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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

SUBMITTER: Richard Sandstrom

PROVIDER: E-GEOD-29983 | 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.

2011-06-30 | GSE29983 | GEO

Orchestration of Floral Initiation by APETALA1

Project description:The MADS-domain transcription factor APETALA1 (AP1) is a key regulator of Arabidopsis flower development. To understand the molecular mechanisms underlying AP1 function, we identified its target genes during floral initiation using a combination of gene expression profiling and genome-wide binding studies. Many of its targets encode transcriptional regulators, including known floral repressors. The latter genes are down-regulated by AP1, suggesting that it initiates floral development by abrogating the inhibitory effects of these genes. While AP1 acts predominantly as a transcriptional repressor during the earliest stages of flower development, regulatory genes known to be required for floral organ formation were found to be activated by AP1 at more advanced stages, indicating a dynamic mode of action. Our results further imply that AP1 orchestrates floral initiation by integrating growth, patterning and hormonal pathways. We used the AP1-GR system to conduct chromatin immunoprecipitation experiments with AP1-specific antibodies followed by deep-sequencing (ChIP-Seq) in order to determine AP1 binding sites on a genome-wide scale. Samples were generated from tissue in which the AP1-GR protein was induced for 2h using a single treatment of 1 uM DEX to the shoot apex. As control, we performed ChIP experiments using the same antibody on uninduced tissue. Experiments were done in two biological replicates.

2010-04-02 | E-GEOD-20176 | biostudies-arrayexpress

Orchestration of floral initiation by APETALA1

Project description:This SuperSeries is composed of the following subset Series: GSE20139: Ath_Agilent_v1_Riechmann array expression profile AP1-GR ap1cal inflorescences - time series (hours) GSE20182: Meyerowitz Lab Arabidopsis Operon Array v4 - 4200A scanner - AP1-GR ap1cal inflorescences - time series (hours) GSE20183: Meyerowitz Lab Arabidopsis Operon Array v4 - 4000B scanner - AP1-GR ap1cal inflorescences - time series (hours) Refer to individual Series

2010-04-02 | E-GEOD-20184 | biostudies-arrayexpress

HNF4A is required to specify glucocorticoid action in the liver - ATACseq

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.

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Developmental dynamics of floral gene regulation [ChIP-Seq]

Project description:Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programmes. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Here, we characterize the dynamic relationship of chromatin accessibility, gene expression and DNA-binding of two MADS-domain proteins during Arabidopsis flower development. The developmental dynamics of DNA-binding of APETALA1 and SEPALLATA3 is largely independent of chromatin accessibility, and our findings suggest that AP1 acts as 'pioneer factor' that modulates chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Our data provide a primer to the idea that cellular differentiation in plants can be associated to dynamic changes in chromatin accessibility, as consequence of the action of master transcription factors. We used the AP1-GR system to conduct chromatin immunoprecipitation experiments with SEP3-specific antibodies and GR atibodies followed by deep-sequencing (ChIP-Seq) in order to determine SEP3 and AP1 binding sites on a genome-wide scale. Samples were generated from tissue in which the AP1-GR protein was induced using a treatment of 1 uM DEX to the shoot apex. The material was collect 2, 4 and 8 days after treatment. As control, we performed ChIP experiments using pre-immune serum at the different time points. Experiments were done in two biological replicates for 4 days and 8 days time-points while one biological replicate was done for control samples and 2 days time-point. The GSE47981 includes expression data that are complementary to the data in the GSE46986 and GSE46894.

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

Ath_Agilent_v1_Riechmann array expression profile AP1-GR ap1cal inflorescences - time series (hours)

Project description:This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a 35S:AP1-GR ap1 cal line to induce a synchronized response activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone treatment. Tissue samples were collected immediately after the treatment, as well as subsequent timepoints. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (Agilent, custom-commercial). Keywords: time course Four sets of biologically independent tissue samples were collected at 0, 2, 4, 8, and 12 hours after the application of dexamethasone (Dex-; activation of the AP1-GR fusion protein) or a mock solution (Mock-; control). Dex- and Mock-derived samples for each timepoint and biological replicate were co-hybridized; one sample was labeled with Cy3 and the other with Cy5. The dyes used for labeling RNA from a given treatment type (Dex and Mock, at a given timepoint) were switched for two of the replicate experiments, to reduce dye-related artifacts. This experimental setup resulted in a total of 5 hybridizations per set (0h, 2h, 4, 8h, and 12h; Dex vs. Mock at each timepoint), and an even number (2) of hybridizations of each dye polarity per timepoint. The combined ratio data results are available as a supplementary file on the Series record.

