Expression data of WT and ced1 under osmotic stress
ABSTRACT: ced1 mutant has reduced expression of NCED3 in response to osmotic stress (polyethylene glycol) treatments compared to the wild type. Other ABA biosynthesis genes are also greatly reduced in ced1 under osmotic stress. We used microarrays to detail the global programme of gene expression under osmotic stress treatment and identified distinct classes of up/down-regulated genes in the stress pathway. Overall design: Arabidopsis seedlings were selected at 16 days with 6hr PEG treatment for RNA extraction and hybridization on Affymetrix microarrays. From Norther data we have known some of well-known stress responsive gene were significantly changed. We sought to obtain whole gene expression to analysis which genes were affected in the osmotic stress pathway.
Project description:ced2 mutant has reduced expression of NCED3 in response to osmotic stress (PEG, polyethylene glycol) treatments compared to the wild type. Other ABA biosynthesis genes are also greatly reduced in ced2 under osmotic stress. We used microarrays to detail the global programme of gene expression under osmotic stress treatment and identified distinct classes of up/down-regulated genes in the stress pathway. Arabidopsis seedlings were selected at 14 days with 6hr PEG treatment for RNA extraction andhybridization to the Arabidopsis ATH1 Gene expression arrays (Agilent Technologies). From Northern data we have known some of well-known stress responsive gene were significantly changed. We sought to obtain whole gene expression to analysis which genes were affected in the osmotic stress pathway.
Project description:ced1 mutant has reduced expression of NCED3 in response to osmotic stress (polyethylene glycol) treatments compared to the wild type. Other ABA biosynthesis genes are also greatly reduced in ced1 under osmotic stress. We used microarrays to detail the global programme of gene expression under osmotic stress treatment and identified distinct classes of up/down-regulated genes in the stress pathway. Arabidopsis seedlings were selected at 16 days with 6hr PEG treatment for RNA extraction and hybridization on Affymetrix microarrays. From Norther data we have known some of well-known stress responsive gene were significantly changed. We sought to obtain whole gene expression to analysis which genes were affected in the osmotic stress pathway.
Project description:In this study genome-wide gene expression profiling was used to analyze mechanisms of drought tolerance in Brassica rapa. Using an Illumina Mi-Seq platform we sequenced RNA from shoot tissues of drought tolerant and drought sensitive B. rapa genotypes in control conditions and after application of osmotic stress. Differentially expressed genes between the different conditions and genotypes were used to identify drought relevant gene networks. Overall design: Two accessions of Brassica rapa with previously-identified contrasting drought responses were exposed to osmotic stress in a hydroponic growth system. Polyethylene glycol (PEG) simulated osmotic stress applied to half of the plants of each accession when plants had 4-5 true leaves while the other half remained with Murashige and Skoog (MS) medium as control for PEG. Total RNA isolated from shoot tissue was used for RNA-sequencing. For each genotype and condition three biological replicates were taken at 4h, 8h and 12h after stress treatment. cDNA libraries were prepared with the TruSeq Stranded Total RNA with Ribo-ZeroTM Plant kit from Illumina. Sequencing was carried out on each library to generate 150 bp PE reads using an Illumina Mi-Seq platform. The transcriptome reads were mapped to the B. rapa cv. Chiifu reference genome v1.5 (Wang et al., 2011) allowing 3 mismatches, then normalised and quantified as FPKM values using the spliced aligner TopHat/Cufflinks (http://ccb.jhu.edu/software/tophat/index.shtml,http://cole-trapnell-lab.github.io/cufflinks/).
