Differential Expression Analysis of wildtype, E12-/- and E47-/- neuronal stem cells
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ABSTRACT:
PROVIDER: PRJNA408140 | ENA |
REPOSITORIES: ENA
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Project description:RNA sequencing of neuronal stem cells from wildtype, E12-/- and E47-/- mice isolated at E14.5
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Project description:Glucocorticoids (GCs) are widely prescribed effective drugs, but their clinical use is compromised by severe side effects including hyperglycemia, hyperlipidemia and obesity. They bind to the Glucocorticoid Receptor (GR), which acts as a ligand-gated transcription factor. The transcriptional activation of metabolic genes by GR is thought to underlie these undesired adverse effects. Using mouse genetics, ChIP-Seq, RNA-Seq and ChIP-MS, we found that the bHLH transcription factor E47 is required for the regulation of hepatic glucose and lipid metabolism by GR in vivo, and that loss of E47 prevents the development of hyperglycemia and hepatic steatosis in response to GCs. Here we show that E47 and GR co-occupy metabolic promoters and enhancers. E47 is needed for the efficient binding of GR to chromatin and for the adequate recruitment of coregulators such as Mediator. Taken together, our results illustrate how GR and E47 regulate hepatic metabolism, and how inhibition of E47 might provide an entry point for novel GC therapies with reduced side effect profiles. These ChIP-MS data sets show IPs for GR in both wildtype and E47 mutant mouse livers treated with the synthetic glucocorticoid Dexamethasone.
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Project description:To elucidate the genome-wide role of Ca2+/ calmodulin inhibition of E2A in regulation of BCR activation, we performed DNA microarray analysis of activated splenic B cells expressing wildtype or CaM-resistant E12 mutant m8N47 with and without anti-IgM treatment for 3 hour.The expression of a remarkably large set of genes differed significantly.
2012-07-11 | GSE35747 | GEO
Project description:To elucidate the genome-wide role of Ca2+/ calmodulin inhibition of E2A in regulation of BCR activation, we performed DNA microarray analysis of activated splenic B cells expressing wildtype or CaM-resistant E12 mutant m8N47 with and without anti-IgM treatment for 3 hour.The expression of a remarkably large set of genes differed significantly. Primary splenic B-lymphocytes were purified from mice heterozygous for the deletion of E2A gene and infected with retroviruses expressing either wildtype or mutant E12 after activation with CD40L plus IL-4 for 14 h. After 12 h incubation, the infection was repeated for 12 h, followed by incubation for a further 22 h post-infection in fresh complete medium with the stimulants to allow expression of GFP and E12. In addition to CD40L plus IL-4, the medium was supplemented with LPS (200 ng/ml) during retroviral infection incubations to improve infection efficiency. To study gene expression following B-cell receptor activation, anti-mouse IgM (2.5 M-NM-<g/ml) was added for 3 hour. For DNA microarray analysis of infected B-lymphocytes, the infected cells were purified with a FACSAria cell sorter instrument (BD Biosciences) using their green fluorescence from expression of the GFP.
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Project description:In maturing T-lineage cells, the helix-loop-helix protein E47 has been shown to enforce a critical proliferation and developmental checkpoint commonly referred to as β selection. To examine how E47 regulates cellular expansion and developmental progression, we have used an E2A deficient lymphoma cell line and DNA microarray analysis to identify immediate E47 target genes. Hierarchical cluster analysis of gene expression patterns revealed that E47 coordinately regulates the expression of genes involved in cell survival, cell growth, lipid metabolism, stress response and lymphoid maturation. These include Cdk6, CD25, Tox, Gadd45a, Gadd45b, Gfi1, Gfi1b, Socs1, Socs3, Id2, Eto2 and Xbp1. We propose a regulatory network linking JAK/STAT mediated signaling, E47 and SOCS proteins in a common pathway. Finally, we suggest that the aberrant activation of Cdk6 in E47 deficient T-lineage cells contributes to the development of lymphoid malignancy. Keywords: gene targets for E47
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Project description:We performed RNA sequencing in different wildtype and E47ko tissues in response to treatment with glucocorticoids. We show a global deregulation of gene expression programs involved in lipid, triglyceride and cholesterol metabolism & transport for E47 mutant liver tissue.
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Project description:In maturing T-lineage cells, the helix-loop-helix protein E47 has been shown to enforce a critical proliferation and developmental checkpoint commonly referred to as β selection. To examine how E47 regulates cellular expansion and developmental progression, we have used an E2A deficient lymphoma cell line and DNA microarray analysis to identify immediate E47 target genes. Hierarchical cluster analysis of gene expression patterns revealed that E47 coordinately regulates the expression of genes involved in cell survival, cell growth, lipid metabolism, stress response and lymphoid maturation. These include Cdk6, CD25, Tox, Gadd45a, Gadd45b, Gfi1, Gfi1b, Socs1, Socs3, Id2, Eto2 and Xbp1. We propose a regulatory network linking JAK/STAT mediated signaling, E47 and SOCS proteins in a common pathway. Finally, we suggest that the aberrant activation of Cdk6 in E47 deficient T-lineage cells contributes to the development of lymphoid malignancy. We used the 1F9 cell line, originally isolated from E2A deficient thymomas. To identify E47 target genes, 1F9 cells were transduced with a retrovirus carrying an E47/estrogen receptor (E47ER) hybrid protein. Control cells were transduced with virus carrying the bHLH region but lacking the N-terminal transactivation domain. Both retroviral constructs also directed the expression of human CD25 (hCD25) to allow rapid isolation of transduced cells. One day post-infection, cells were incubated with 4-hydroxytamoxifen (4-OHT) for a period of six hours, to activate the E47ER fusion protein. hCD25 positive cells were purified using magnetic beads, RNA was isolated and used to generate probes for hybridization to murine oligonucleotide microarrays.
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Project description:E47 represses Foxp3 transcription, albeit indirectly through the activation of unknown negative regulatory of Foxp3 transcription. To identify target genes of E47 in regulatory T cells, we compared gene expression profiles of Treg cells overexpressing E47 compared to control-vector transduced cells.
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