Epigenetic mutant gene expression analysis
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Tuncay Baubec
PROVIDER: E-GEOD-18977 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This experiment was designed to identify transcripts which are changed in plants deficient for evolutionary conserved EST1B gene. A mutation in est1b leads to a constitutive up-regulation of a PAD4-dependent pathogen response pathway. To eliminate secondary effects of the constitutive pathogen response in est1b mutants we will analyze transcriptoms in plants in which lack PAD4. Keywords: Expression profilling by array 6 samples were used in this experiment
2009-11-17 | E-GEOD-18979 | biostudies-arrayexpress
Project description:The aim of this project is to identify endogenous targets of yet unidentified epigenetic mutants. Mutants were discovered in a forward genetic approach using T-DNA insertion mutagenesis. Pools of 25 seedlings, grown in-vitro, will be used to examine changes in gene expression. 9 samples were used in this experiment.
2009-12-09 | E-GEOD-19269 | biostudies-arrayexpress
Project description:A number of RNA encoding different functions have been detected in the plant vasculature. An RNase L inhibitor, similar to that present in humans have been identified in the phloem sap of cucurbits. We are interested in analyze the role of this putative inhibitor on the transcript levels that could be present in the vasculature and mainly in the phloem stream. For this purpose, we obtained an RLI T-DNA insertion mutant and generated A. thaliana overexpressing lines using the ORF of the two alleles found in the database. Keywords: Expression profilling by array 6 samples were used in this experiment
2009-11-17 | E-GEOD-18981 | biostudies-arrayexpress
Project description:Plants live in soils that vary considerably, both spatially and over time, in terms of nutrient composition and pH. Consistently, plants have to recognize and adapt to these changes by altering their structure and metabolism. The goal of this array analysis is to characterize the global transcriptional response to external pH changes in roots, which to date is almost unexplored. Arabidopsis thaliana (Columbia-0) were grown in hydroponic cultures in basic nutrient solution. Two days before treatment the media was shifted to nutrient solution containing 5mM MES, pH 6. At the time of the treatment start (4 hours after light on) the plants were shifted to nutrient solutions of pH 4.5 and 6.0 (control). Root RNA samples from time point 1 and 8 hour after treatment start is used for array analyzes. Keywords: Expression profilling by array 12 samples were used in this experiment
2009-11-17 | E-GEOD-18982 | biostudies-arrayexpress
Project description:In plant axillary bud dormancy and outgrowth are regulated by phytohormones, but it is still unknown about its molecular mechanism. We reveal that Arabidopsis axillary buds located at axil of rosette leaves show dormancy and that this is broken by the decapitation of main stem, resulting in the bud outgrowth. To investigate about the molecular mechanisms of dormancy and outgrowth, we carried out gene expression analysis during axillary shoot outgrowth in Arabidopsis wild type Columbia accession. Since axillary buds did not initiate outgrowth (dormancy) at 5 day after bolting of main stem, we used 5-day bolted plants as a control (before decapitation). Then, main stems were decapitated, and axillary shoots were collected at 24 hours after decapitation (named as growing shoot). Total RNA was prepared from either control or growing shoots and used for the microarray analysis. We carried out duplicate microarray analysis using independent plant materials.Ref):Tatematsu et al., Plant Physiol. 138: 757-766 (2005). Keywords: Expression profilling by array 4 samples were used in this experiment
2009-11-17 | E-GEOD-18987 | biostudies-arrayexpress
Project description:We characterized two independent insertional mutants of the AtEXO70A1 gene, encoding a subunit of the exocyst complex. Homozygous mutants exhibit a suite of phenotypic defects: polar growth of root hairs and stigmatic papillae is disturbed; organs are generally smaller; plants show loss of apical dominance and an indeterminate growth where instead of floral meristems new lateral inflorescences are initiated in a reiterative manner; exo70A1 mutants have dramatically reduced fertility. These results suggest that EXO70A1 is involved in cell and organ morphogenesis. Keywords: Expression profiling by array 4 samples were used in this experiment
2009-11-17 | E-GEOD-18986 | biostudies-arrayexpress
