E-GEOD-54049 - Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis

Status
Released on 23 June 2014, last updated on 1 December 2015
Organism
Arabidopsis thaliana
Samples (47)
Array (1)
Protocols (7)
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.
Experiment type
transcription profiling by array 
Contacts
Alessia Para, Amy Marshall-Colon, Bastiaan O Bargmann, Christopher Hackley, Gabriel Krouk, Gloria M Coruzzi, Kenneth D Birnbaum, Kranthi Varala, Molly B Edwards, Nancy J Francoeur, Tara M Moran, W R McCombie, Ying Li
Citation
Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis. Para A, Li Y, Marshall-Colón A, Varala K, Francoeur NJ, Moran TM, Edwards MB, Hackley C, Bargmann BO, Birnbaum KD, McCombie WR, Krouk G, Coruzzi GM. , Europe PMC 24958886
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-54049.idf.txt
Sample and data relationshipE-GEOD-54049.sdrf.txt
Raw data (1)E-GEOD-54049.raw.1.zip
Processed data (1)E-GEOD-54049.processed.1.zip
Array designA-AFFY-2.adf.txt
Links