Chromatin mechanism of DELLA-mediated gene repression and Gibberellin-induced gene activation in rice
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ABSTRACT:
ORGANISM(S): Oryza sativa Japonica Group
PROVIDER: GSE226812 | GEO | 2023/08/11
REPOSITORIES: GEO
Similar Datasets
Project description:Many years after the discovery of GID1 as the GA receptor, the belief in the existence of GA-binding protein (GBP) in aleurone cells still persists. Actually, some recent reviews and textbooks still contain information about the possibility of an alternative GA perception mechanism mediated by GBPs. Thus, to finally clarify this issue, we examined the expression of GA-regulated genes using rice embryoless half-seeds of four kinds of GA signaling mutants, each one independently carrying mutated GID1, DELLA, and GA-related F-box, which are all encoded by single genes in rice, allowing for convenient study of the GA perception system. The comprehensive microarray analysis using these rice mutants revealed that all genes tested to be responsive to GA in the wild-type (WT) aleurone cells consistently did not respond to GA in the gid1 or slr1 mutant.
2014-12-19 | GSE64290 | GEO
Project description:Many years after the discovery of GID1 as the GA receptor, the belief in the existence of GA-binding protein (GBP) in aleurone cells still persists. Actually, some recent reviews and textbooks still contain information about the possibility of an alternative GA perception mechanism mediated by GBPs. Thus, to finally clarify this issue, we examined the expression of GA-regulated genes using rice embryoless half-seeds of four kinds of GA signaling mutants, each one independently carrying mutated GID1, DELLA, and GA-related F-box, which are all encoded by single genes in rice, allowing for convenient study of the GA perception system. The comprehensive microarray analysis using these rice mutants revealed that all genes tested to be responsive to GA in the wild-type (WT) aleurone cells consistently did not respond to GA in the gid1 or slr1 mutant. All microarray experiments were performed according to the manufacturerM-bM-^@M-^Ys manual. The Feature Extraction software (Agilent Technologies) was used to delineate and measure the Cy3 and Cy5 signal intensities of each spot in the array. The resulting data were normalized using the Variance-stabilizing normalization (VSN) algorithm.
2014-12-19 | E-GEOD-64290 | biostudies-arrayexpress
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
Project description:The goal of this study was to search for DELLA-independent GA-regulated genes in tomato. RNA deep sequencing (RNA-seq) was performed to GA-treated M82 and pro∆GRAS mutant. Using a two fold increased or decreased cutoff we identified 81 GA-up regulated and 15 GA-down regulated genes, from which five genes were DELLA-independent.
2015-07-09 | GSE68018 | GEO
Project description:Brassinosteroid (BR) and gibberellin (GA) promote many similar developmental responses in plants; but their relationship remains unclear. Here we show that BR and GA act interdependently through a direct interaction between the BR-activated BZR1 and GAinactivated DELLA transcription regulators. GA promotion of cell elongation required BR signaling, whereas BR or active BZR1 can suppresssed the GA-deficient dwarf phenotype. DELLAs directly interacted with BZR1 and inhibited BZR1-DNA binding both in vitro and in vivo. Genome-wide analysis defined a BZR1-dependent GA-regulated transcriptome, which is enriched with light-regulated genes and genes involved in cell wall synthesis and photosynthesis/chloroplast. GA promotion of hypocotyl elongation requires both BZR1 and the phytochrome interacting factors (PIFs), as well as their common downstream targets PREs. The results demonstrate that GA releases DELLA-mediated inhibition of BZR1, and that the DELLA-BZR1-PIF4 interaction defines a core transcription module that mediates coordinated growth regulation by GA, BR and light signals.
