Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA394581 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5829640.fastq.gz | Fastqsanger.gz | |||
| SRR5829641.fastq.gz | Fastqsanger.gz |
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Project description:We report novel function of NPR1 coactivator that regulates cold acclimation by promoting cold-induced gene expression.
2018-08-31 | GSE101483 | GEO
Project description:MicroRNAs (miRNAs) play vital roles in various biological processes by leading to mRNA cleavage or translational repression, and are also involved in multiple stress conditions. However, the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study, high-throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control (28°C, 30 days) and cold-acclimation (18°C, 30 days) conditions. A total of 414 miRNAs, 349 known and 65 novel, were identified. Among those miRNAs, 24 (19 known and 5 novel) were up-regulated, and 23 (9 known and 14 novel) were down-regulated in cold acclimated cells. The Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses indicated that the known differentially expressed miRNAs (DE-miRNA) are involved in cold acclimation by regulation of phosphorylation, cell junction, intracellular signal transduction, ECM-receptor interaction and so on. Moreover, dre-miR-100-3p inhibitor or dre-miR-16b mimics could protect ZF4 cells under cold stress, indicating the involvement of miRNA in cold acclimation. In summary, the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation.
2019-12-17 | GSE134399 | GEO
Project description:Functions of Arabidopsis REI1-LIKE (REIL) proteins, two homologs of a yeast ribosome biogenesis protein (RBP) that takes part in the late cytoplasmic steps of 60S ribosomal subunit maturation, were characterized by systems analyses of the 10°C cold acclimating reil1-1 reil2-1 double mutant compared to Col-0 wildtype. The mutant lacked both REIL proteins, was strongly growth inhibited in the cold and complemented by constitutive expression of N-terminal FLUORESCENT PROTEIN (FP)-REIL1 and FP-REIL2 fusion proteins under control of the UBIQUITIN 10 promoter. Wildtype acclimation to 10°C causes relative accumulation of cytosolic ribosome subunits and rRNA. Expression of cytosolic ribosomal genes, known cytosolic RBPs, translation initiation- and elongation-factors was activated. Conserved function of Arabidopsis REIL proteins was indicated by delay of these processes in reil1-1 reil2-1, cytosolic localization of FP-REIL proteins and native REIL protein interactions with 60S containing ribosome fractions. Non-acclimated reil1-1 reil2-1 triggered plant specific metabolic and transcriptomic cold acclimation responses that included activation of the DREB/CBF-regulon with a preference for the cold acclimation factors, CBF1/DREB1B, CBF2/DREB1C, and CBF3/DREB1A. Cold-acclimating reil1-1 reil2-1 maintained cellular integrity and acquired freezing tolerance but did not activate FLOWERING LOCUS T expression in mature leaves. This block was independent of FLOWERING LOCUS C and AGAMOUS-LIKE 19 mediated vernalization. We conclude that Arabidopsis REIL proteins enhance accumulation of cytosolic ribosome subunits after cold shift and either directly or indirectly feedback on temperature perception by suppression of premature cold acclimation at optimized temperature and by triggering growth and the vegetative to generative phase transition in the cold. Transcriptomic profiling demonstrated a hidden acclimation phenotype of the morphologically inconspicuous reil1-1reil2-1 mutant under optimized temperature conditions. Premature triggering of cold acclimation, a severe growth defect at 10°C and compensation responses indicate that REIL function may extend beyond cytosolic ribosome biogenesis towards translation initiation.
2018-02-01 | GSE101111 | GEO
Project description:Small noncoding RNA (sncRNA), including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs) are key gene regulators in eukaryotes, playing critical roles in plant development and stress tolerance. Trans-acting siRNAs (ta-siRNAs), which are secondary siRNAs triggered by miRNAs, and siRNAs from natural antisense transcripts (nat-siRNAs) are two well-studied classes of endo-siRNAs. In order to understand sncRNAsM-bM-^@M-^Y roles in plant cold response and stress acclimation, we studied miRNAs and endo-siRNAs in Cassava (Manihot esculenta), a major source of food for the world populations in tropical regions. Combining Next-Generation sequencing and computational and experimental analyses, we profiled and characterized sncRNA species and mRNA genes from the plants that experienced severe and moderate cold stresses, that underwent further severe cold stress after cold acclimation at moderate stress, and that grew under the normal condition. We also included Castor bean (Ricinus communis) to understand conservation of sncRNAs. In addition to known miRNAs, we identified dozens of novel miRNAs as well as ta-siRNA-yielding and nat-siRNA-yielding loci in Cassava and Castor bean, respectively. Among the expressed sncRNAs, many sncRNAs were differentially expressed under cold stresses. Our study provided the results on gene regulation by sncRNAs in cold acclimation of Euphorbiaceous plants and the role of sncRNA-mediated pathways affected by cold stress and stress acclimation in Cassava. Examination of small RNA populations in Cassava cultivar SC124 under the normal condition (NC), gradual cold acclimation (CA), cold shock (CS) and stress acclimation Cold stress after cold acclimation (CCA).
