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Next Generation Sequencing of tomato WT, M82 and pro∆GRAS mutant treated with Gibberellin

ABSTRACT: 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.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE68018 | GEO | 2015/07/09

SECONDARY ACCESSION(S): PRJNA281504

REPOSITORIES: GEO

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Next Generation Sequencing of tomato WT, M82 and pro∆GRAS mutant treated with Gibberellin

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

Brassinosteroid, gibberellin, and phytochrome impinge on a common transcription module in Arabidopsis

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.

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Project description:GA treatment of wild-type rice and use of DELLA protein mutant for RNA-seq and ChIP-seq. Explaining the chromatin mechanisms of DELLA-mediated gene repression and GA signalling-induced gene activation.

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Brassinosteroid, gibberellin, and phytochrome impinge on a common transcription module in Arabidopsis

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Probing the Existence of an Alternative Gibberellin Receptor(s) in Rice Aleurone Cells

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.

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Gibberellin-induced gene expression in maize mesocotyl under deep-sowing condition

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. In two independent experiments, we generate 10-day-old maize mesocotyl-specific gene expression profiles through comparing genome-wide expression patterns of GA3 treatment and UCZ (a GA biosynthesis inhibitor) treatment under 20 cm deep-sowing condition in darkness by using 17,555 Affymetrix maize whole genome array.

2009-03-07 | E-GEOD-15048 | biostudies-arrayexpress

Arabidopsis mutants treated with flg22, Alternaria brassicicola, Methyl jasmonate and Pst DC3000 bacteria

Project description:Gibberellin (GA) promotes plant growth by destabilizing DELLA proteins. DELLA proteins integrate multiple hormonal and environmental stress responses. We investigated the role of GA and DELLA proteins in plant defence. We used microarrays to detail the global programme of gene expression controlled by DELLA proteins and identified distinct classes of differentially regulated genes in response to pathogens, hormones or pathogen elicitors.

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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

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