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
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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: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: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:Comparison of gene expression profile of human pluripotent stem cells (clone hCBiPS2) expanded in batch-fed and perfusion stirred bioreactors after 0, 3 and 7 days.
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Project description:Retinaldehyde dehydrogenases convert retinal into all-trans retinoic acid (ATRA), thereby regulating cell differentiation and cancer stem cell proliferation. Chemical tools and methods are valuable commodities to study aldehyde dehydrogenase (ALDH) activity in human cells. Here, we describe the design, synthesis and application of LEI-945, a first-in-class activity-based probe modeled on retinal that reports on individual ALDHs in cancer cells. Comparative chemical proteomics with LEI-945 explained the ability of various breast cancer cell lines to produce ATRA via retinaldehyde dehydrogenases isozymes, whereas the ALDEFLUORTM assay could not. Competitive chemical proteomics using LEI-945 revealed that the ALDH inhibitor NCT-505 inhibited both ALDH1A1 and ALDH1A3 in MDA-MB-468 breast cancer cells inducing a cell cycle arrest in the G1 phase as well as cell death through necrosis. Our results show that LEI-945 holds promise to guide the discovery of ALDH-based therapeutics
2019-12-18 | PXD015495 | Pride
Project description:Brown adipose tissue (BAT) is a thermogenic organ that dissipates stored energy as heat to maintain body temperature in infants and small mammals. This process may also provide protection from development of diet-induced obesity. We found that the bioactive lipid mediator lysophosphatidic acid (LPA) markedly decreases differentiation of cultured primary brown adipocyte precursors, while potent selective inhibitors of the LPA-generating enzyme autotaxin (ATX) promote differentiation. Transgenic mice overexpressing ATX exhibited reduced expression of BAT-related genes in peripheral white adipose tissue and accumulated significantly more fat than wild-type controls when fed a high fat diet. Our results indicate that ATX and its product LPA are physiologically relevant negative regulators of brown fat adipogenesis and suggest that a decrease in peripheral brown adipose tissue results in increased susceptibility to diet-induced obesity in mice. Primary BAT cell cultures were established as previously reported with some minor modifications (Cannon B., 2001; Néchad M., 1983). Four- to 6-week-old mice were euthanized under aseptic conditions and interscapular BAT (IBAT) dissected, finely minced in digestion buffer containing 123 mM NaCl, 5mM HCl, 1.3 mM CaCl2, 5mM glucose, 1.5% (w/v) crude bovine serum albumin fraction V, 100 mM HEPES, 0.2% collagenase type II (Sigma-Aldrich Corp., St. Louis, MO), pH 7.4, and digested in 10 ml of the same buffer for 30 min at 37°C. The supernatant obtained was then filtered using a 250 µm nylon mesh and kept in ice for 15 minutes to allow fat droplets and mature cells to float. The resulting infranatant was filtered through a 30 µm nylon mesh to enrich the fraction with precursor cells and centrifuged at 700g for 10 min. The pellet obtained was washed once in warm DMEM and resuspended in DMEM medium containing 10% newborn calf serum, 10 mM HEPES, 4mM glutamine, 25 µg/ml sodium ascorbate (Sigma-Aldrich Corp., St. Louis, MO)., 100U/ml penicillin and 100mg/ml streptomycin. Cells were seeded onto 35mm dish plates. Insulin treatment was started on day 1 at 50 nM and the concentration increased to 100 nM at day 5 and 200 nM at day 7. Differentiated/confluent cells were collected for biochemical analysis (~day 9). To identify genes regulated by ATX and LPA signaling, 9 DIV primary BAT cultures were treated with the vehicle (DMSO), specific ATX inhibitor HA155 (2.5µM), or LPA (1-Oleoly-LPA, 5µM) (Avanti Polar Lipids, AL, USA) during differentiation. Treatment of the BAT cultures did not affect confluence or markers of proliferation. RNA was extracted from three cultures per condition using TRIzol reagent (Invitrogen, Carlsbad, CA) as described previously (Blalock EM., 2003).
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