Gene expression of hormone-treated U2OS cells expressing GR alleles
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE45407 | GEO | 2014/07/15
SECONDARY ACCESSION(S): PRJNA193692
REPOSITORIES: GEO
Similar Datasets
Project description:The glucocorticoid receptor (GR) binds to DNA in at least three stoichiometric ratios to regulate gene expression. The dimeric binding of GR to a 15 base pair core sequence has been well studied, and is associated with activation of gene expression. Monomeric GR has been associated with repression. GR has also been shown to form tetramers on DNA in live cells. The role of DNA sequence in directing DNA-binding stoichiometry and subsequent gene regulation is not clear. We took an unbiased approach using SELEX-seq to calculate comprehensive monomeric- and dimeric-binding profiles for GR. The monomeric site is composed of a canonical half-site, but is distinguished from the dimer site by a downstream TTTg motif and the absence of a second half-site. To probe the mechanism of how this motif favors monomeric binding, we performed Spec-/Coop-seq. The TTTg increases monomeric affinity while decreasing cooperative dimeric binding. Crystal structures indicated that TTTg results in a narrowed minor groove bringing residues Y455 and K471 of GR into the proximity of DNA, increasing affinity. Interestingly, although monomeric binding is more often associated with repression of gene expression than dimeric binding, the trend is not significant. Consistent with live-cell imaging, a meta-analysis of GR:DNA structures reveals that, regardless of binding sequence, GR binds to DNA as a dimer of dimers using highly similar interfaces. This suggests that the functional stoichiometry of GR in the cell is tetrameric, and that sequence may modulate GR activity.
2018-12-01 | GSE107584 | GEO
Project description:The glucocorticoid receptor (GR) is a ubiquitously expressed transcription factor that controls metabolic and homeostatic processes essential for life. Although numerous crystal structures of the GR ligand-binding domain (GR-LBD) have been reported, the functional oligomeric state of the full-length receptor, which is essential for its transcriptional activity, remains disputed. Here we present five new crystal structures of agonist-bound GR-LBD, along with a thorough analysis of previous structural work. Biologically relevant homodimers were identified by studying a battery of GR point mutants including crosslinking assays in solution and quantitative fluorescence microscopy in live cells. Our results highlight the relevance of non-canonical dimerization modes for GR, especially of contacts made by loop L1-3 residues such as Tyr545. Our work unveils likely pathophysiologically relevant quaternary assemblies of the nuclear receptor with important implications for glucocorticoid action and drug design.
2023-03-11 | PXD028039 | Pride
Project description:Prednisone is anti-inflammatory glucocorticoid (GC), and GC-based therapy is most used combination chemotherapy for treating aggressive B-cell lymphomas. However, there are still gaps in our understanding of specific mechanism of GC’s action for its cytotoxicity. By performing multi-omics approaches, we identified new GR targets and how these targets control the b-cell receptor signaling networks, providing a mechanistic framework upon which to base combination therapies.
2024-05-02 | PXD041891 | Pride
Project description:The glucocorticoid receptor (GR) is a nuclear hormone receptor critical to the regulation of energy metabolism and the inflammatory response. The actions of GR are highly dependent on cell type and environmental context. Here, we demonstrate the necessity for liver lineage-determining factor hepatocyte nuclear factor 4A (HNF4A) in defining liver-specificity of GR action. In normal mouse liver, the HNF4 motif lies adjacent to the glucocorticoid response element (GRE) at GR binding sites found within regions of open chromatin. In the absence of HNF4A, the liver GR cistrome is remodelled, with both loss and gain of GR recruitment evident. Loss of chromatin accessibility at HNF4A-marked sites leads to loss of GR binding at weak GRE motifs. GR binding is gained at sites characterised by strong GRE motifs, which typically show GR recruitment in non-liver tissues. The functional importance of these HNF4A-regulated GR sites is further demonstrated by evidence of an altered transcriptional response to glucocorticoid treatment in the Hnf4a-null liver.
2022-01-20 | E-MTAB-10266 | biostudies-arrayexpress
Project description:The glucocorticoid receptor (GR) is a nuclear hormone receptor critical to the regulation of energy metabolism and the inflammatory response. The actions of GR have been shown to be highly dependent on context. Here, we demonstrate the necessity for liver lineage-determining factor hepatocyte nuclear factor 4A (HNF4A) in defining tissue-specificity of GR action. In normal liver, the HNF4 motif lies adjacent to the glucocorticoid response element (GRE) at GR binding sites found within regions of open chromatin. In the absence of HNF4A, the liver GR cistrome is remodelled, with both loss and gain of GR recruitment evident. Lost sites are characterised by HNF4 motifs and weak GRE motifs. Gained sites are characterised by strong GRE motifs, and typically show GR recruitment in non-liver tissues. These RNA-seq data demonstrate the functional importance of these HNF4A-regulated GR sites by showing evidence of an altered transcriptional response to glucocorticoid treatment in the Hnf4a-null liver. In Hnf6-null liver, a far more minor effect on the glucocorticoid response is observed.
2021-04-09 | E-MTAB-10247 | biostudies-arrayexpress
Project description:The glucocorticoid receptor (GR) is a nuclear hormone receptor critical to the regulation of energy metabolism and the inflammatory response. The actions of GR have been shown to be highly dependent on context. Here, we performed GR ChIP-seq in mouse liver to demonstrate the necessity for liver lineage-determining factor hepatocyte nuclear factor 4A (HNF4A) in defining tissue-specificity of GR action. In normal liver, the HNF4 motif lies adjacent to the glucocorticoid response element (GRE) at GR binding sites found within regions of open chromatin. In the absence of HNF4A, the liver GR cistrome is remodelled, with both loss and gain of GR recruitment evident. Lost sites are characterised by HNF4 motifs and weak GRE motifs. Gained sites are characterised by strong GRE motifs, and typically show GR recruitment in non-liver tissues. The functional importance of these HNF4A-regulated GR sites is further demonstrated by evidence of an altered transcriptional response to glucocorticoid treatment in the Hnf4a-null liver.
