Expression data from Arabidopsis thaliana
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE21601 | GEO | 2010/08/25
SECONDARY ACCESSION(S): PRJNA127141
REPOSITORIES: GEO
Similar Datasets
Project description:Nitrogen and light are two major regulators of plant metabolism and development. While genes involved in the control of each of these signals have begun to be identified, regulators that integrate gene responses to nitrogen and light signals have yet to be determined. Here, we evaluate the role of bZIP1, a transcription factor involved in light and nitrogen sensing, by exposing wild-type (WT) and bZIP1 T-DNA null mutant plants to a combinatorial space of N and L treatment conditions. We use ANOVA analysis combined with clustering and Boolean modeling, to evaluate the role of bZIP1 in mediating L and N signaling genome-wide. Arabidopsis thaliana were growth on basal MS salts (custom-made; GIBCO) with 0.5 mM KNO3, 3 mM sucrose and 0.8% BactoAgar at pH 5.7. After 14 days under long-day (16 h light: 8 h dark) conditions with light intensity of 50 μE.m-2.s-1 and at 22°C, plants were transferred to new plates containing 20 mM KNO3 and 20 mM NH4NO3 (referred here as 1xN: concentrations in MS media) in the absence or presence of light for 2 h at the start of their light cycle.
2010-08-25 | E-GEOD-21601 | biostudies-arrayexpress
Project description:The goal of this work is to identify the gene regulatory hubs that control nitrogen-use in Oryza sativa, one of the most important crop plants, by using a combination of genomics, bioinformatics and systems biology approaches. Here, we evaluate the role of bZIP1, a transcription factor involved in light and nitrogen sensing, by exposing wild-type (WT) and bZIP1 T-DNA null mutant plants to a combinatorial space of N and L treatment conditions. We use ANOVA analysis combined with clustering and Boolean modeling, to evaluate the role of bZIP1 in mediating L and N signaling genome-wide. We also study the interspecies conservation, comparing rice with Arabidopsis thaliana nitrogen transcriptomes, to help identify conserved nitrogen regulation.
2015-06-10 | E-GEOD-38102 | biostudies-arrayexpress
Project description:To identify potential transient interactions between a TF and its targets, we developed an approach that can identify primary targets based either on TF-induced regulation or TF-binding, assayed in the same samples. Our studies focused on the TF bZIP1 (BASIC LEUCINE ZIPPER 1), a central integrator of cellular and metabolic signaling. To discern the mechanisms by which bZIP1 regulates a gene netowork in response to a nitrogen (N)-signal perceived in vivo, we perturbed both bZIP1 and the N-signal that it transduces in a cell-based transient expression system called TARGET (Transient Assay Reporting Genome-wide Effects of Transcription factors). To identify the genome-wide targets of bZIP1 in response to a N-signal, we transiently perturbed both the TF and the signal in the TARGET cell-based system. Specifically, bZIP1 was transiently overexpressed in root protoplasts following transfection with a 35S::GR::bZIP1 construct containing an RFP (red fluorescent protein) selectable marker gene. bZIP1 transfected cells were sequentially treated with: i) an inorganic nitrogen signal (+/-N), ii) cycloheximide (CHX) to block the synthesis of proteins, and iii) dexamethasone (DEX) to induce nuclear import of the GR::bZIP1 protein. To identify both the TF-regulated and the TF-bound genes, transcriptome analysis of transfected cells and micro-ChIP data (using anti-GR antibodies), were carried out in parallel . This submission represents transcriptome component of study.
2014-06-23 | E-GEOD-54049 | biostudies-arrayexpress
Project description:To identify potential transient interactions between a TF and its targets, we developed an approach that can identify primary targets based either on TF-induced regulation or TF-binding, assayed in the same samples. Our studies focused on the TF bZIP1 (BASIC LEUCINE ZIPPER 1), a central integrator of cellular and metabolic signaling. To discern the mechanisms by which bZIP1 regulates a gene netowork in response to a nitrogen (N)-signal perceived in vivo, we perturbed both bZIP1 and the N-signal that it transduces in a cell-based transient expression system called TARGET (Transient Assay Reporting Genome-wide Effects of Transcription factors).