2010-04-02 | E-GEOD-20139 | biostudies-arrayexpress

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

Project description:Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programmes. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Here, we characterize the dynamic relationship of chromatin accessibility, gene expression and DNA-binding of two MADS-domain proteins during Arabidopsis flower development. The developmental dynamics of DNA-binding of APETALA1 and SEPALLATA3 is largely independent of chromatin accessibility, and our findings suggest that AP1 acts as M-bM-^@M-^Xpioneer factorM-bM-^@M-^Y that modulates chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Our data provide a primer to the idea that cellular differentiation in plants can be associated to dynamic changes in chromatin accessibility, as consequence of the action of master transcription factors. We used the AP1-GR system to conduct DNaseI hypersensitivity experiments at different stages of flower development. Samples were generated from tissue in which the AP1-GR protein was induced using a treatment of 1 uM DEX to the shoot apex. The material was collect before treatment and 2, 4 and 8 days after treatment. As control, naked DNA from wild-type inflorescences was used. Experiments were done in two biological replicates. The GSE47981 includes expression data that are complementary to the data in the GSE46986 and GSE46894.

2014-02-03 | E-GEOD-46894 | biostudies-arrayexpress

Ath_Agilent_v2_Riechmann array expression profile AP1-GR ap1cal inflorescences - chx experiment

2011-01-01 | E-GEOD-20175 | biostudies-arrayexpress

Meyerowitz Lab Arabidopsis Operon Array v4 - 4200A scanner - AP1-GR ap1cal inflorescences - time series (hours)

Project description:This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a 35S:AP1-GR ap1 cal line to induce a synchronized response activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone treatment. Tissue samples were collected immediately after the treatment, as well as subsequent timepoints. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (non-commercial; Meyerowitz Lab Arabidopsis Operon Array v4). Keywords: time course Four sets of biologically independent tissue samples were collect at 0, 2, 4 ,8, and 12 hours after the application of dexamethasone (Dex-; activation of the AP1-GR fusion protein) or a mock solution (Mock-; control). In each of the biological replicates of the time course experiments, all the samples derived from dexamethasone (Dex)-treated plants were labeled with one dye (i.e., Cy3), and all the samples derived from the corresponding Mock-treated plants were labeled with the alternative dye (i.e., Cy5). The dyes used for labeling RNA from a given treatment type (Dex and Mock) were switched for two of the replicate experiments, to reduce dye-related artifacts. Dex- and Mock-derived samples for each timepoint and biological replicate were co-hybridized. This experimental setup resulted in a total of 5 hybridizations per set (0h, 2h, 4, 8h, and 12h; Dex vs. Mock at each timepoint), and two biological replicate sets labeled with each dye polarity (Mock-Cy3/Dex-Cy5, and vice versa). The combined ratio data results are available as a supplementary file on the Series record.

2010-04-02 | E-GEOD-20182 | biostudies-arrayexpress

Meyerowitz Lab Arabidopsis Operon Array v4 - 4000B scanner - AP1-GR ap1cal inflorescences - time series (hours)

Project description:This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a 35S:AP1-GR ap1 cal line to induce a synchronized response activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone treatment. Tissue samples were collected immediately after the treatment, as well as subsequent timepoints. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (non-commercial; Meyerowitz Lab Arabidopsis Operon Array v4). Keywords: time course Four sets of biologically independent tissue samples were collect at 0, 2, 4 ,8, and 12 hours after the application of dexamethasone (Dex-; activation of the AP1-GR fusion protein) or a mock solution (Mock-; control). In each of the biological replicates of the time course experiments, all the samples derived from dexamethasone (Dex)-treated plants were labeled with one dye (i.e., Cy3), and all the samples derived from the corresponding Mock-treated plants were labeled with the alternative dye (i.e., Cy5). The dyes used for labeling RNA from a given treatment type (Dex and Mock) were switched for two of the replicate experiments, to reduce dye-related artifacts. Dex- and Mock-derived samples for each timepoint and biological replicate were co-hybridized. This experimental setup resulted in a total of 5 hybridizations per set (0h, 2h, 4, 8h, and 12h; Dex vs. Mock at each timepoint), and two biological replicate sets labeled with each dye polarity (Mock-Cy3/Dex-Cy5, and vice versa). The combined ratio data results are available as a supplementary file on the Series record.

2010-04-02 | E-GEOD-20183 | biostudies-arrayexpress

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