Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

A1-2 expression analysis of GR activation

ABSTRACT: 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

ORGANISM(S): Homo sapiens

SUBMITTER: NIEHS Microarray Core

PROVIDER: E-GEOD-30592 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Analysis of chromatin dynamics during glucocorticoid receptor activation.

Burd Craig J CJ Ward James M JM Crusselle-Davis Valerie J VJ Kissling Grace E GE Phadke Dhiral D Shah Ruchir R RR Archer Trevor K TK

Molecular and cellular biology 20120326 10

Steroid hormone receptors initiate a genetic program 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). We looked at dynamic changes in FAIRE signals during GR activation specifically at regions of receptor interaction. We found a distribution of GR-responsive regions with diverse ...[more]

PMID: 22451486

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Project description:These tracks display a synthesis of evidence from different assays as part of the four Open Chromatin track sets. This track displays open chromatin regions and/or transcription factor binding sites identified in multiple cell types by one or more complementary methodologies, DNaseI hypersensitivity (HS) (Duke DNaseI HS), Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (UNC FAIRE), and chromatin immunoprecipitation (ChIP) for select regulatory factors (UTA TFBS). Each methodology was performed on the same cell type using identical growth conditions. (Note: Data for some or all ChIP experiments may not be available for all cell types). Regions that overlap between methodologies identify regulatory elements that are cross-validated indicating high confidence regions. In addition, multiple lines of evidence suggest that regions detected by a single assay (e.g., DNase-only or FAIRE-only) are also biologically relevant (Song et al., submitted). DNaseI HS data: DNaseI is an enzyme that has long been used to map general chromatin accessibility, and DNaseI "hypersensitivity" is a feature of active cis-regulatory sequences.The use of this method has led to the discovery of functional regulatory elements that include promoters, enhancers, silencers, insulators, locus control regions, and novel elements. DNaseI hypersensitivity signifies chromatin accessibility following binding of trans-acting factors in place of a canonical nucleosome. FAIRE data: FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements) is a method to isolate and identify nucleosome-depleted regions of the genome. FAIRE was initially discovered in yeast and subsequently shown to identify active regulatory elements in human cells (Giresi et al., 2007). Similar to DNaseI HS, FAIRE appears to identify functional regulatory elements that include promoters, enhancers, silencers, insulators, locus control regions and novel elements. ChIP data: ChIP (Chromatin Immunoprecipitation) is a method to identify the specific location of proteins that are directly or indirectly bound to genomic DNA. By identifying the binding location of sequence-specific transcription factors, general transcription machinery components, and chromatin factors, ChIP can help in the functional annotation of the open chromatin regions identified by DNaseI HS mapping and FAIRE. Input data: As a background control experiment, we sequenced the input genomic DNA sample that was used for ChIP. Crosslinked chromatin is sheared and the crosslinks are reversed without carrying out the immunoprecipitation step. This sample is otherwise processed in a manner identical to the ChIP sample as described below. The input track is useful in revealing potential artifacts arising from the sequence alignment process such as copy number differences between the reference genome and the sequenced samples, as well as regions of poor sequence alignability. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each site, the maximum F-Seq Density Signal value has been calculated for each assay that was performed in that cell type. F-Seq employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Significant regions, or peaks, were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05 (DNaseI HS, ChIP) or 0.1 (FAIRE) threshold were considered significant. See assay specific description pages ( Duke DNaseI HS, UNC FAIRE and UTA TFBS) for more details. A Fisher's Combined P-value for DNaseI HS and FAIRE was calculated using Fisher's combined probability test. First, a test statistic is calculated using the formula x^2 = -2*sum(ln(pi)) where pi are the p-values calculated for DNaseI HS and FAIRE. X2 follows a chi-squared distribution, thus a combined p-value can be assigned to this test statistic.

Project description:This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Terry Furey mailto:tsfurey@duke.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). These tracks display a synthesis of evidence from different assays as part of the four Open Chromatin track sets. This track displays open chromatin regions and/or transcription factor binding sites identified in multiple cell types by one or more complementary methodologies, DNaseI hypersensitivity (HS) (Duke DNaseI HS), Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (UNC FAIRE), and chromatin immunoprecipitation (ChIP) for select regulatory factors (UTA TFBS). Each methodology was performed on the same cell type using identical growth conditions. (Note: Data for some or all ChIP experiments may not be available for all cell types). Regions that overlap between methodologies identify regulatory elements that are cross-validated indicating high confidence regions. In addition, multiple lines of evidence suggest that regions detected by a single assay (e.g., DNase-only or FAIRE-only) are also biologically relevant (Song et al., submitted). DNaseI HS data: DNaseI is an enzyme that has long been used to map general chromatin accessibility, and DNaseI "hypersensitivity" is a feature of active cis-regulatory sequences.The use of this method has led to the discovery of functional regulatory elements that include promoters, enhancers, silencers, insulators, locus control regions, and novel elements. DNaseI hypersensitivity signifies chromatin accessibility following binding of trans-acting factors in place of a canonical nucleosome. FAIRE data: FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements) is a method to isolate and identify nucleosome-depleted regions of the genome. FAIRE was initially discovered in yeast and subsequently shown to identify active regulatory elements in human cells (Giresi et al., 2007). Similar to DNaseI HS, FAIRE appears to identify functional regulatory elements that include promoters, enhancers, silencers, insulators, locus control regions and novel elements. ChIP data: ChIP (Chromatin Immunoprecipitation) is a method to identify the specific location of proteins that are directly or indirectly bound to genomic DNA. By identifying the binding location of sequence-specific transcription factors, general transcription machinery components, and chromatin factors, ChIP can help in the functional annotation of the open chromatin regions identified by DNaseI HS mapping and FAIRE. Input data: As a background control experiment, we sequenced the input genomic DNA sample that was used for ChIP. Crosslinked chromatin is sheared and the crosslinks are reversed without carrying out the immunoprecipitation step. This sample is otherwise processed in a manner identical to the ChIP sample as described below. The input track is useful in revealing potential artifacts arising from the sequence alignment process such as copy number differences between the reference genome and the sequenced samples, as well as regions of poor sequence alignability. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each site, the maximum F-Seq Density Signal value has been calculated for each assay that was performed in that cell type. F-Seq employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Significant regions, or peaks, were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05 (DNaseI HS, ChIP) or 0.1 (FAIRE) threshold were considered significant. See assay specific description pages ( Duke DNaseI HS, UNC FAIRE and UTA TFBS) for more details. A Fisher's Combined P-value for DNaseI HS and FAIRE was calculated using Fisher's combined probability test. First, a test statistic is calculated using the formula x^2 = -2*sum(ln(pi)) where pi are the p-values calculated for DNaseI HS and FAIRE. X2 follows a chi-squared distribution, thus a combined p-value can be assigned to this test statistic.

Dataset Information

A1-2 expression analysis of GR activation

Publications

Analysis of chromatin dynamics during glucocorticoid receptor activation.

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