2014-06-23 | GSE54049 | GEO
Project description:BACKGROUND:Dynamic transcriptional regulation is critical for an organism's response to environmental signals and yet remains elusive to capture. Such transcriptional regulation is mediated by master transcription factors (TF) that control large gene regulatory networks. Recently, we described a dynamic mode of TF regulation named "hit-and-run". This model proposes that master TF can interact transiently with a set of targets, but the transcription of these transient targets continues after the TF dissociation from the target promoter. However, experimental evidence validating active transcription of the transient TF-targets is still lacking. RESULTS:Here, we show that active transcription continues after transient TF-target interactions by tracking de novo synthesis of RNAs made in response to TF nuclear import. To do this, we introduced an affinity-labeled 4-thiouracil (4tU) nucleobase to specifically isolate newly synthesized transcripts following conditional TF nuclear import. Thus, we extended the TARGET system (Transient Assay Reporting Genome-wide Effects of Transcription factors) to include 4tU-labeling and named this new technology TARGET-tU. Our proof-of-principle example is the master TF Basic Leucine Zipper 1 (bZIP1), a central integrator of metabolic signaling in plants. Using TARGET-tU, we captured newly synthesized mRNAs made in response to bZIP1 nuclear import at a time when bZIP1 is no longer detectably bound to its target. Thus, the analysis of de novo transcripomics demonstrates that bZIP1 may act as a catalyst TF to initiate a transcriptional complex ("hit"), after which active transcription by RNA polymerase continues without the TF being bound to the gene promoter ("run"). CONCLUSION:Our findings provide experimental proof for active transcription of transient TF-targets supporting a "hit-and-run" mode of action. This dynamic regulatory model allows a master TF to catalytically propagate rapid and broad transcriptional responses to changes in environment. Thus, the functional read-out of de novo transcripts produced by transient TF-target interactions allowed us to capture new models for genome-wide transcriptional control. Root protoplasts were transfected with 35S::GR::bZIP1 or Empty vector (EV=pJD385_35S::GR) constructs and cells were sequentially treated with: i) the nitrogen signal (N), ii) cycloheximide (CHX), iii) dexamethasone (DEX; for review see Bargmann et. al 2013). Cells were exposed to 4tU to affinity-label newly synthesized transcripts prior RNA extraction followed by specific pull down of 4tu-fractions and hybridization on Arabidopsis ATH1 microarray chips.
2016-02-08 | E-GEOD-69389 | biostudies-arrayexpress
Project description:Understanding the structure and interplay of cellular signalling pathways is one of the great challenges in molecular biology. Boolean Networks can infer signalling networks from observations of protein activation. In situations where it is difficult to assess protein activation directly, Nested Effect Models are an alternative. They derive the network structure indirectly from downstream effects of pathway perturbations. To date, Nested Effect Models cannot resolve signalling details like the formation of signalling complexes or the activation of proteins by multiple alternative input signals. Here we introduce Boolean Nested Effect Models (B-NEM). B-NEMs combine the use of downstream effects with the higher resolution of signalling pathway structures in Boolean Networks. We show that B-NEMs accurately reconstruct signal flows in simulated data. Using B-NEM we then resolve BCR signalling via PI3K and TAK1 kinases in BL2 lymphoma cell lines. 84 BL2 cell-line samples were hybridized to HGU133+2 Affymetrix GeneChips.
2015-12-10 | E-GEOD-68761 | biostudies-arrayexpress
Project description:Understanding the structure and interplay of cellular signalling pathways is one of the great challenges in molecular biology. Boolean Networks can infer signalling networks from observations of protein activation. In situations where it is difficult to assess protein activation directly, Nested Effect Models are an alternative. They derive the network structure indirectly from downstream effects of pathway perturbations. To date, Nested Effect Models cannot resolve signalling details like the formation of signalling complexes or the activation of proteins by multiple alternative input signals. Here we introduce Boolean Nested Effect Models (B-NEM). B-NEMs combine the use of downstream effects with the higher resolution of signalling pathway structures in Boolean Networks. We show that B-NEMs accurately reconstruct signal flows in simulated data. Using B-NEM we then resolve BCR signalling via PI3K and TAK1 kinases in BL2 lymphoma cell lines.
2015-12-10 | GSE68761 | GEO
Project description:When light and exogenous nitrogen levels are limiting, the AtWRKY1 transcription factor mediates regulatory crosstalk between nitrogen and light signaling pathways in an energy conservation mechanism. Transcriptome experiments were performed for WT and wrky1 mutant lines under no treatment; N treatment; light treatment; or combination treatment.
2017-08-01 | GSE76278 | GEO
Project description:Liver samples were collected from zebrafish females (3 months old). Vitellogenic females were maintained under conditions of 14 h light: 10 h dark. Non-vitellogenic females were obtained by exposing females to 6 h light/18 h dark regime.
2009-10-01 | E-MEXP-1572 | biostudies-arrayexpress