2014-07-05 | E-GEOD-52177 | biostudies-arrayexpress
Project description:Earlier findings indicated that light plays a critical role in the development of frost tolerance in winter cereals. However, the exact mechanism is still poorly understood. In the present work the effects of light during the cold acclimation period were studied in chilling-sensitive maize plants. The results show that although exposure to relatively high light intensities during cold acclimation at 15 °C causes various stress symptoms, it enhances the effectiveness of acclimation to chilling conditions (5 °C in the light). Interestingly, certain stress responses were light-dependent not only in the leaves, but also in the roots. A microarray study was also conducted to achieve a better understanding of the interaction of low temperature and light intensity during the cold hardening period. Numerous genes significantly differentially expressed were observed in almost all assimilation and metabolic pathways. Acclimation at moderately low temperature and low light intensity reduced the level of soluble sugars, while chilling increased it. Greater accumulation during hardening was detected at relatively high light intensity. It seems that the photoinhibition induced by low temperature is a necessary evil for cold acclimation processes in plants.
2020-12-31 | GSE107913 | GEO
Project description:Background: The prevalence of type 2 diabetes has increased dramatically in recent decades. Increasing brown adipose tissue (BAT) mass and activity has recently emerged as an interesting approach to not only increase energy expenditure, but also improve glucose homeostasis. BAT can be recruited by prolonged cold exposure in lean, healthy humans. Here, we tested whether cold acclimation could have therapeutic value for patients with type 2 diabetes by improving insulin sensitivity. Methods: Eight type 2 diabetic patients (age 59.3±5.8 years, BMI 29.8±3.2 kg/m2) followed a cold acclimation protocol, consisting of intermittent cold exposure (6 hours/day, 14-14.5 °C) for 12 consecutive days. Before and after cold acclimation, cold-induced BAT activity was assessed by [18F]FDG-PET/CT scanning, insulin sensitivity at thermoneutrality by a hyperinsulinemic-euglycemic clamp, and muscle and WAT biopsies were taken. Results: Cold-induced BAT activity was low, but increased in all patients upon cold acclimation (SUV from 0.40±0.29 to 0.63±0.78, p<0.05). Interestingly, insulin sensitivity showed a very pronounced 40% increase upon cold acclimation (glucose rate of disappearance from 14.9±4.1 to 20.5±6.9 μmol kg-1 min-1, p<0.05). A 40% increase in insulin sensitivity cannot be explained by BAT glucose uptake, in fact basal skeletal muscle GLUT4 content and translocation was markedly increased after cold acclimation, without effects on insulin signaling or AMPk activation. Conclusions: Regular mild cold exposure has marked effects on insulin sensitivity, which are accompanied by small increases in BAT activity and more pronounced effects on skeletal muscle. These data suggest a novel therapeutic option for the treatment of type 2 diabetes.
2015-07-05 | GSE67297 | GEO
Project description:Stress acclimation is an effective mechanism that plants acquired for adaption to dynamic environmental conditions. After undergoing cold acclimation, plants become more tolerant to cold stress. In order to understand the mechanism of cold acclimation, we performed a systematic, comprehensive study of cold response and acclimation in Cassava (Manihot esculenta), a staple crop and major food source in the tropical regions of the world. We profiled mRNA genes and small-RNA species, using next generation sequencing, and performed an integrative analysis of the transcriptome and microRNAome of Cassava across the normal condition, a moderate cold stress at 14°C, a harsh stress at 4°C after cold acclimation at 14°C, and a cold shock from 24°C to 4°C. Two results from the analysis were striking. First, the moderate stress and cold shock, despite a difference of 10°C between the two, triggered comparable degrees of perturbation to the transcriptome; in contrary, further harsh stress after cold acclimation resulted in a much smaller degree of transcriptome variation. Second and more importantly, about two thirds of the up- or down-regulated genes after moderate stress reversed their expression to down- or up-regulation, respectively, under harsh stress after cold acclimation, resulting in a genome-wide rewiring of regulatory networks. MicroRNAs, which are key post-transcriptional gene regulators, were major players in this massive rewiring of genetic circuitry. Further, a function enrichment analysis of the perturbed genes revealed that cold acclimation helped the plant to develop immunity to further harsh stress by exclusively inducing genes with functions of nutrient reservoir; in contrast, many genes with functions of viral reproduction were induced by cold shock. Our study revealed, for the first time, the molecular basis of stress acclimation in plants, and shed lights on the role of microRNA gene regulation in cold response and acclimation in Euphorbia.
