Analysis of gene expression profiles of the cold-inducible RNA-binding protein knockdown BHK21 (Cirp−/−BHK21) cells
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE54425 | GEO | 2017/01/01
SECONDARY ACCESSION(S): PRJNA236602
REPOSITORIES: GEO
Similar Datasets
Project description:In mammalian tissues circadian gene expression can be driven by local oscillators or systemic signals controlled by the master pacemaker in the suprachiasmatic nucleus. Here we show that simulated body temperature cycles, but not peripheral oscillators, can control the rhythmic expression of Cold-Inducible RNA binding Protein (CIRP) in cultured fibroblasts. In turn, loss-of-function experiments indicate that CIRP is required for high amplitude circadian gene expression. The transcriptome-wide identification of CIRP-bound RNAs by a biotin-streptavidin based CLIP-seq procedure revealed several CIRP-bound transcripts encoding circadian oscillator proteins. One of these, CLOCK, accumulated to particularly low levels in CIRP-depleted fibroblasts. Since ectopic expression of CLOCK improved circadian gene expression in these cells, we surmise that CIRP confers robustness to circadian oscillators via the regulation of CLOCK expression. Identification of CIRP-interacting RNA molecules in NIH3T3 cells and RNA expression in NIH3T3 cells treated with Control or CIRP siRNA after incubation of the cells at 33M-BM-0C for 8 hours
2012-08-24 | E-GEOD-37685 | biostudies-arrayexpress
Project description:In mammalian tissues circadian gene expression can be driven by local oscillators or systemic signals controlled by the master pacemaker in the suprachiasmatic nucleus. Here we show that simulated body temperature cycles, but not peripheral oscillators, can control the rhythmic expression of Cold-Inducible RNA binding Protein (CIRP) in cultured fibroblasts. In turn, loss-of-function experiments indicate that CIRP is required for high amplitude circadian gene expression. The transcriptome-wide identification of CIRP-bound RNAs by a biotin-streptavidin based CLIP-seq procedure revealed several CIRP-bound transcripts encoding circadian oscillator proteins. One of these, CLOCK, accumulated to particularly low levels in CIRP-depleted fibroblasts. Since ectopic expression of CLOCK improved circadian gene expression in these cells, we surmise that CIRP confers robustness to circadian oscillators via the regulation of CLOCK expression.
2012-08-24 | GSE37685 | GEO
Project description:Cold-inducible RNA-binding protein (CIRP) is a ubiquitous intracellular RNA chaperon, which serves as a damage-associated molecular pattern (DAMP) when released outside the cells upon stimulation by inflammation and infection. It has been shown that CIRP promotes splenic CD4+ and CD8+ T-cell activation in vivo and predisposes CD4+ T cells to a Th1 hyperinflammatory response profile in vitro. However, the effect and underlying mechanisms of CIRP on Th17/Treg differentiation is still unclear. This study reveals the transcriptomic changes of mouse Naïve CD4+ T cells induced by Recombinant Mouse CIRP (rmCIRP) in vitro.
2023-06-30 | GSE234044 | GEO
Project description:We explored the microevolutionary trends of CTCF binding evolution by preforming ChIP-seq experiments in five closely related Mus strains, subspecies and species: Mus musculus domesticus, Mus musculus castaneus, Mus spretus, Mus caroli and Mus pahari. All experiments were performed in adult male liver samples in 3 biological replicates and with an input control set. Complementary RNA-seq data from this same study have been deposited in ArrayExpress under accession numebr E-MTAB-5768 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5768 ).
