Arabidopsis thaliana
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PROVIDER: PRJNA96017 | ENA |
REPOSITORIES: ENA
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Project description:Plants must properly integrate noisy temperature signals to monitor seasonal progression. However, the global regulatory landscape underlying cold acclimation and adaption of plants to noisy and fluctuating natural cold conditions remain poorly investigated. Here, we perform a deep-coverage RNA-seq to investigate the transcriptome dynamics of Arabidopsis thaliana plants grown over weeks of a fluctuating temperature regime, mimicking natural cold conditions of autumn and early winter, or grown using an average daily temperature profile without any temperature fluctuations. We show that progressive cold induces three main patterns of transcriptional response: dynamic-, cooling- and chilling-responsive gene activation. Progressive cold induces a complex network of regulators that could be responsible for the regulation of distinct transcriptional programs. Surprisingly, we find only small differences in cold-responsive gene expression between average and fluctuating conditions. We also highlight that temperature before time is the principal driver of cold transcriptional reprogramming. By combining RNA-seq and ATAC-seq data, we observe that the induction of cold-responsive genes is associated with an increase of promoter accessibility whereas down-regulated genes do not lose accessibility, allowing plants to rapidly reactivate transcription after the return of favourable conditions.
2026-09-10 | GSE283017 | GEO
Project description:Plants must properly integrate noisy temperature signals to monitor seasonal progression. However, the global regulatory landscape underlying cold acclimation and adaption of plants to noisy and fluctuating natural cold conditions remain poorly investigated. Here, we perform a deep-coverage RNA-seq to investigate the transcriptome dynamics of Arabidopsis thaliana plants grown over weeks of a fluctuating temperature regime, mimicking natural cold conditions of autumn and early winter, or grown using an average daily temperature profile without any temperature fluctuations. We show that progressive cold induces three main patterns of transcriptional response: dynamic-, cooling- and chilling-responsive gene activation. Progressive cold induces a complex network of regulators that could be responsible for the regulation of distinct transcriptional programs. Surprisingly, we find only small differences in cold-responsive gene expression between average and fluctuating conditions. We also highlight that temperature before time is the principal driver of cold transcriptional reprogramming. By combining RNA-seq and ATAC-seq data, we observe that the induction of cold-responsive genes is associated with an increase of promoter accessibility whereas down-regulated genes do not lose accessibility, allowing plants to rapidly reactivate transcription after the return of favourable conditions.
2026-09-10 | GSE283016 | GEO
Project description:Plants in temperate regions have evolved mechanisms to survive sudden temperature drops. Previous reports have indicated that the cold acclimation mechanism is light-dependent and does not fully operate under a low light intensity. In these studies, plants were grown under a long-day photoperiod and were more sensitive to freezing stress. However, winter annuals like Arabidopsis thaliana Col-0 germinate in the fall, overwinter as rosettes, and therefore must acclimate under short photoperiods and low irradiance. The role of light intensity was analysed in plants grown under a short-day photoperiod at the growth stage 1.14. Plants were acclimated at 4 °C for seven days under 100 and 20 μmol m-2s-1 PPFD for control and limited-light conditions, respectively. All cold acclimated plants accumulated molecular markers reportedly associated with acquired freezing tolerance, including proline, sucrose, CBFs, and COR gene protein products dehydrins and low-temperature-responsive proteins LTIs. Observed changes indicated that low PPFD did not inhibit the cold acclimation process, and the freezing stress experiment confirmed similar survival rates. The molecular analysis found distinct PPFD-specific adaptation mechanisms that were manifested in contrasting content of anthocyanins, cytokinin conjugates, abundances of proteins forming photosystems, and enzymes of protein, energy, and ROS metabolism pathways. Finally, this study led to the identification of putative proteins and metabolite markers correlating with susceptibility to freezing stress of non-acclimated plants grown under low PPFD. Our data show that Arabidopsis plants grown under short-day photoperiod can be fully cold-acclimated under limited light conditions, employing standard and PPFD-specific pathways.
