Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DELLA protein direct targets in Arabidopsis

ABSTRACT: 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. Keywords: Dexamethasone treatment, gibberellin treatment, time course, transgene effect

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE8741 | GEO | 2007/11/21

SECONDARY ACCESSION(S): PRJNA105285

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

Phosphorylation Promotes DELLA Activity by Enhancing Its Binding to Histone H2A at Target Chromatin in Arabidopsis

Project description:DELLA proteins are conserved master growth regulators that play a central role in controlling plant development in response to internal and environmental cues. DELLAs function as transcription regulators, which are recruited to target promoters by binding to transcription factors (TFs) and histone H2A via its GRAS domain. Recent studies showed that DELLA stability is regulated post-translationally via two mechanisms, phytohormone gibberellin-induced polyubiquitination for its rapid degradation, and Small Ubiquitin-like Modifier (SUMO)-conjugation to alter its accumulation. Moreover, DELLA activity is dynamically modulated by two distinct glycosylations: DELLA-TF interactions are enhanced by O-fucosylation, but inhibited by O-linked N-acetylglucosamine (O-GlcNAc) modification. However, the role of DELLA phosphorylation remains unclear. Here, we identified phosphorylation sites in REPRESSOR OF ga1-3 (RGA, an AtDELLA) purified from Arabidopsis by tandem mass spectrometry analysis, and showed that phosphorylation of the RGA LKS-peptide in the poly-S/T region enhances RGA-H2A interaction and RGA association with target promoters. Interestingly, phosphorylation does not affect RGA-TF interactions. Our study has uncovered that phosphorylation is a new regulatory mechanism of DELLA activity.

2024-08-08 | PXD046004 | Pride

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

Transcriptional effects after the expression of MYB30, MYB55 or MYB110 gene

Project description:Transcriptional profiling of rice transgenic calli which were stably transformed with the vector containing the dexamethasone (DEX)-inducible promoter and each of three MYB gene (MYB30, MYB55 or MYB110) or control. Calli were treated with DEX for 4 h to induce transgene expression. Ethanol was the solvent of DEX and used as control.

2018-04-22 | GSE77912 | GEO

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

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.

2008-06-18 | E-GEOD-10019 | biostudies-arrayexpress

Transcription profiling of Arabidopsis rosettes from plants over-expressing OBP1 to identify candidate target genes

Project description:In order to identify candidate target genes of the OBP1 (At3g50410) transcription factor we used dexamethasone inducible system (Lloyd et al, 1994). A single inducible over-expression line was compared to an empty vector control line 10h after DEX induction to identify candidate genes that were confirmed by quantitative RT-PCR.

2008-11-03 | E-MEXP-1360 | biostudies-arrayexpress

The PFYRE Subdomain in Master Growth Repressor DELLA is Essential for Its Association with Target Chromatin via Histone H2A Binding

Project description:The DELLA genes encode conserved master growth repressors in plants, and they are also known as ‘Green Revolution’ genes because of their pivotal role in modulating stature of the high-yielding wheat varieties, which were crucial for the success of the ‘Green Revolution’ in the 1960s. At the cellular level, DELLA proteins are nuclear-localized transcription regulators, which play a central role in controlling plant development in response to internal and environmental cues. Recent studies indicate that DELLAs regulate expression of target genes via direct protein-protein interaction of their C-terminal GRAS domain with hundreds of key transcription factors (TFs) and epigenetic regulators. However, the molecular mechanism of DELLA-mediated transcription reprogramming remains unclear. Here, by characterizing missense alleles of an Arabidopsis DELLA, REPRESSOR OF ga1-3 (RGA), we unveil a novel function of the PFYRE subdomain within its GRAS domain for binding to histone H2A via pulldown and co-IP assays. ChIP-Seq analysis further show that this activity is essential for RGA association with its target chromatin globally. Our results indicate that although DELLAs are recruited to target gene promoters by binding to TFs via its LHR1 subdomain, DELLA-H2A interaction via its PFYRE subdomain is necessary to stabilize the TF-DELLA-H2A complex at the target chromatin. This study provides new insight into the two distinct key modular functions in DELLA for its genome-wide transcription regulation in plants. The assay for transposase-accessible chromatin using sequencing (ATAC-seq) for RGA vs rga-11 and RGA treated with GA or mock.

2023-06-27 | GSE233124 | GEO

Overexpression of the receptor-like kinase BIR1 gene causes SOBIR1- and EDS1-dependent cell death phenotypes in Arabidopsis

Project description:In order to understand the downstream biological processes and pathways associated to BIR1 induction, we conducted a global transcriptome RNA-Seq assay in Arabidopsis wild-type (WT) and transgenic plants with a dexamethasone (DEX) inducible BIR1-mCherry transgene (ine 9, L9).

2023-06-15 | GSE234036 | GEO

The PFYRE Subdomain in Master Growth Repressor DELLA is Essential for Its Association with Target Chromatin via Histone H2A Binding

Project description:The DELLA genes encode conserved master growth repressors in plants, and they are also known as ‘Green Revolution’ genes because of their pivotal role in modulating stature of the high-yielding wheat varieties, which were crucial for the success of the ‘Green Revolution’ in the 1960s. At the cellular level, DELLA proteins are nuclear-localized transcription regulators, which play a central role in controlling plant development in response to internal and environmental cues. Recent studies indicate that DELLAs regulate expression of target genes via direct protein-protein interaction of their C-terminal GRAS domain with hundreds of key transcription factors (TFs) and epigenetic regulators. However, the molecular mechanism of DELLA-mediated transcription reprogramming remains unclear. Here, by characterizing missense alleles of an Arabidopsis DELLA, REPRESSOR OF ga1-3 (RGA), we unveil a novel function of the PFYRE subdomain within its GRAS domain for binding to histone H2A via pulldown and co-IP assays. ChIP-Seq analysis further show that this activity is essential for RGA association with its target chromatin globally. Our results indicate that although DELLAs are recruited to target gene promoters by binding to TFs via its LHR1 subdomain, DELLA-H2A interaction via its PFYRE subdomain is necessary to stabilize the TF-DELLA-H2A complex at the target chromatin. This study provides new insight into the two distinct key modular functions in DELLA for its genome-wide transcription regulation in plants. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RGA, rga-11 as well as the negative control sly1 dP and sly1 dQ.

2023-06-27 | GSE220898 | GEO

Early gibberellin responses in Arabidopsis

Project description:The aim is to identify early gibberellin responsive genes in a gibberellin deficient strain such as ga1-3. Such genes are likely regulated by DELLA proteins which are master gibberellin repressors. DELLA proteins are rapidly degraded after gibberellin treatment, but their direct target genes still need to be elucidated. Keywords: hormone response, gibberellin treatment

2007-11-21 | GSE8739 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data