Arabidopsis response to four days of limited light treatment -
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Kinga Rutowicz
PROVIDER: E-MTAB-2803 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Experiment was designed to compare the transcriptomic response of wild type and h1.3 Arabidopsis plants (Ler) to combined low light and drought conditions. H1.3 is highly upregulated by these experimental conditions
2015-03-31 | E-MTAB-2806 | biostudies-arrayexpress
Project description:Linker histones (H1s) are conserved and ubiquitous structural components of eukaryotic chromatin. Multiple non-allelic variants of H1 co-exist in animals and plants, differ in their DNA/nucleosome binding properties and have been implicated in the control of genetic programs during development and differentiation. To study the genome-wide distribution of Arabidopsis H1 variants, ChIP-on-chip technology was used .
2015-07-29 | E-MTAB-2804 | biostudies-arrayexpress
Project description:Background Protein synthesis is a highly energy demanding process and is regulated according to energy availability in plant cells. Light and sugar availability affect mRNA translation but the specific roles of these factors remain unclear. In this study, sucrose was applied to Arabidopsis seedlings kept in the light or in the dark, in order to distinguish sucrose and light effects on transcription and translation. These were studied using microarray analysis of steady state mRNA and mRNA bound to translating ribosomes. Results Steady state mRNA levels were affected differently by sucrose in the light and in the dark but general translation increased to a similar extend in both conditions. Alterations in polysomal mRNA association closely followed the changes induced on the transcript level. However, for 243 mRNAs, a change in ribosome occupancy was observed after sucrose treatment in the light, but not in the dark condition. Many of these mRNAs are annotated as encoding ribosomal proteins, supporting specific translational regulation of this group of transcripts. Unexpectedly, the numbers of ribosomes bound to each mRNA decreased for mRNAs with increased ribosome occupancy. Conclusions Our results suggest that sucrose regulate translation of these 243 mRNAs but specifically in the light, through a novel regulatory mechanism. Our data sows that increased polysomal association is not necessarily leading to more ribosomes per transcript, suggesting a mechanism of translational induction not solely dependent on increased translation initiation rates. Four different samples groups were used: Control, Darkness, Sucrose, Simultaneous Darkness and sucrose treatments. All sample groups was represented by both total mRNA hybridization and of mRNAs from polysomal enrichment. All sample groups were represented by three biological replicates.
2015-01-28 | E-GEOD-59306 | 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:Transcription profiling of shoot apices of the myo mutant was compared with shoot apices of WT (background Ler).
2009-07-22 | E-MEXP-1735 | biostudies-arrayexpress
Project description:To identify genes of the guard cell transkriptome of Arabidopsis thaliana enriched guard cell samples were compared with total leaf tissue. Genes of the abscisic acid and humidity response of Arabidopsis thaliana guard cells were identified by treatment with ABA-Spray and low humidity. Ost1-2 and slac1-3 mutants were compared to their wildtype. total samples analysed are 35: 4 biolocigal independent replicates of: total leaf (COL-0) vs. enriched guard cells (COL-0); ABA-sprayed enriched guard cells (gl1-1) vs. control-sprayed enriched guard cells (gl1-1); enriched guard cells (slac1-3) vs. enriched guard cells (gl1-1);guard cells (ost1-2) vs. guard cells (ler);low humidity(20%rh) treated enriched guard cells (COL-0) vs. high humidity(80%) treated enriched guard cells (COL0)
2013-06-04 | E-GEOD-38639 | biostudies-arrayexpress
Project description:Leaf growth is a complex developmental process that is continuously fine-tuned by the environment. Various abiotic stresses, including mild drought stress, have been shown to inhibit leaf growth in Arabidopsis thaliana (Arabidopsis), but the underlying mechanisms remain largely unknown. Here we identify the redundant Arabidopsis transcription factors ETHYLENE RESPONSE FACTOR 5 (ERF5) and ERF6 as master regulators which adapt leaf growth to environmental changes. ERF5 and ERF6 gene expression is induced very rapidly and specifically in actively growing leaves after sudden exposure to osmotic stress that mimics mild drought. Subsequently, enhanced ERF6 expression inhibits cell proliferation and leaf growth by a process involving GA and DELLA signaling. Using an ERF6 inducible overexpression line, we demonstrate that the GA-degrading enzyme GA2-OX6 is transcriptionally