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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of Arabidopsis steroid inducible RGA expressor transgenic to identify RGA downstream genes

ABSTRACT: To understand the transcriptional program controlled by RGA, we took advantage of a functional steroid-inducible RGA proteins system in combination with microarray analysis to identify RGA target genes. Experiment Overall Design: We firstly compared the transcriptomes in ga1-3rgargl2RGA-GR inflorescence without flowers later than stage 12 induced by dexamesone- relative to mock-treatment, which revealed the differentially expressed genes corresponding to the RGA protein activity induced by dexamesone.As negative controls to exclude unexpected effects of transgenic T-DNA and Dex itself, RNAs derived from nontransgenic plants (ga1-3 rga rgl2) inflorescences treated with Dex were used. Three sets of biological independent replicates were collected.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Hao Yu

PROVIDER: E-GEOD-10019 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Global identification of DELLA target genes during Arabidopsis flower development.

Hou Xingliang X Hu Wen-Wei WW Shen Lisha L Lee Li Yen Candy LY Tao Zhen Z Han Jin-Hua JH Yu Hao H

Plant physiology 20080523 3

Gibberellin (GA) plays important roles in regulating many aspects of plant development. GA derepresses its signaling pathway by promoting the degradation of DELLA proteins, a family of nuclear growth repressors. Although the floral organ identity is established in flowers of the GA-deficient mutant ga1-3, the growth of all floral organs is severely retarded. In particular, abortive anther development in ga1-3 results in male sterility. Genetic analysis has revealed that various combinations of n ...[more]

PMID: 18502975

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Identification of target genes of the DELLA protein RGL2 during the repression of seed germination

Project description:To shed light on the genetic events downstream of DELLA proteins, we have employed a microarray expression profiling of Arabidopsis thaliana seeds to identify target genes of the DELLA protein RGL2. Seeds of the germinating ga1-3 rga-t2 rgl2-1 and the non-germinating ga1-3 rga-t2 mutant were stratified, and RNA was extracted after five days. Transcript profiles of the non-germinating seeds closely resemble profiles of dormant seeds, and several transcription factors involved in light- and phytohormone-regulated signalling pathways appear to be up-regulated, suggesting that RGL2 controls various physiological aspects to inhibit seed germination. Gene expression five days after stratification was measured in ga1-3 rga-t2 seeds, using seeds of the ga1-3 rga-t2 rgl2-1 mutant as reference. Two biological replicates were performed for each sample.

2012-08-31 | E-GEOD-40485 | biostudies-arrayexpress

Identification of target genes of the DELLA protein RGL2 during the repression of seed germination

2012-08-31 | GSE40485 | GEO

Identification of RGA downstream genes by using steroid-inducible system

2008-05-28 | GSE10019 | GEO

Genome-wide binding sites for RGA in Arabidopsis inflorescence apices

Project description:The Arabidopsis thaliana REPRESSOR OF GA gene (RGA) encodes a DELLA protein that associates with multiple transcription factors to control plant growth in response to the hormone gibberellin (GA) (1). As part of a screen for genes that mediate the function of RGA in stem growth and shoot meristem function, we performed ChIP-seq to identify genome-wide loci associated with RGA in inflorescence apices. To detect genes controlled by RGA in a gain-of-function semi-dwarf background, we used a GFP-tagged, gibberellin-insensitive version of RGA (RGAp:GFP-rga-delta17) (2). (1) J.-M. Daviere, P. Achard, Gibberellin signaling in plants. Development 140, 1147-1151 (2013). (2) A. Dill, T. P. Sun, Synergistic derepression of gibberellin signaling by removing RGA and GAI function in Arabidopsis thaliana. Genetics 159, 777-785 (2001).

2017-08-15 | GSE94926 | GEO

Transcription profiling by array of Arabidopsis mutant for ga1, rga and rgl and with dexamethasone-induced expressing of RGA

Project description:To understand the transcriptional program controlled by RGA, we took advantage of a functional steroid-inducible RGA proteins system in combination with microarray analysis to identify RGA target genes. Experiment Overall Design: We firstly compared the transcriptomes in ga1-3rgargl2RGA-GR inflorescence without flowers later than stage 12 induced by dexamesone- relative to mock-treatment, which revealed the differentially expressed genes corresponding to the RGA protein activity induced by dexamesone.As negative controls to exclude unexpected effects of transgenic T-DNA and Dex itself, RNAs derived from nontransgenic plants (ga1-3 rga rgl2) inflorescences treated with Dex were used. Three sets of biological independent replicates were collected.