2012-06-25 | GSE35408 | GEO
Project description:In order to elucidate the molecular mechanism of gibberellin (GA)-induced mesocotyl elongation, gene expression profiling analyses were performed in a deep-sowing tolerant maize inbred line 3681-4. Gene expression studies combing Affymetrix GeneChip analysis and Real-time PCR were employed to determine the molecular mechanism underlying GA promotion of maize mesocotyl elongation. These studies showed that the GA receptor GID1, the transcriptional factor MYB, and the genes encoding DELLA protein DWRF8, kinases, Raf, LRR, RLCK, and involved in flavonoid biosynthesis, aminosugars metabolism, cell wall synthesis and modification, might play critical roles in maize mesocotyl elongation.
2009-03-07 | GSE15048 | GEO
Project description:The goal of this study was to search for DELLA-independent GA-regulated genes in tomato. RNA deep sequencing (RNA-seq) was performed to GA-treated M82 and pro∆GRAS mutant. Using a two fold increased or decreased cutoff we identified 81 GA-up regulated and 15 GA-down regulated genes, from which five genes were DELLA-independent. M82 and pro∆GRAS seedlings were treated with Paclobutrazol (10mg/l) once a day for three days followed by a single GA3 application (100 µM). Three hours after the GA treatment, young leaves were collected and RNA was extracted for Illumina HiSeq 2500 sequencing. A total of eight samples were analyzed, each treatment had two biological replicates.
2015-07-09 | E-GEOD-68018 | biostudies-arrayexpress
Project description:Brassinosteroid (BR) and gibberellin (GA) promote many similar developmental responses in plants; but their relationship remains unclear. Here we show that BR and GA act interdependently through a direct interaction between the BR-activated BZR1 and GAinactivated DELLA transcription regulators. GA promotion of cell elongation required BR signaling, whereas BR or active BZR1 can suppresssed the GA-deficient dwarf phenotype. DELLAs directly interacted with BZR1 and inhibited BZR1-DNA binding both in vitro and in vivo. Genome-wide analysis defined a BZR1-dependent GA-regulated transcriptome, which is enriched with light-regulated genes and genes involved in cell wall synthesis and photosynthesis/chloroplast. GA promotion of hypocotyl elongation requires both BZR1 and the phytochrome interacting factors (PIFs), as well as their common downstream targets PREs. The results demonstrate that GA releases DELLA-mediated inhibition of BZR1, and that the DELLA-BZR1-PIF4 interaction defines a core transcription module that mediates coordinated growth regulation by GA, BR and light signals. Wild type Arabidopsis and bzr1-1D were grown in media containing 1 uM PAC and 0 or 2 uM PPZ for 4.5 days in dark, then treated with 10 uM GA3 or mock solution for 12 hr. Total RNA was extracted with Spectrum Plant Total RNA Kit (Sigma) and the mRNA sequencing libraries were constructed with barcodes using TruSeqTM RNA Sample Preparation Kit (Illumina). Six barcoded libraries were pooled together and sequenced by Illumina HiSeq2000.
2012-06-25 | E-GEOD-35408 | biostudies-arrayexpress
Project description:To understand how GA functions in regulating embryo development, a genome-wide transcriptomic analysis was carried out using 9DAF seeds dissected from siliques of dellaq (rga28 gai rgl1 rgl2) and the wild-type (col-0-2) grown in full-spectrum white fluorescent light at 22°C under long day conditions (16 h light/8 h dark). Then we found that GA regulates embryo development via DELLA-LEC1interaction, a subsequent genome-wide transcriptomic analysis was carried out using 9DAF seeds dissected from siliques of lec1-4 and the wild-type (col-0-1) in the same growth condition. Basing on the criteria of 1.5-fold cutoff for the genes with 5% false discovery rate, we first identified the differentially expressed genes in dellaq vs col-0-2, lec1-4 vs Col-0-1 subsets, which are referred to as DELLA and LEC1 regulated genes. These data reveal that DELLAs and LEC1 co-target a set of common genes in late embryogenesis, strongly supporting the role of DELLA-LEC1 in embryo development.
2018-02-15 | GSE108544 | GEO
Project description:To identify in vivo DELLA interacting proteins in rice, we used the SLR1-FLAG transgenic material to perform IP-MS analysis.
2023-03-07 | PXD040644 | iProX