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Transcriptional profiles between mp mutant seedlings and transgenics carrying the dexamethasone-inducible GR-bdl protein

ABSTRACT: In order to identify targets of the transcription factor AUXIN RESPONSE FACTOR5 / MONOPTEROS (ARF5/MP), we compared transcriptomes of mp-B4149 mutant seedlings (9 day-old) and seedlings carrying the dexamethasone-inducible version of the MP inhibitor protein BODENLOS (GR-bdl). Without dexamethasone (DEX) treatment, this line is identical to the wild-type, while DEX treatment leads to strong inhibition of ARF-dependent transcription. To remove all endogenous MP-inhibiting Aux/IAA proteins, we treated mp or GR-bdl seedlings during 1 hour with auxin (50 micromolar Indole-3-Acetic Acid), either with or without a pretreatment with 10 micromolar DEX for 1 hour. Genes that are activated by MP are expected to br downregulated in mp seedlings and in the GR-bdl line afer DEX treatment. We used biological duplicates for each of the three treatments. Keywords: Transcriptional profiling of transcription factor targets

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE13881 | GEO | 2010/04/01

SECONDARY ACCESSION(S): PRJNA110351

REPOSITORIES: GEO

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Transcriptional profiles between mp mutant seedlings and transgenics carrying the dexamethasone-inducible GR-bdl protein

Project description:In order to identify targets of the transcription factor AUXIN RESPONSE FACTOR5 / MONOPTEROS (ARF5/MP), we compared transcriptomes of mp-B4149 mutant seedlings (9 day-old) and seedlings carrying the dexamethasone-inducible version of the MP inhibitor protein BODENLOS (GR-bdl). Without dexamethasone (DEX) treatment, this line is identical to the wild-type, while DEX treatment leads to strong inhibition of ARF-dependent transcription. To remove all endogenous MP-inhibiting Aux/IAA proteins, we treated mp or GR-bdl seedlings during 1 hour with auxin (50 micromolar Indole-3-Acetic Acid), either with or without a pretreatment with 10 micromolar DEX for 1 hour. Genes that are activated by MP are expected to br downregulated in mp seedlings and in the GR-bdl line afer DEX treatment. We used biological duplicates for each of the three treatments. Keywords: Transcriptional profiling of transcription factor targets Mp mutant and GR-bdl seeds were germinated on solid 1/2MS media, and transferred to liquid medium after 9 days of horizontal growth. Duplicate cultures were generated for mp mutants, and quadruplicates for the GR-bdl line. 10 micromolar DEX was added to both mp cultures and to two of the GR-bdl cultures, and seedlings were gently shaken during 1 hour. Then, 50 micromolar IAA was added to all 6 cultures and seedlings were incubated with gentle shaking for another hour. Total RNA was isolated from the seedlings using a QIAgen RNeasy kit, and reverse transcription, in-vitro transcription, cRNA labling and fragemntation was done according to established methods (Schmid et al., Nature Genetics [2005] 37, 501-506). Labeled cRNA was hybridized to Arabidopsis ATH1 arrays.

2010-04-12 | E-GEOD-13881 | biostudies-arrayexpress

Transcription profiling of Arabidopsis wild type or mp mutant seedlings treated with auxin

Project description:Comparison of mp mutant seedlings with transgenics carrying a dexamethasone-inducible GR-bodenlos gene. Seedlings were pretreated with control medium or medium containing dexamethasone, followed by a 1 hour auxin treatment, and expression profiles were compared using Affymetrix ATH1 arrays.

2010-05-01 | E-MEXP-1948 | biostudies-arrayexpress

Transcriptome analysis of genes regulated by INDEHISCENT (IND) transcription factor under the control of the 35S promoter after treatment with auxin

Project description:IND is a regulator of fruit development in Arabidopsis thaliana. To identify genes regulated by IND we performed array based transcriptome analysis of Dexamethasone (DEX) inducible IND transgenic seedlings. One week old 35S::IND:GR seedlings were treated with DMSO, Auxin, DEX and Auxin plus DEX for 6 h. Three biological independent experiments were performed.

