Response to1 µM dexamethasone in MEF cells expressing GR dimer deficient mutant receptors
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ABSTRACT:
PROVIDER: PRJNA783901 | ENA |
REPOSITORIES: ENA
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Project description:The glucocorticoid (GC) receptor (GR) is essential in development and inflammation. Healthy GRdim/dim mice with reduced dimerization propensity due to a point mutation (A465T) at the dimer interface of the GR DNA binding domain (DBD) (here GRD/D) have helped to define GR monomer and dimer functions of GR. Since GRD/D retains residual dimerization capacity, we generated the dimer-nullifying double mutant GRD+L/D+L mice, featuring an additional mutation (I634A) in the ligand binding domain (LBD) of GR. These mice are perinatally lethal, as are GRL/L mice, displaying improper lung and skin formation. We used embryonic fibroblasts, high and low doses of dexamethasone (Dex), nuclear translocation, RNAseq, dimerization assays and ligand binding assays (and Kd values), we suggest that the lethal phenotype is due to insufficient ligand binding. The data suggest cross talk between GR dimerization potential and ligand affinity. We conclude that a mutation as subtle as this I634A, at a position not directly involved in ligand interactions senso stricto, can thus still influence ligand binding and have a lethal outcome.
2021-12-03 | GSE189620 | GEO
Project description:The glucocorticoid (GC) receptor (GR) is essential in development and inflammation. Healthy GRdim/dim mice with reduced dimerization propensity due to a point mutation (A465T) at the dimer interface of the GR DNA binding domain (DBD) (here GRD/D) have helped to define GR monomer and dimer functions of GR. Since GRD/D retains residual dimerization capacity, we generated the dimer-nullifying double mutant GRD+L/D+L mice, featuring an additional mutation (I634A) in the ligand binding domain (LBD) of GR. These mice are perinatally lethal, as are GRL/L mice, displaying improper lung and skin formation. We used embryonic fibroblasts, high and low doses of dexamethasone (Dex), nuclear translocation, RNAseq, dimerization assays and ligand binding assays (and Kd values), we suggest that the lethal phenotype is due to insufficient ligand binding. The data suggest cross talk between GR dimerization potential and ligand affinity. We conclude that a mutation as subtle as this I634A, at a position not directly involved in ligand interactions senso stricto, can thus still influence ligand binding and have a lethal outcome.
2021-11-29 | GSE189356 | GEO
Project description:Response to 10 nM dexamethasone in MEF cells expressing GR dimer deficient mutant receptors
| PRJNA782638 | ENA
Project description:In order to identify relevant target genes of RAX1 (AT5G23000) involved in meristem initiation in Arabidopsis we generated dexamethasone inducible lines expressing either a mCherry-RAX1-GR or a mCherry-GR (mock construct) fusion protein. We analysed differential gene regulation after 4 hours of dexamethasone or mock treatment in 14 day-old seedlings. Paired-end sequencing was performed using 3 biological replicate for each genotype and differentially expressed genes were identified for the interaction of genotype and treatment.
2019-07-01 | E-MTAB-7050 | biostudies-arrayexpress
Project description:We performed ChIP-seq targeting the glucocorticoid receptor (GR) in the U2OS-GR cell line and the androgen receptor (AR) in the U2OS-AR cell line. The cell lines are derived from U2OS ATTC:HTB-96 and stably transfected with an expression construct for either rat GR or human AR, respectively. The U2OS-GR cells were treated with dexamethasone (1 µM) for 90 minutes. The U2OS-AR cells were treated with R1881 (5 nM) for 4 hours.
2021-03-09 | E-MTAB-9616 | biostudies-arrayexpress
Project description:We performed ChIP-seq in the GR18 cell line (derived from U2OS ATTC:HTB-96, stably transfected with an expression construct for GR), upon glucocorticoid (dexamethasone)treatment for 90 minutes. Cells were cross-linked with 1% formaldehyde for 3 minutes.
