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E-GEOD-30592 - Expression profile of A1-2 cells treated with 100 nM Dexamethasone or ethanol vehicle for 8h

Status
Released on 28 February 2012, last updated on 12 August 2015
Organism
Homo sapiens
Samples (6)
Array (1)
Protocols (8)
Description
A1-2 cells treated with 100 nM Dexamethasone or ethanol vehicle for 8h. The ability of steroid hormone receptors to initiate a genetic program is tightly regulated by the chromatin environment of the responsive regions. Using the glucocorticoid receptor (GR) as a model factor for transcriptional initiation, we classified chromatin structure through Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE), a technique designed to identify regulatory regions and open chromatin within the genome. We looked at dynamic changes in FAIRE signals prior to and following activation of GR with its ligand, dexamethesone, specifically at regions of receptor interaction. We have found a distribution of GR responsive regions that respond to activation by varying degrees of chromatin modulation. The majority of regions that demonstrate GR interaction also demonstrate increases in FAIRE signal in response to ligand. Most of these GR responsive regions fell within a narrow window of FAIRE signal in the basal chromatin state, suggesting a preferred chromatin structure for GR recruitment. Supporting this notion, global FAIRE-seq data indicated an enrichment of signal surrounding the GR binding site prior to activation. FAIRE signal induction correlated to an increase in nuclease sensitivity and overall FAIRE signal also represented a general accessibility of the chromatin. Further investigation into the requirement of ATPase-dependent chromatin remodeling showed response element specific effects of Brg-1 knockdown. FAIRE induction was universally decreased by Brg-1 depletion, but to varying degrees in a target specific manner. Taken together, these data suggest classes of nuclear receptor response regions that react to activation through different chromatin regulatory events and identify a novel identifier of chromatin structure that classifies the majority of response elements tested. Experiment performed in triplicate. 3 biological replicates of A1-2 cells treated with dexamethasone and 3 biological replicates of A1-2 cells treated with ethanol
Experiment type
transcription profiling by array 
Contacts
NIEHS Microarray Core <microarray@niehs.nih.gov>, Craig J Burd, Dhiral Phadke, Grace E Kissling, Ruchir R Shah, Trevor K Archer, Valerie J Davis
Citation
Analysis of chromatin dynamics during glucocorticoid receptor activation. Burd CJ, Ward JM, Crusselle-Davis VJ, Kissling GE, Phadke D, Shah RR, Archer TK.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-30592.idf.txt
Sample and data relationshipE-GEOD-30592.sdrf.txt
Raw data (1)E-GEOD-30592.raw.1.zip
Processed data (1)E-GEOD-30592.processed.1.zip
Array designA-AGIL-28.adf.txt
Links