Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Alice Pajoro
PROVIDER: E-GEOD-46987 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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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
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.
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Project description:This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a pAP1: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) Four sets of biologically independent tissue samples were collect before DEX-induction (day 0, 0d), as well as at 2 days, 4 days and 8 days after the treatment. Samples for each timepoint and biological replicate were co-hybridized as indicated; one sample was labeled with Cy3 and the other with Cy5. The dyes used for labeling RNA from a given timepoint were switched for two of the replicate experiments, to reduce dye-related artifacts. This experimental setup resulted in a total of 3 hybridizations per set (0days vs 2days, 2days vs 4days, and 4days vs 8days), and an even number (2) of hybridizations of each dye polarity per comparison.
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2013-07-01 | E-GEOD-45938 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE38358: Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA (ChIP-Seq) GSE38362: Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA (mRNA) Refer to individual Series
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Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
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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 or dexamethasone+cycloheximide treatment. Tissue samples were collected at 3hrs after the treatment. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (Agilent, custom-commercial). We treated inflorescences of 35S:AP1-GR ap1-1 cal-1 plants with a dexamethasone-containing or a mock solution, or with identical solutions that contained in addition 10 M-NM-<M cycloheximide. Tissue was collected 3 hours after the treatment. Samples from each of the four biological replicates resulted in a set of four hybridization pairs: Mock vs. Dex, Mock vs. Chx, Mock vs. Dex+Chx, and Chx vs. Dex+Chx. Dye polarities were switched between biological replicates.
2011-01-01 | E-GEOD-20175 | biostudies-arrayexpress
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
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.
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