2019-03-11 | E-MTAB-7747 | biostudies-arrayexpress
Project description:We performed ChIP-seq targeting the H3K27ac, H3K4me1, H3K27me3 and H3K9me3 in the U2OS-GR and U2OS-AR cell lines. The cell lines are derived from U2OS ATTC:HTB-96 and stably transfected with an expression construct for either rat GR or human AR, respectively. The U2OS-GR cells were treated with dexamethasone (1 µM) or vehicle (ethanol) for 90 minutes. The U2OS-AR cells were treated with R1881 (5 nM) or vehicle (DMSO) for 4 hours.
2021-03-09 | E-MTAB-9617 | biostudies-arrayexpress
Project description:In order to identify targets of the transcription factor AUXIN RESPONSE FACTOR5 / MONOPTEROS (ARF5/MP), we compared transcriptomes of mp-B4149 mutant seedlings (9 day-old) and seedlings carrying the dexamethasone-inducible version of the MP inhibitor protein BODENLOS (GR-bdl). Without dexamethasone (DEX) treatment, this line is identical to the wild-type, while DEX treatment leads to strong inhibition of ARF-dependent transcription. To remove all endogenous MP-inhibiting Aux/IAA proteins, we treated mp or GR-bdl seedlings during 1 hour with auxin (50 micromolar Indole-3-Acetic Acid), either with or without a pretreatment with 10 micromolar DEX for 1 hour. Genes that are activated by MP are expected to br downregulated in mp seedlings and in the GR-bdl line afer DEX treatment. We used biological duplicates for each of the three treatments. Keywords: Transcriptional profiling of transcription factor targets
2010-04-01 | GSE13881 | GEO
Project description:To quantify functional enhancers, we performed STARR-seq (Self-Transcribing Active Regulatory Region sequencing) in the U2OS-GR and the U2OS-AR cell lines (derived from U2OS ATTC:HTB-96, stably transfected with an expression construct for rat GR or human AR, respectively). U2OS-GR cells were treated with dexamethasone (1 µM) or vehicle (ethanol) for 14 hours. U2OS-AR cells were treated with R1881 (5 nM) or vehicle (DMSO) for 14 hours. To limit the number of putative enhancers, the STARR library contained genomic regions isolated by FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements) from dexamethasone-treated U2OS-GR cells to include regions that gain accessibility upon GR activation. We added unique molecular identifiers (UMIs) during the reverse transcription stage to facilitate quantitative measurements of enhancer activity for each fragment. The UMI for each read is present within the sequence identifier line (directly following the y coordinate and separated by a ':') of the fastq files.
2021-03-09 | E-MTAB-9614 | biostudies-arrayexpress
Project description:In order to identify targets of the transcription factor AUXIN RESPONSE FACTOR5 / MONOPTEROS (ARF5/MP), we compared transcriptomes of mp-B4149 mutant seedlings (9 day-old) and seedlings carrying the dexamethasone-inducible version of the MP inhibitor protein BODENLOS (GR-bdl). Without dexamethasone (DEX) treatment, this line is identical to the wild-type, while DEX treatment leads to strong inhibition of ARF-dependent transcription. To remove all endogenous MP-inhibiting Aux/IAA proteins, we treated mp or GR-bdl seedlings during 1 hour with auxin (50 micromolar Indole-3-Acetic Acid), either with or without a pretreatment with 10 micromolar DEX for 1 hour. Genes that are activated by MP are expected to br downregulated in mp seedlings and in the GR-bdl line afer DEX treatment. We used biological duplicates for each of the three treatments. Keywords: Transcriptional profiling of transcription factor targets Mp mutant and GR-bdl seeds were germinated on solid 1/2MS media, and transferred to liquid medium after 9 days of horizontal growth. Duplicate cultures were generated for mp mutants, and quadruplicates for the GR-bdl line. 10 micromolar DEX was added to both mp cultures and to two of the GR-bdl cultures, and seedlings were gently shaken during 1 hour. Then, 50 micromolar IAA was added to all 6 cultures and seedlings were incubated with gentle shaking for another hour. Total RNA was isolated from the seedlings using a QIAgen RNeasy kit, and reverse transcription, in-vitro transcription, cRNA labling and fragemntation was done according to established methods (Schmid et al., Nature Genetics [2005] 37, 501-506). Labeled cRNA was hybridized to Arabidopsis ATH1 arrays.
2010-04-12 | E-GEOD-13881 | biostudies-arrayexpress