2021-04-09 | E-MTAB-10224 | biostudies-arrayexpress
Project description:Long-term glucocorticoid treatment in multiple myeloma is hampered by deleterious side effects. Glucocorticoids bind to the glucocorticoid receptor (GR), which is a crucial drug target because its activation triggers myeloma cell death. The mineralocorticoid receptor (MR) is a closely related nuclear receptor but its impact on glucocorticoid responsiveness in myeloma is unknown. Here we reveal a functional crosstalk between GR and MR that culminates in improved myeloma cell killing. We show that the GR agonist Dexamethasone (Dex) downregulates MR levels in a GR-dependent way in myeloma cells. Co-treatment of Dex with the MR antagonist Spironolactone enhances Dex-induced cell killing in (primary) myeloma cells. The crosstalk is further evidenced by an endogenous interaction between GR and MR in myeloma cells that is ligand-inducible and by a distinctive gene expression profile. Our study demonstrates that GR-MR crosstalk is therapeutically relevant in myeloma and presents a glucocorticoid-based dose-reduction strategy that could diminish glucocorticoid-related side effects in patients.
2023-08-23 | GSE200313 | GEO
Project description:Glucocorticoid Receptor (GR) suppresses inflammation by activating anti-inflammatory and repressing pro-inflammatory genes. GR-interacting protein (GRIP)1 of the p160 family has emerged as a unique GR corepressor in macrophages (MΦ), however, whether GRIP1 contributes to GR-activated transcription, and what dictates its context-specific coactivator vs. corepressor properties is unknown. We report that loss of GRIP1 in human and mouse MΦ attenuated GR-mediated induction of several anti-inflammatory targets, revealing a non-redundant function of GRIP1 in coactivation. Moreover, glucocorticoid treatment of quiescent MΦ globally directed GRIP1 toward GR-bound genomic sites dominated by classic palindromic GREs, suggesting its dedicated role as a GR coactivator. Further, GRIP1 N-terminal region was phosphorylated at a serine cluster by Cyclin-Dependent Kinase (CDK)9, which was recruited into GC-induced GR:GRIP1:CDK9 ternary complexes, producing distinct GRIP1 phospho-isoforms at different GREs even associated with the same gene. Functionally, phosphorylation potentiated GRIP1 coactivator properties by facilitating its recruitment and/or creating novel protein:protein interaction surfaces in a GRE-specific manner. Strikingly, GRIP1 function as a GR corepressor was phosphorylation-independent; consistently, no phospho-GRIP1 or CDK9 was detected at GR transrepression sites near pro-inflammatory genes. Thus, liganded GR in MΦ restricts actions of its own coregulator via CDK9-mediated phosphorylation to a subset of complexes driving anti-inflammatory gene transcription.
2017-09-29 | GSE99887 | GEO
Project description:The Glucocorticoid Receptor (GR) is both one of the most widely used clinical drug targets and a very potent metabolic regulator. GR belongs to the nuclear hormone receptor family of ligand-gated transcription factors that govern mammalian physiology. Upon ligand binding, GR enters the nucleus to regulate gene expression both positively and negatively. It is known to bind to consensus DNA sequences termed glucocorticoid response elements (GREs), but the mechanisms determining transcriptional activation versus repression remain an unresolved molecular paradox. Prevailing models suggest that tethering of GR to AP-1 or NF-κB via protein-protein interactions, rather than direct DNA binding, specifies negative regulation. However, here we show that the repression of inflammatory genes as well as all other glucocorticoid responses, require direct DNA binding of GR. Generating GR point mutant mice that retain the ability to tether via protein-protein interactions while unable to recognize DNA sequences, we demonstrate that response element recognition via the Zinc finger is absolutely required for both transcriptional activation and repression. We have used ChIP-Seq and RNA-Seq in inflammatory and metabolic cells and tissues together with proteomics to reveal that DNA binding of GR is necessary for the assembly of a functional SWI/SNF coregulator complex. Generally, the desired anti-inflammatory actions of GR are attributed to the silencing of inflammatory genes, while its adverse effects are believed to result from the transcriptional upregulation of metabolic targets. Our findings not only challenge classical models and dogmas of GR mediated gene regulation, but will provide an important basis for the development of novel immunosuppressants with reduced side effect profiles.
2020-07-07 | PXD013772 | Pride
Project description:We have applied next-generation sequencing technology to obtain high through-put profiling of glucocorticoid receptor (GR) DNA binding in whole hippocampus from male rat brain. By obtaining sequence from immunoprecipitated, sonicated chromatin, we have generated genome-wide binding maps for GR in two contexts, testing whether chromatin is primed for GR binding according to the animal's acute experience. In one context (stressed) adrenalectomised rats are infused with corticosterone while undergoing restraint stress. In the second context (non-stressed control) rats are infused with the same corticosterone profile but restraint stress is omitted. We find that GR binding was highly similar suggesting factors other than GR binding may account for any context-dependent alterations in GR function associated with acute stress. We show that GR is positioned near to genes associated with structural and functional organisation of the hippocampus at largely intergenic and intronic sites. Glucocorticoid response element sequences support a majority of GR binding in this tissue but may be reinforced by NF-1 and/or basic-helix loop helix transcription factors binding their nearby recognition motifs. We found little evidence for tethering of GR to other factors, or for the usage of negative glucocorticoid response elements.
2017-02-20 | GSE94008 | GEO