Genome-wide validation of the direct regulated targets for 33 nitrogen-early response transcription factors
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE117857 | GEO | 2019/03/14
REPOSITORIES: GEO
Similar Datasets
Project description:The effects of nitrogen and cycloheximide treatments on nitrogen response and TF-target identification was tested in the cell-based TARGET assay. For protoplast experiments, Arabidopsis plants were grown on low nitrogen (1mM KNO3) and after 10 days protoplasts were generated from root tissue. Cells were transfected with a vector containing the GR-TGA4 fusion or GR-only empty vector and incubated overnight. In the morning, samples were pre-treated with nitrogen as specified for 2 hours, and +/-cycloheximide for 20 minutes, before TF entry into the nucleus was induced with dexamethasone. 3 hours after dex treatment samples were FACS sorted into RNA extraction buffer. For whole roots, Arabidopsis were grown in liquid media with low nitrogen (1 mM KNO3) in Phytatrays for 11 days. In the morning and at the same time as the protoplasts, the plants were transferred to fresh media containing either 20 mM KCL or 20mM KNO3 + 20mM NH4NO3 for 5 hours. Roots were harvested and immediately frozen in liquid N2.
2019-03-14 | GSE128209 | GEO
Project description:The direct targets of 16 TFs were identified using the TARGET system. Arabidopsis plants were grown on 1/2X MS media and after 10 days protoplasts were generated from root tissue, Cells were transfected with a vector containing the GR-TF fusion and incubated overnight. Each experiment also included a GR-only empty vector control. In the morning, samples were pre-treated with cycloheximide for 20 minutes, before TF entry into the nucleus was induced with dexamethasone. 3 hours after dex treatment samples were FACS sorted into RNA extraction buffer and RNA-seq libraries were generated. Transcriptional response to each TF compared to empty vector was assayed.
2020-06-13 | GSE152405 | GEO
Project description:Transcriptomic profiling was carried out for leaves of Lotus japonicus plants grown with different mineral nitrogen sources (NO3-, NH4+ or NH4NO3) or under conditions of biological nitrogen fixation (Nod). Nodulated plants were inoculated with Mesorhizobium loti and watered with nitrogen-free âHornumâ medium supplemented with 3 mM KCl. Plants under different nitrogen nutritions were watered with âHornumâ nutrient solution containing 10 mM KNO3 (NO3- plants) or with 10 mM NH4Cl supplemented with 3 mM KCl (NH4+ plants) or with 5 mM NH4NO3 supplemented with 3 mM KNO3 (NH4NO3 plants). After all the plants reached the size of 7 trifoils, leaf tissue was harvested. Every harvest involved at least three independent biological replicates for each treatment.
2016-05-17 | E-MTAB-4177 | biostudies-arrayexpress
Project description:ra05-09_urea - urea - What are the transcriptomic plant responses to urea nitrogen supply ? - Columbia Arabidopsis ecotype were grown hydroponically on 0.5 mM NH4NO3 as sole nitrogen source during 35 days under short days. Plants were then placed on 3 nutrient solutions supplemented, either with 1 mM NH4NO3, or with 0.5 mM NH4NO3 + 0.5 mM Urea, or with 1 mM Urea. Root and shoot samples were harvested separately 7 days after these different nitrogen treatments Keywords: treated vs untreated comparison
2007-10-16 | GSE9258 | GEO
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: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:ngs2020_24_era-nitrogen-What genes are affected in the era1 mutant compared to the WT?-Characterize the effect of nitrogen nutrition (0 mM, 2mM and 10 mM NH4NO3) on development and metabolism in era1 and WT at the rosette stage at the onset of flower bud. Library construction with Quantseq 3seq sequencing
2023-02-08 | GSE208151 | GEO
Project description:To comprehensively investigate the effects of glutathione on the gene expression, the microarray analysis was performed in the glutathione-fed wild-type Arabidopsis thaliana. Wild-type Arabidopsis (ecotype Columbia-0) were fed with 1 mM oxidized glutathione (GSSG) and 2 mM reduced glutathione (GSH) for comparison at equal nitrogen equivalents. To examine the effects of glutathione other than nitrogen at equal nitrogen equivalents, plants were fed with 3 mM NH4NO3. Plants grown by water were used as a control.
2023-08-01 | GSE228403 | 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:The organs of multicellular species are comprised of cell types that must function together to perform specific tasks. One critical organ function is responding to internal or external change but little is known about how responses are tailored to specific cell types or coordinated among them on a global level. Here we use cellular profiling of five Arabidopsis root cell types in response to a limiting resource, nitrogen, to uncover a vast and predominantly cell-specific response that was largely undetectable using traditional methods. These methods reveal a new class of cell-specific nitrogen responses. As a proof-of-principle, we dissected one cell-specific response circuit that mediates nitrogen-induced changes in root branching from pericycle cells. Thus, cellular response profiling links gene modules to discrete functions in specific cell types. Experiment Overall Design: The whole experiment was carried out in triplicate with 84 chips in total (28 experiments). The nitrogen response in 5 FACS-sorted root cell types (LRC, lateral root cap; EpiC, epidermis and cortex; EndoP, endodermis and pericycle; Peri, pericycle; Stele, stele), protoplasts and Col-0 whole roots was assayed using microarrays. 5mM KNO3 was used as a nitrogen treatment for 2 hours. 5mM KCl was used as a control treatment for the same length of time. 1mM MSX in combination with 5mM KNO3 (or with 5mM KCl as a control) was used to block the assimilation of KNO3, and 5mM Gln added to restore it in order to separate KNO3 effects from assimilated-nitrogen effects. 5mM KNO3 was either maintained in the protoplast-generating solution (continuous treat) or not (transitory treat) to test how to best preserve the cellular nitrogen-response during the 1 hr protoplast generating procedure. As controls we used protoplasts, whole roots frozen directly after the 2hr treatment or 3.5hr treatment, or whole roots incubated in protoplast-generating solution (minus enzymes; transitory or continuous treated) and then frozen. After FACS-sorting or mock FACS-sorting cells were frozen.
2008-06-15 | E-GEOD-7631 | biostudies-arrayexpress