2014-08-18 | GSE52176 | GEO
Project description:Background: The prevalence of type 2 diabetes has increased dramatically in recent decades. Increasing brown adipose tissue (BAT) mass and activity has recently emerged as an interesting approach to not only increase energy expenditure, but also improve glucose homeostasis. BAT can be recruited by prolonged cold exposure in lean, healthy humans. Here, we tested whether cold acclimation could have therapeutic value for patients with type 2 diabetes by improving insulin sensitivity. Methods: Eight type 2 diabetic patients (age 59.3±5.8 years, BMI 29.8±3.2 kg/m2) followed a cold acclimation protocol, consisting of intermittent cold exposure (6 hours/day, 14-14.5 °C) for 12 consecutive days. Before and after cold acclimation, cold-induced BAT activity was assessed by [18F]FDG-PET/CT scanning, insulin sensitivity at thermoneutrality by a hyperinsulinemic-euglycemic clamp, and muscle and WAT biopsies were taken. Results: Cold-induced BAT activity was low, but increased in all patients upon cold acclimation (SUV from 0.40±0.29 to 0.63±0.78, p<0.05). Interestingly, insulin sensitivity showed a very pronounced 40% increase upon cold acclimation (glucose rate of disappearance from 14.9±4.1 to 20.5±6.9 μmol kg-1 min-1, p<0.05). A 40% increase in insulin sensitivity cannot be explained by BAT glucose uptake, in fact basal skeletal muscle GLUT4 content and translocation was markedly increased after cold acclimation, without effects on insulin signaling or AMPk activation. Conclusions: Regular mild cold exposure has marked effects on insulin sensitivity, which are accompanied by small increases in BAT activity and more pronounced effects on skeletal muscle. These data suggest a novel therapeutic option for the treatment of type 2 diabetes. Microarray analysis was performed on abdominal subcutaneous white adipose tissue samples from human type 2 diabetic patients before, and after 10 days of cold acclimation. A total of 14 samples, from 7 subjects, were used for the microarray analysis.
2015-07-05 | E-GEOD-67297 | biostudies-arrayexpress
Project description:Intertidal zone organisms can experience transient freezing temperatures during winter low tides, but their extreme cold tolerance mechanisms are not known. Petrolisthes cinctipes is a temperate mid-high intertidal zone crab species that can experience wintertime habitat temperatures below the freezing point of seawater. We examined how cold tolerance changed during the initial phase of thermal acclimation to cold and warm temperatures, as well as the persistence of cold tolerance during long-term thermal acclimation. Thermal acclimation for as little as 6 hours at 8˚C enhanced crab tolerance during a 1h exposure to -2°C relative to crabs acclimated to 18˚C. Potential mechanisms for this enhanced tolerance were elucidated using cDNA microarrays to probe for differences in gene expression in cardiac tissue of warm and cold acclimated crabs during the first day of thermal acclimation. No changes in gene expression were detected until 12h of thermal acclimation. Genes strongly upregulated in warm acclimated crabs represented immune response and extracellular / intercellular processes, suggesting that warm acclimated crabs had a generalized stress response and may have been remodelling tissues or altering intercellular processes. Genes strongly upregulated in cold acclimated crabs included many that are involved in glucose production suggesting that cold acclimation involves increasing intracellular glucose as a cryoprotectant. Structural cytoskeletal proteins were also strongly represented among the genes upregulated in only cold acclimated crabs. There were no consistent changes in composition or the level of unsaturation of membrane phospholipid fatty acids with cold acclimation, which suggests that neither short- nor long-term changes in cold tolerance are mediated by changes in membrane fatty acid composition. Overall, our study demonstrates that initial changes in cold tolerance are likely not regulated by transcriptomic responses, but that gene expression-related changes in homeostasis begin within 12 hours – the length of a tidal cycle. all array data and raw images archived at the Porcelain Crab Array Database (http://array.sfsu.edu)
2012-03-01 | GSE35307 | GEO