Project description:Histone phosphorylation plays key roles in stress-induced transcriptional reprogramming in metazoans but its function(s) in land plants has remained relatively unexplored. Here we report that an Arabidopsis mutant defective in At3g03940 and At5g18190, encoding closely related Ser/Thr protein kinases, shows pleiotropic phenotypes including dwarfism and hypersensitivity to osmotic/salt stress. The double mutant has reduced global levels of phosphorylated histone H3 threonine 3 (H3T3ph), which are not enhanced, unlike the response in the wild type, by drought-like treatments. Genome-wide analyses revealed increased H3T3ph, slight enhancement in trimethylated histone H3 lysine 4 (H3K4me3), and a modest decrease in histone H3 occupancy in pericentromeric/knob regions of wild type plants under osmotic stress. However, despite these changes in heterochromatin, transposons and repeats remained largely transcriptionally repressed. In contrast, this reorganization of heterochromatin was mostly absent in the double mutant, which even under normal conditions exhibited lower H3T3ph levels in pericentromeric regions, and a few transposons and repeat sequences showed modest transcriptional activation. Interestingly, within actively transcribed protein-coding genes, H3T3ph density was minimal in 5’ genic regions, coincidental with a peak of H3K4me3 accumulation. This pattern was not affected in the double mutant, implying the existence of additional H3T3 protein kinases in Arabidopsis. Our results suggest that At3g03940 and At5g18190 are involved in the phosphorylation of H3T3 in pericentromeric/knob regions and that this repressive epigenetic mark may be important for maintaining proper heterochromatic organization and, possibly, chromosome function(s). Columbia-0 and double mutant at3g03940/at518190 knockdown plants were grown in 12 hr light for 3 weeks in pots with soil covered with miracloth to prevent soil contamination of leaf tissues. Control was kept in normal watered state, for other samples (peg) drought stress was induced by treatment with 30% Polyethylene glycol (PEG 6,000) for 5 hours. Pulldowns on H3, H3K4, and H3T3 were performed on all samples with 3-4 replicates.
Project description:The study was conducted to identify differentially expressed polyethylene glycol (PEG) induced water stress responsive genes in E. grandis. Forty day old rooted cutting of E. grandis was subjected to -0.225 MPa PEG treatment and total RNA was isolated from leaves of water treated control and PEG treated samples after three hours of treatment. The differential expression of water stress responsive genes was analyzed using microarray technique. Agilent two-color experiment, Organism: Eucalyptus,Custom Agilent Eucalyptus 8x60k Microarray Gene expression (AMADID: 59849 ) designed by Genotypic Technology Pvt.Ltd.
Project description:Despite the potential of the endoplasmic reticulum (ER) stress response to accommodate adaptive pathways, its integration with other environmental-induced responses is poorly understood in plants. Here, we performed global expression profiling on soybean leaves exposed to polyethylene glycol treatment or to unfolded protein response (UPR) inducers to identify integrated networks between osmotic and ER stress-induced adaptive responses. The results unmasked the major branches of the ER-stress response, which includes enhancing protein folding and degradation in the ER, as well as specific osmotically regulated changes linked to cellular responses induced by dehydration. However, a small proportion (5.5%) of total up-regulated genes represented a shared response that seemed to integrate the two signaling pathways. These co-regulated genes were considered downstream targets based on similar induction kinetics and a synergistic response to the combination of osmotic- and ER-stress-inducing treatments. Genes in this integrated pathway with the strongest synergistic induction encoded proteins with diverse roles. Two of them contained a plant-specific development and cell death (DCD) domain while another had homology to proteins with an ubiquitin-associated (UBA) domain. A NAC domain-containing protein exhibited robust early kinetics of induction consistent with a role as a transfactor. This integrated pathway diverged further from characterized ER-specific branches of UPR as downstream targets were inversely regulated by osmotic stress. Collectively, our results describe a novel branch of the ER stress response that integrates the osmotic signal to potentiate transcription of shared target genes. Keywords: stress response Overall design: In all experiments two independent biological replicates were used. For each biological replicate, two hybridizations were performed, with dye-swap.
Project description:This study utilized next generation sequencing technology (RNA-Seq) to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) to elucidate those genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought. We examined the mRNA of 9 day old Sorghum bicolor (BTx623) from 2 tissue types (roots and shoots) for 2 treatments (20 uM ABA and 20% PEG) with corresponding controls (0.2M NaOH and H2O) for 27 hrs prior to harvesting, each done in triplicate biological replicates - resulting in 24 unique runs
Project description:To explore the transcriptomic global response to osmotic stress in roots, 18 mRNA-seq libraries were generated from three triploid banana genotypes grown under mild osmotic stress (5% PEG) and control conditions.
Project description:Time course of the transcriptome of desiccation-sensitive 2.7-2.9 mm-long radicles of Medicago truncatula seeds at different time points during incubation in a polyethylene glycol (PEG) solution at -1.7 MPa and 10°C, resulting in a gradual re-establishment of desiccation tolerance. Gene profiling was also performed on embryos before (14 days after pollination) and after acquisition of desiccation tolerance during maturation (20 days after pollination).
Project description:We characterized the polyethylene glycol (PEG)-responding desiccome from the most geographically widespread Gram-positive nitrogen-fixing plant symbiont, i.e. Frankia alni, by next-generation proteomics.