induced by ERF6 and that consequently DELLA proteins are stabilized. As a result, ERF6 gain-of-function lines are dwarfed and hypersensitive to osmotic stress, while growth of erf5erf6 loss-of-function mutants is less affected by stress. Next to its role in plant growth under stress, ERF6 also activates the expression of a plethora of osmotic stress-responsive genes, including the well-known stress tolerance genes STZ, MYB51 and WRKY33. Interestingly, the activation of the stress tolerance genes by ERF6 occurs independently from the ERF6-mediated growth inhibition. Together, these data fit into a leaf growth regulatory model in which ERF5 and ERF6 form a missing link between the previously observed stress-induced 1-aminocyclopropane-1-carboxylic acid (ACC) accumulation and DELLA-mediated cell cycle exit and execute a dual role by regulating both stress tolerance and growth-inhibition. Samples were obtained from three independent experiments and from multiple plates within the experiment. Whole seedlings were harvested rapidly in an excess of RNAlater® solution (Ambion), and after overnight storage at 4°C, dissected under a binocular microscope on a cooling plate with precision microscissors. Dissected leaves were transferred to a new tube, frozen in liquid nitrogen, and ground with a Retsch machine and 3-mm metal balls. RNA was extracted with TriZol (Invitrogen) and further purified with the RNeasy Mini Kit (Qiagen). DNA digestion was done on columns with RNase-free DNase I (Roche). For the identification of genome-wide expression changes, samples of the strong ERF6-overexpressing line (ERF6IOE-S) and the control line (GFP:IOE) were harvested 4 h after transfer to DEX. Two µg of pure RNA samples were hybridized to AGRONOMICS1 Arabidopsis Tiling Arrays (Rehrauer et al., 2010) at the VIB Microarray Facility (Leuven, Belgium).
2013-04-06 | E-GEOD-45830 | biostudies-arrayexpress
Project description:To identify genes of the guard cell transcriptome of Arabidopsis thaliana enriched guard cell samples of ost1-2 and slac1-5 mutants were compared to their wildtype. Total samples analysed are 11: biological independent replicates of: enriched guard cells (slac1-5) vs. enriched guard cells (gl1-1); enriched guard cells (ost1-2) vs. guard cells (ler);
2013-11-20 | E-GEOD-42470 | biostudies-arrayexpress
Project description:Early leaf growth is sustained by cell proliferation and subsequent cell expansion that initiates at the leaf tip and proceeds in a basipetal direction. Using detailed kinematic and gene expression studies to map these stages during early development of the third leaf of Arabidopsis thaliana we showed that the cell cycle arrest front did not progress gradually down the leaf, but rather was established and abolished abruptly. Interestingly, leaf greening and stomatal patterning followed a similar basipetal pattern, but proliferative pavement cell and formative meristemoid divisions were uncoordinated in respect to onset and persistence. Genes differentially expressed during the transition from cell proliferation to expansion were enriched in genes involved in cell cycle, photosynthesis, and chloroplast retrograde signaling. Proliferating primordia treated with norflurazon, a chemical inhibitor of retrograde signaling, showed inhibited onset of cell expansion. Hence, differentiation of the photosynthetic machinery is important for regulating the exit from proliferation. GSM839070-GSM839081: Total RNA was extracted using RNeasy plant mini kit (Qiagen) from leaf 3 of Arabidopsis seedlings grown in vitro and treated or not treated with norflurazon (NF) at 8 days after stratification (DAS) and harvested 24 and 48 hours after treatment. RNA from three biological repeats of each timepoint and treatment were submitted to AGRONOMICS1 array hybridization. GSM839082-GSM839099: Total RNAs were extracted using RNeasy plant mini kit (Qiagen) from leaf 3 of Arabidopsis seedlings 8, 9, 10, 11, 12, and 13 days after stratification (DAS) and grown in vitro. RNAs from three biological repeats of each timepoint were submitted to AGRONOMICS1 array hybridization.
2012-01-17 | E-GEOD-33936 | biostudies-arrayexpress
Project description:To assess plasticity in genetic regulation of gene expression in Arabidopsis thaliana, genome wide gene expression variation was analyzed in a Ler/Cvi recombinant inbred line (RIL) population treated with low-light. The variation in expression could be explained for many genes by expression quantitative trait loci (eQTLs), which were compared to a previous genetical genomics study in the same untreated population. Please note Characteristics[StrainOrLine] is the population of 162 recombinant inbred lines between the accessions Ler x Cvi. Ler and Cvi are the names of the parental accessions.
2013-03-01 | E-MTAB-1357 | biostudies-arrayexpress