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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Comparison of exon profiles before and after hormone induction

ABSTRACT: Exon array analysis component. Development, differentiation, and response to environmental stimuli are characterized by sequential changes in cellular state initiated by the de novo binding of induced or temporally regulated transcriptional factors to their cognate genomic sites. The mechanism whereby a given regulatory factor selects a limited number of in vivo targets from myriads of potential genomic binding sites is undetermined. Here we show that up to 95% of induced de novo genomic binding by the glucocorticoid receptor, a paradigmatic ligandactivated transcription factor, is targeted to preexisting foci of accessible chromatin. Factor binding invariably potentiates chromatin accessibility. Cellselective de novo genomic occupancy patterns appear to be comprehensively predetermined by cellspecific differences in baseline chromatin accessibility patterns, with secondary contributions from local sequence features. The results define a novel framework for understanding regulatory factorgenome interactions, and provide a molecular basis for the tissueselectivity of steroid pharmaceuticals and other agents that intersect the living genome. Time course of dexamethasone treatment of 2 cell types from a zero hour untreated control, 2 hour, 4 hour and 8hr treatment times. This is part of a larger study: Chromatin accessibility predetermines de novo steroid receptor binding. There are 2 replicates per cell line per time point except in the case of 8hr Dex treated AtT-20 where a second replicate was unavailable.

ORGANISM(S): Mus musculus

SUBMITTER: Richard Sandstrom

PROVIDER: E-GEOD-26189 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Comparison of gene expression profiles for hormone induction in the presence and absence of AP1 binding.

Project description:Gene expression array analysis component. Ligand-dependent transcription by the nuclear receptor glucocorticoid receptor (GR) is mediated by interactions with co-regulators. The role of these interactions in determining selective binding of GR to regulatory elements remains unclear. Recent findings indicate a large fraction of genomic GR binding coincides with chromatin that is accessible prior to hormone treatment, suggesting that receptor binding is dictated by proteins that maintain chromatin in an open state. Combining nucleolytic cleavage and chromatin immunoprecipitation with high-throughput sequencing, we identify the activator protein 1 (AP1) as a major partner for productive GR-chromatin interactions. AP1 is critical for GR-regulated transcription and recruitment to co-occupied regulatory elements, illustrating an extensive AP1-GR interaction network. Importantly, the maintenance of baseline chromatin accessibility facilitates GR recruitment and is dependent on AP1 binding. We propose a model where the basal occupancy of transcription factors act to prime chromatin and direct inducible transcription factors to select regions in the genome. Dexamethasone treatment of cells at zero hour untreated control and 4 hour treatment times, in the absence and presence of acidic-fos (A-fos), an AP1 dominant negative. A-fos expression is under tetracycline control (Tet-Off). This is part of a larger study: Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding. There are 2 replicates per condition per time point.

2011-06-30 | E-GEOD-29983 | biostudies-arrayexpress

Comparison of exon profiles before and after hormone induction

Project description:Exon array analysis component. Development, differentiation, and response to environmental stimuli are characterized by sequential changes in cellular state initiated by the de novo binding of induced or temporally regulated transcriptional factors to their cognate genomic sites. The mechanism whereby a given regulatory factor selects a limited number of in vivo targets from myriads of potential genomic binding sites is undetermined. Here we show that up to 95% of induced de novo genomic binding by the glucocorticoid receptor, a paradigmatic ligandactivated transcription factor, is targeted to preexisting foci of accessible chromatin. Factor binding invariably potentiates chromatin accessibility. Cellselective de novo genomic occupancy patterns appear to be comprehensively predetermined by cellspecific differences in baseline chromatin accessibility patterns, with secondary contributions from local sequence features. The results define a novel framework for understanding regulatory factorgenome interactions, and provide a molecular basis for the tissueselectivity of steroid pharmaceuticals and other agents that intersect the living genome.

2010-12-21 | GSE26189 | GEO

Evolution of diapause in the African killifish by remodeling ancient gene regulatory landscape

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2013-06-01 | E-GEOD-46832 | biostudies-arrayexpress

SUMOylation regulates chromatin protein network and accessibility at glucocorticoid receptor-binding sites

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SPOCD1 is a novel executor of piRNA-directed DNA methylation that links MIWI2 to the de novo DNA methylation machiner

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Developmental dynamics of DNA accessibility during flower development [DNaseI-Seq]

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2014-02-03 | E-GEOD-46986 | biostudies-arrayexpress

DNase02

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2013-05-01 | E-TABM-1219 | biostudies-arrayexpress

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