Project description:The genomic response to low levels of nitrate was studied in Arabidopsis using the Affymetrix ATH1 chip containing more than 22,500 probe sets. Arabidopsis plants were grown hydroponically in sterile liquid culture on ammonium as the sole source of nitrogen for 10 d, then treated with 250 um nitrate for 20 min. The response to nitrate was much stronger in roots (1,176 genes showing increased or decreased mRNA levels) than in shoots (183 responding genes). In addition to known nitrate-responsive genes (e.g. those encoding nitrate transporters, nitrate reductase, nitrite reductase, ferredoxin reductase, and enzymes in the pentose phosphate pathway), genes encoding novel metabolic and potential regulatory proteins were found. These genes encode enzymes in glycolysis (glucose-6-phosphate isomerase and phosphoglycerate mutase), in trehalose-6-P metabolism (trehalose-6-P synthase and trehalose-6-P phosphatase), in iron transport/metabolism (nicotianamine synthase), and in sulfate uptake/reduction. In many cases, only a few select genes out of several in small gene families were induced by nitrate. These results show that the effect of nitrate on gene expression is substantial (affecting almost 10% of the genes with detectable mRNA levels) yet selective and affects many genes involved in carbon and nutrient metabolism. Keywords: Expression profilling by array 8 samples were used in this experiment
2009-11-17 | E-GEOD-18984 | biostudies-arrayexpress
Project description:In addition to the canonical RNAi pathways that targets mRNAs in the cytoplasm, several RNA-dependent pathways operate in the nucleus to induce sequence-specific epigenetic modifications. One specialized type of RNAi-mediated pathway is RNA-directed DNA methylation (RdDM). During RdDM, nuclear DNA with sequence identity to the trigger dsRNA is de novo methylated at almost all cytosine residues, providing a mark for the formation of transcriptionally silent heterochromatin. Genetic forward screens identified the RPD3-like histone deacetylase HDA6 as the enzyme responsible for the histone deacetylation step of RdDM and suggest that HDA6 might have acquired specific functions for RNA-directed transcriptional silencing processes [Aufsatz et al., 2002a; Aufsatz et al., 2002b]. Complete loss-of-function mutants for AtHDA6 (rts1-1; RNA-mediated transcriptional gene silencing) exhibit reactivation of RdDM-silenced promoters, despite the continuous presence of the silencing-inducing RNA signal. One of the found mutant alleles, rts1-5, has an amino acid substitution located at a conserved position within the HDAC domain (Naumann et al., manuscript in preparation). This mutant is characterized by strong reactivation of an RdDM-silenced target promoter, despite maintaining wild-type levels of cytosine methylation. An evaluation of the transcription pattern among the mutants with opposite methylation phenotype and wild-type plants should show which genes are differentially regulated between the mutants in comparison to wild-type plants. Keywords: Expression profiling by array 9 samples were used in this experiment
2009-11-17 | E-GEOD-18988 | biostudies-arrayexpress
Project description:Maternal environment is an important regultor of seed dormancy, but the mechanisms underlying the process are poorly understood. We have found that genes in the circadian clock control dormancy, in part through their regulation of the canonical photoperiod pathway known from research into flowering time control. In this experiment we compare the affects of altering seed maturation temperature or maternal photoperiod on dry seed transcriptomes, and the photoperiod-insenstive ft-1 mutant to wt type Ler. In this way we are identifying gene expression programmes which result from the seed's response to maternal environmental experience. Keywords: Expression profilling by array 12 samples were used in this experiment
2011-04-21 | E-GEOD-28747 | biostudies-arrayexpress
Project description:The aim of the experiment is to look at transcriptional changes in null mutants of APS kinase. There are four APS kinase isoforms in Arabidopsis, we are interested in the double mutant APK1/APK2, created by crossing two single salk lines. The transcriptomes of WT (Col-0) plants and the double knockout (ab) will be compared. The plants were grown under controlled environment conditions of 10h day, 14h night, 22 degrees centigrade, 60% humidity for five weeks. 10 whole rosettes were pooled for each replicate, there are three replicates for each genotype. Keywords: Expression profiling by array 6 samples were used in this experiment
2009-11-17 | E-GEOD-18980 | biostudies-arrayexpress