2018-03-06 | E-MTAB-5769 | biostudies-arrayexpress
Project description:We compared gene expression differences in the polytypic species complex Mus musculus (Mus musculus musculus, Mus musculus domesticus, Mus musculus castaneus and Mus musculus ssp) with that of Mus spretus via oligonucleotide microarrays representing more than 20,000 genes. Analysis of the results by two way ANOVA statistics suggests that the most genes with significant differences in expression levels among the subspecies are found in liver and kidney and the least in testis. This picture is different when one compares with Mus spretus, where the largest number of differences is found in testis. Keywords: multi-species comparison
2006-12-13 | GSE2597 | GEO
Project description:The aim of the study was to investigate whether the trefoil peptide genes, in concerted action with a miRNA regulatory network, were contributing to nutritional maintrenance. Using a Tff3 knock-out mouse model, 21 specific miRNAs were noted to be significantly deregulated when compared to the wild type strain. n = 6 mus musculus wild type samples and n = 6 knock-down experiments have been screened for a currently known mus musculus miRNAs and validated by TaqMan
2010-09-20 | E-GEOD-23819 | biostudies-arrayexpress
Project description:The aim of the study was to investigate whether the trefoil peptide genes, in concerted action with a miRNA regulatory network, were contributing to nutritional maintrenance. Using a Tff2 knock-out mouse model, 48 specific miRNAs were noted to be significantly deregulated when compared to the wild type strain. n = 6 mus musculus wild type samples and n = 6 knock-down experiments have been screened for a currently known mus musculus miRNAs and validated by TaqMan
2012-01-01 | E-GEOD-25815 | biostudies-arrayexpress
Project description:BackgroundNeuroinflammation is a key cascade after cerebral ischemia. Excessive production of proinflammatory mediators in ischemia exacerbates brain injury. Cold-inducible RNA-binding protein (CIRP) is a newly discovered proinflammatory mediator that can be released into the circulation during hemorrhage or septic shock. Here, we examine the involvement of CIRP in brain injury during ischemic stroke.MethodsStroke was induced by middle cerebral artery occlusion (MCAO). In vitro hypoxia was conducted in a hypoxia chamber containing 1% oxygen. CIRP and tumor necrosis factor-α (TNF-α) levels were assessed by RT-PCR and Western blot analysis.ResultsCIRP is elevated along with an upregulation of TNF-α expression in mouse brain after MCAO. In CIRP-deficient mice, the brain infarct volume, induction of TNF-α, and activation of microglia are markedly reduced after MCAO. Using microglial BV2 cells, we demonstrate that hypoxia induces the expression, translocation, and release of CIRP, which is associated with an increase of TNF-α levels. Addition of recombinant murine (rm) CIRP directly induces TNF-α release from BV2 cells and such induction is inhibited by neutralizing antisera to CIRP. Moreover, rmCIRP activates the NF-κB signaling pathway in BV2 cells. The conditioned medium from BV2 cells exposed to hypoxia triggers the apoptotic cascade by increasing caspase activity and decreasing Bcl-2 expression in neural SH-SY5Y cells, which is inhibited by antisera to CIRP.ConclusionExtracellular CIRP is a detrimental factor in stimulating inflammation to cause neuronal damage in cerebral ischemia.General significanceDevelopment of an anti-CIRP therapy may benefit patients with brain ischemia.
| S-EPMC4061249 | biostudies-literature
Project description:We analyzed KDM1A (LSD1) occupancy in the Xi during somatic cell reprogramming of female mouse cells. We use MEFs from hybrid embryos by crossing male Mus spretus and female Mus musculus domesticus C57BL/6J to distiguish genome DNA from the Xi. We found a possible physical and/or functional regulation of KDM1A during the X chromosome reactivation in the intiation site on the Xi.
2022-01-01 | GSE157479 | GEO
Project description:Cold-inducible RNA-binding protein (CIRP) is a cold-shock protein which can be induced after exposure to a moderate cold-shock in different species ranging from amphibians to humans. Expression of CIRP can also be regulated by hypoxia, UV radiation, glucose deprivation, heat stress and H2O2, suggesting that CIRP is a general stress-response protein. In response to stress, CIRP can migrate from the nucleus to the cytoplasm and regulate mRNA stability through its binding site on the 3'-UTR of its targeted mRNAs. Through the regulation of its targets, CIRP has been implicated in multiple cellular process such as cell proliferation, cell survival, circadian modulation, telomere maintenance and tumor formation and progression. In addition, CIRP can also exert its functions by directly interacting with intracellular signaling proteins. Moreover, CIRP can be secreted out of cells. Extracellular CIRP functions as a damage-associated molecular pattern to promote inflammatory responses and plays an important role in both acute and chronic inflammatory diseases. Here, we summarize novel findings of CIRP investigation and hope to provide insights into the role of CIRP in cell biology and diseases.
| S-EPMC5674272 | biostudies-literature