2017-07-05 | E-MTAB-3812 | biostudies-arrayexpress

Transcription targets of ASYMMETRIC LEAVES 2 (AS2), KANADI1 (KAN), REVOLUTA (REV) and SHOOT MERISTEMLESS (STM) genes

Project description:Dexamethasone applied to WT, GR-AS2, GR-KAN1, GR-REV and GR-STM seedlings and expression measured at 0, 30, 60 and 120 minutes after Dex application.

2016-07-01 | GSE70796 | GEO

Arabidopsis thaliana

Project description:Transcriptional profiles between mp mutant seedlings and transgenics carrying the dexamethasone-inducible GR-bdl protein

| PRJNA110351 | ENA

Analysis of genes regulated by an Arabidopsis transcription factor, Dof3.2

Project description:To obtain information on which genes are regulated by an Arabidopsis transcription factor Dof3.2, we treated Arabidopsis transgenic 35S::Dof3.2-GR seedlings with dexamethasone (DEX), then performed DNA microarray analyses. T3 homozygous Dof3.2-GR transgenic line was used.

2020-03-01 | GSE58064 | GEO

Transcription targets of ASYMMETRIC LEAVES 2 (AS2), KANADI1 (KAN), REVOLUTA (REV) and SHOOT MERISTEMLESS (STM) genes

Project description:Dexamethasone applied to WT, GR-AS2, GR-KAN1, GR-REV and GR-STM seedlings and expression measured at 0, 30, 60 and 120 minutes after Dex application. SRA Series SRP051213 BioProject PRJNA258547. All reps are bio reps. Expression values are geometric normalized FPKM values from Tophat/Cufflinks reads and mappings.

2016-07-01 | E-GEOD-70796 | biostudies-arrayexpress

Identification of target genes of ABI3 [Agilent 44k]

Project description:ABI3 is a key regulator of seed development in Arabidopsis and other plants.To identify genes regulated by ABI3 we performed array based transcriptome analysis of Dexamethasone inducible ABI3 transgenic seedlings. ABI3 mostly in concert with abscisic acid (ABA) was found to activate genes specifically expressed during the maturation phase of seed development. Two weeks old wildtype and 35S::ABI3::GR seedlings were treated with ABA, Dexamethasone (DEX) and ABA plus Dexamethasone for 4 h. Two biological independent experiments were performed. Wildtype was induced to control for DEX-induction of genes.

2012-05-31 | E-GEOD-33951 | biostudies-arrayexpress

Identification of BABY BOOM downstream targets

Project description:A glucocorticoid-regulated BBM protein (35S:BBM-GR) was used in combination with microarray analysis to identify genes directly activated by BBM. We employed the system described by (Lloyd et al., 1994) in which dexamethasone (DEX) and cycloheximide (CHX) are applied together to respectively, induce nuclear localization of the BBM-GR protein and prevent translation of the primary targets mRNAs. In this way it is possible to identify direct targets of a transcriptional activator by comparing gene expression profiles between DEX+CHX-treated transgenic and wild-type tissues. The ability of the 35S:BBM GR construct to induce somatic embryogenesis in Arabidopsis seedlings was determined by phenotypic observation of 35S:BBM GR seeds germinated and grown in the presence of 10 µM dexamethasone (DEX). As in 35S:BBM seedlings, we observed somatic embryo formation on the cotyledons, first leaves and shoot meristem of DEX-treated 35S:BBM GR seedlings. We identified a set of 20 genes (including BBM itself) and our analysis indicates that BBM directly activates a signaling pathway comprising transcription factors and other signaling molecules, but which does not initially include genes known to induce somatic embryogenesis, such as LEC1, LEC2 or WUS. The functions of the BBM target genes are unknown, however a number of them have recently been identified in microarray screens for meristem-expressed genes. The identification of BBM-interacting partners and downstream targets provides new tools for unraveling pathways related to plant cell growth and organogenesis. Keywords: transcriptional activation

2008-09-22 | GSE3399 | GEO

Arabidopsis Forever Young Flower (FYF): 35S::FYF+GR

Project description:Transcriptional profiling of 35S::FYF+GR transgenic plant's floral buds(DEX treat) compared to 35S::FYF+GR transgenic plant's floral buds(mock treat). DEX : Dexamethasone

2015-06-01 | GSE69411 | GEO

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