2021-07-08 | PXD025234 | Pride
Project description:Arabidopsis sfr mutants are deficient in cold acclimation during exposure to coolnon-freezing temperatures. Although not visibly affected by the cold they have lost the ability to survive subsequent freezing. We plan to investigate how the sfr2 and sfr6 mutants respond to low temperature on the gene expression level. Wild type plants that have undergone identical treatments in parallel are necessary controls. The cold treatment of plants in the rosette stage (soil grown in a 8/16 hours day/night cycle) will be carried out in a cooled growth chamber at 4 degrees for 24 hours (same light regimetreatment starting/ending at the 4th hour of light). The aerial parts of the treated and untreated plants will be collected and frozen immediately in liquid nitrogen for RNA extraction. Comparison of the cold response of thousands of Arabidopsis genes in the wild type to the situation in our freezing sensitive mutants will enhance our understanding of the cold response itself and illuminate the effect of the mutations on the cold acclimation process. Experimenter name = Irene Bramke Experimenter phone = 01784 44 3770 Experimenter fax = 01784 43 4326 Experimenter address = Royal Holloway Experimenter address = University of London Experimenter address = School of Biological Sciences Experimenter address = Bourne Building Experimenter address = Laboratory 406 Experimenter zip/postal_code = TW20 OEX Experimenter country = UK Keywords: growth_condition_design; genetic_modification_design
2007-01-08 | GSE5711 | GEO
Project description:The goal of the project is to determine proteomic changes occuring in Arabidopsis thalina plants overexpressing Phospholipid:diacylglycerol acyltransferase 1 (PDAT1) gene. This modification resulted in prolongation of plant lifespan together with profound increase of cold and hot tolerance, asdescribed in Demski et.al, 2020. In this study we have compared Arabidopsis leaf proteomes of wild-type plandt and two independently created overexpressor strains grown in normal conditions.
2025-08-21 | PXD043240 | Pride
Project description:Plants have developed various mechanisms of stress response, including stress memory. Epigenetic mechanisms play a vital role in plants' stress memory. In this experiment, DNA methylation dynamics in primed and non-primed A. thaliana plants was evaluated under cold stress to understand the role of epigenetic mechanisms in cold stress responses and memory.
2026-03-13 | E-MTAB-16110 | biostudies-arrayexpress
Project description:Arabidopsis sfr mutants are deficient in cold acclimation during exposure to coolnon-freezing temperatures. Although not visibly affected by the cold they have lost the ability to survive subsequent freezing. We plan to investigate how the sfr2 and sfr6 mutants respond to low temperature on the gene expression level. Wild type plants that have undergone identical treatments in parallel are necessary controls. The cold treatment of plants in the rosette stage (soil grown in a 8/16 hours day/night cycle) will be carried out in a cooled growth chamber at 4 degrees for 24 hours (same light regimetreatment starting/ending at the 4th hour of light). The aerial parts of the treated and untreated plants will be collected and frozen immediately in liquid nitrogen for RNA extraction. Comparison of the cold response of thousands of Arabidopsis genes in the wild type to the situation in our freezing sensitive mutants will enhance our understanding of the cold response itself and illuminate the effect of the mutations on the cold acclimation process. Experimenter name = Irene Bramke; Experimenter phone = 01784 44 3770; Experimenter fax = 01784 43 4326; Experimenter address = Royal Holloway; Experimenter address = University of London; Experimenter address = School of Biological Sciences; Experimenter address = Bourne Building; Experimenter address = Laboratory 406; Experimenter zip/postal_code = TW20 OEX; Experimenter country = UK Experiment Overall Design: 6 samples were used in this experiment
2008-06-14 | E-GEOD-5711 | biostudies-arrayexpress
Project description:Arabidopsis thaliana and Eutrema salsugineum show the ability to cold acclimate. However, the degree of freezing tolerance depends in both cases on the accession. To elucidate the transcriptional basis of this differencial freezing tolerance, we performed where we grew plants under control conditions (20°C/18°C day/night) or under cold conditions (additional 4°C for 2 weeks). Rosettes were harvested from non-acclimated and cold acclimated plants for RNA isolation. Expression patterns were compared between treatments, accessions and species.
2018-01-01 | GSE100108 | GEO
Project description:Transcriptome analysis of dark-grown cop1 and cop1BBX22-GFPox plants
| PRJNA127763 | ENA