localization, SKN-1 transcriptional activity remains largely unaffected. Interestingly, RNA-Seq revealed that loss of trx-1 elicits a general, organism-wide down-regulation of several classes of genes; those encoding for collagens and lipid transport and localization being most prevalent. However, one prominent lipase-related gene, lips-6, is highly up regulated upon loss of trx-1 in a skn-1-dependent manner. Together, these results uncover a novel role for a thioredoxin in regulating intestinal SKN-1 nuclear localization in a cell non-autonomous manner, thereby contributing to the understanding of the processes involved in maintaining redox homeostasis throughout an organism. Four samples were analyzed: Two nematode strains were analyzed, each under non-stressed and stressed (10mM NaAs) conditions
2016-04-01 | E-GEOD-77976 | biostudies-arrayexpress
Project description:The Caenorhabditis elegans oxidative stress response transcription factor, SKN-1, is essential for the maintenance of redox homeostasis and is a functional ortholog of the Nrf family of transcription factors. The numerous levels of regulation that govern these transcription factors underscore their importance. Here, we add a thioredoxin, encoded by trx-1, to the expansive list of SKN-1 regulators. We report that loss of trx-1 promotes nuclear localization of intestinal SKN-1 in a redox-independent, cell non-autonomous fashion from the ASJ neurons. Furthermore, this regulation is not general to the thioredoxin family, as two other C. elegans thioredoxins TRX-2 and TRX-3 do not play a role in this process. Moreover, TRX-1-dependent regulation requires signaling from the p38 MAPK signaling pathway. However, while TRX-1 regulates SKN-1 nuclear localization, SKN-1 transcriptional activity remains largely unaffected. Interestingly, RNA-Seq revealed that loss of trx-1 elicits a general, organism-wide down-regulation of several classes of genes; those encoding for collagens and lipid transport and localization being most prevalent. However, one prominent lipase-related gene, lips-6, is highly up regulated upon loss of trx-1 in a skn-1-dependent manner. Together, these results uncover a novel role for a thioredoxin in regulating intestinal SKN-1 nuclear localization in a cell non-autonomous manner, thereby contributing to the understanding of the processes involved in maintaining redox homeostasis throughout an organism.
2016-04-01 | GSE77976 | GEO
Project description:A long intergenic non-coding RNA regulates nuclear localization of DNA methyl transferase-1
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Project description:To elucidate the role of HNRNPU in regulation of lncRNAs nuclear localization, we knocked down HNRNPU in K562 cells using short interfering RNAs and performed subcellular RNA-seq using nuclear or cytosolic RNAs
2021-01-23 | GSE165310 | GEO
Project description:RNA-seq Analysis of U87: Ctrl, U87:EGFR, U87:EGFRvIII, U87:EGFR+EGFRvIII and U87:EGFR+EGFRvIII KRAS KO
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Project description:DNA methyl-transferase-1 or DNMT1 maintains DNA methylation in the genome and is important for regulating gene expression in cells. Aberrant changes in DNMT1 activity and DNA methylation are commonly observed in cancers and many other diseases. Recently, a number of long intergenic non-protein-coding RNAs or lincRNAs have been shown to play a role in regulating DNMT1 activity. CCDC26 is a nuclear lincRNA which is frequently mutated in cancers and is a hotbed for disease-associated single nucleotide changes. However, the functional mechanism of CCDC26 is not understood. Here, we show that this lincRNA is concentrated on the nuclear periphery. Strikingly, in the absence of CCDC26 lincRNA, DNMT1 is mis-located in the cytoplasm and the genomic DNA is significantly hypomethylated. This is accompanied by double stranded DNA breaks and increased cell death. These results point to a previously unrecognized mechanism of lincRNA mediated subcellular localization of DNMT1 and regulation of DNA methylation.
2021-03-16 | GSE105029 | GEO
Project description:Since the sequencing of the human genome, one of the biggest surprises has been the annotation of thousands of long noncoding RNAs (lncRNAs). Although lncRNAs and mRNAs are similar in many ways, it has become clear they differ in localization properties with lncRNAs being more nuclear enriched and in several cases exclusively nuclear. Yet the RNA based sequences that determine nuclear localization remain poorly understood. Towards the goal of systematically dissecting the lncRNA sequences that impart nuclear enrichment, we developed a massively parallel reporter assay (MPRA). Unlike previous MPRAs that determine motifs important for transcriptional regulation, we have modified this approach to identify sequences sufficient for RNA nuclear enrichment for 38 lncRNAs. Using this approach, we identified 109 distinct, conserved nuclear enrichment regions, originating from 29 distinct lncRNAs. We also discovered two shorter motifs that are enriched in our nuclear enrichment regions—one specific to XIST, and a more general motif found in 21 different lncRNAs. We further validated the autonomous functionality of the XIST motif and three nuclear enrichment regions by single molecule RNA FISH. Taken together, these results give the first glimpse of sequence elements responsible for the nuclear enrichment of this critical class of RNA molecules.
2018-01-10 | GSE98828 | GEO