Transcriptomic changes upon NaCl treatment dependent on GA biosynthesis and signaling.
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE195912 | GEO | 2022/02/08
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptomic changes upon NaCl treatment dependent on GA biosynthesis and signaling.
| PRJNA802649 | ENA
Project description:This work aimed to characterize the molecular differences of SUMO1-SLR1 and SLR1 in rice (Oryza sativa cv. Nipponbare) shoots subjected to salt stress and to identify novel SLR1 interactors. Because DELLA proteins regulate gene expression, we exposed SLR1-OX, SUMO1SLR1-OX, and Nipponbare genetic background to high salt concentrations (120 mM NaCl) during 8 hours at the seedling stage and collected samples for subsequent RNA-seq analysis. Functional annotation of SLR1-OX DEGs showed enrichment of gene ontology (GO) terms associated with diterpenoid biosynthesis, highlighting the impact of SLR1 on GA metabolism. After functional annotation of DEGs specific to SUMO1SLR1-OX, we found a significant over-representation of GO terms associated with defense response and gibberellin dioxygenase activity. We also found a salt stress-dependent induction of GA20ox2 and GA2ox3 genes in SUMO1SLR1-OX. GA20ox2 and GA2ox3 encode enzymes involved in the regulation of active GA (GA4) levels. Therefore, it is reasonable to hypothesize that SLR1 SUMOylation could adjust active GA homeostasis upon exposure to salt stress.
2024-09-01 | E-MTAB-14289 | 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.
2012-06-25 | GSE35408 | GEO
Project description:We used whole-genome microarrays to identify differentially expressed genes in leaves of GA-deficient (35S::PcGA2ox) and/or GA-insensitive (35S::rgl1) transgenics as compared to WT poplar (717-1B4 genotype). Our work suggests that the molecular machinery that reduces gibberellins (GAs) concentration and signaling is a major route for restraining growth under both immediate and imminent adverse conditions. We show that inhibition of growth as a result of water deprivation and short days (SDs) coincides with up-regulation of several DELLA and GA2ox encoding genes in poplar. Likewise, GA-deficient and GA-insensitive transgenics, with up-regulated GA2ox and DELLA domain proteins, elicited a hypersensitive growth inhibition in response to both drought and SDs. Because the GA-modified transgenic showed accelerated response to drought and SD, we hypothesized that the mechanisms associated with these responses are constitutively elevated even under control conditions (well-watered, long day photoperiod). Therefore, we used whole-genome poplar microarray to study transcriptome level changes in the leaves of transgenic compared to WT plants grown under control environment.
2014-01-01 | GSE38390 | GEO
Project description:A comparative transcriptomic study of the impact of salt toxicity on rice plant (Oryza sativa L.; cv 'I Kong Pao') after short term (48 hours) exposure to NaCl (200 mM) or Na2SO4 (100 mM). Twenty five days old rice seedlings were exposed to 0, 200 mM NaCl or 100 mM Na2SO4 for 48 hours in hydroponic culture. Comparison between control and salt-stressed plants were done at the shoot and the root levels. The essays were replicated twice on two independent plant cultures.
2020-03-27 | GSE147572 | GEO
Project description:We used whole-genome microarrays to identify differentially expressed genes in leaves of GA-deficient (35S::PcGA2ox) and/or GA-insensitive (35S::rgl1) transgenics as compared to WT poplar (717-1B4 genotype). Our work suggests that the molecular machinery that reduces gibberellins (GAs) concentration and signaling is a major route for restraining growth under both immediate and imminent adverse conditions. We show that inhibition of growth as a result of water deprivation and short days (SDs) coincides with up-regulation of several DELLA and GA2ox encoding genes in poplar. Likewise, GA-deficient and GA-insensitive transgenics, with up-regulated GA2ox and DELLA domain proteins, elicited a hypersensitive growth inhibition in response to both drought and SDs. Because the GA-modified transgenic showed accelerated response to drought and SD, we hypothesized that the mechanisms associated with these responses are constitutively elevated even under control conditions (well-watered, long day photoperiod). Therefore, we used whole-genome poplar microarray to study transcriptome level changes in the leaves of transgenic compared to WT plants grown under control environment. Genetic background for all plants was INRA 717-1B clone (Populus tremula x Populus alba). Expression analysis was preformed on three individual genotypes; wild-type (WT, untransformed control), 35S::PcGA2ox and 35S::rgl1. Leaves from two independent biological replicates per genotype were used, each pooled from 20 clonally propagated plants.
2014-01-01 | E-GEOD-38390 | biostudies-arrayexpress
Project description:au07-08_nacl - nacl - Small RNAs induced under salt stress. - Arabidopsis seedlings have been treated with 150 mM NaCl in orden to determine small RNAs specifically induced by this stress. Keywords: treated vs untreated comparison
2008-04-07 | GSE10420 | 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. 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: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
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