2014-07-03 | E-GEOD-10019 | ExpressionAtlas

rga response

Project description:comparison of the transcriptionnal response of the rga mutant and the wild type in S. agalactiae NEM316 strain

2012-05-21 | E-MEXP-3236 | biostudies-arrayexpress

RNA-sequencing of estradiol inducible DOF6 overexpression (DOF6ioex) and rgl2-13 DOF6ioex seeds imbibed in mock or 50µM estradiol for 8h

Project description:The DELLA protein RGA-LIKE2 (RGL2) is a key transcriptional repressor of gibberellic acid (GA) signaling that regulates seed germination.RGL2 lacks a DNA binding domain and requires a transcription factor to induce GATA12 expression. Our data show that this RGL2-containing protein complex includes DNA BINDING1 ZINC FINGER6 (DOF6), which is a known negative regulator of germination in freshly harvested seeds. The RGL2-DOF6 complex regulates primary seed dormancy in Arabidopsis by regulating downstreming targets.

2023-12-25 | GSE200271 | GEO

DELLA protein direct targets in Arabidopsis

2007-11-21 | GSE8741 | GEO

RGA binding sites in Arabidopsis thaliana seedlings

Project description:DELLA proteins act as hubs that relay environmental information to the multiple transcriptional circuits that control growth and development through physical interaction with transcription factors from different families. We have analyzed the presence of one DELLA protein at the Arabidopsis genome by chromatin immunoprecipitation coupled to large-scale sequencing and we find that it binds at the promoters of multiple genes. Enrichment analysis shows a strong preference for cis elements recognized by specific transcription factor families. In particular, we demonstrate that DELLA proteins are recruited by type-B ARABIDOPSIS RESPONSE REGULATORS (ARR) to the promoters of cytokinin-regulated genes, where they act as transcriptional co-activators. The biological relevance of this mechanism is underpinned by the necessity of simultaneous presence of DELLAs and ARRs to restrict root meristem growth and to promote photomorphogenesis. Provided are 3 biological replicates analysing RGA binding sites in Arabidopsis seedlings. ChIP-seq was performed on plants expressing RGA-GFP under the native RGA promoter and on non-transgenic control plants as reference

2015-07-23 | E-GEOD-59187 | biostudies-arrayexpress

Transcription profiling of Arabidopsis transgenic lines with a gibberellin non responsive DELLA protein vs control to identify DELLA protein direct targets

Project description:The aim of this study is to identify early DELLA protein-responsive genes using a Dexamethasone (DEX)-inducible system. Two transgenic lines were used: one induces the expression of a dominant, gibberellin non-responsive DELLA protein (rga-delta17); the other is a control line that carries the same vector, but lacks the rga-delta17 transgene. By comparing the gene expression changes in the line that expresses the rga-delta17 protein in the presence or absence of DEX it is possible to identify putative targets of DELLA proteins. An empty vector transgenic line was included in this study to identify genes that might be regulated by the DEX inducible system that are not dependent on the DELLA protein. Experiment Overall Design: Seedlings of both transgenic lines were pretreated for 16 h with 2 uM GA4 to enhance gibberellin responses. Because DELLA proteins are strong signaling repressors, this pretreatment should maximize the effect of DELLA induction. Eight-day old seedlings were treated with 2 uM GA4 or a combination of 2 uM GA4 plus 10 uM DEX to induce the rga-delta17 transgene. Three biological replicas for the transgenic line that carries the DEX-inducible rga-delta17 transgene were generated at 2h and 4h. For the empty vector line, only 2 biological replicas were generated at 4h of treatment with 2 uM GA with or without 10 uM DEX.

2008-06-16 | E-GEOD-8741 | biostudies-arrayexpress

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