ArticlePlant physiology2008
Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome.
Article in Plant physiology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 116 papers, 1 of them a synthesis that pooled it.
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Who cites it
116 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Abiotic Stress in Crop Production.International journal of molecular sciences · 2023Pooled it
- The Core Circadian Clock GenePlants (Basel, Switzerland) · 2026Article
- CsPRR7 negatively regulates cold tolerance by repressing CsCBF3 in tea plants.Plant cell reports · 2026Article
- Chromatin remodeling at the C-REPEAT BINDING FACTOR cluster controls growth retardation at low ambient temperature.The Plant cell · 2026Article
- Temperature compensation of the Arabidopsis circadian clock.Npj biological timing and sleep · 2025Review
- Low temperature abolishes human cellular circadian rhythm through Hopf bifurcation.NPJ systems biology and applications · 2025Article
- Coincidence of the threshold temperature of seasonal switching for diel transcriptomic oscillations and growth.Plant & cell physiology · 2025Article
- The circadian clock of Populus affects physiological, transcriptional and metabolomic responses to osmotic and ionic components of salt stress.Npj biological timing and sleep · 2025Article
- Wound-induced transcriptional dynamics in rice.Crop health · 2025Article
- Diurnal dynamics of different circadian transcription modules in Chinese pine needles and roots during dormancy induction.BMC plant biology · 2025Article
- Molecular and biochemical components associated with chilling tolerance in tomato: comparison of different developmental stages.Molecular horticulture · 2024Article
- Circadian and environmental signal integration in a natural population ofProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Transcriptome dynamics inFrontiers in plant science · 2024Article
- Genome-wide circadian gating of a cold temperature response in bread wheat.PLoS genetics · 2023Article
- Chilling stress drives organ-specific transcriptional cascades and dampens diurnal oscillation in tomato.Horticulture research · 2023Article
- Clock-regulated coactivators selectively control gene expression in response to different temperature stress conditions inProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Machine learning extracts marks of thiamine's role in cold acclimation in the transcriptome ofFrontiers in plant science · 2023Article
- A Transferable Machine Learning Framework for Predicting Transcriptional Responses of Genes Across Species.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Rice CIRCADIAN CLOCK ASSOCIATED 1 transcriptionally regulates ABA signaling to confer multiple abiotic stress tolerance.Plant physiology · 2022Article
- Identification and Characterization ofInternational journal of molecular sciences · 2022Article
56 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In plants, low temperature causes massive transcriptional changes, many of which are presumed to be involved in the process of cold acclimation. Given the diversity of developmental and environmental factors between experiments, it is surprising that their influence on the identification of cold-responsive genes is largely unknown. A systematic investigation of genes responding to 1 d of cold treatment revealed that diurnal- and circadian-regulated genes are responsible for the majority of the substantial variation between experiments. This is contrary to the widespread assumption that these effects are eliminated using paired diurnal controls. To identify the molecular basis for this variation, we performed targeted expression analyses of diurnal and circadian time courses in Arabidopsis (Arabidopsis thaliana). We show that, after a short initial cold response, in diurnal conditions cold reduces the amplitude of cycles for clock components and dampens or disrupts the cycles of output genes, while in continuous light all cycles become arrhythmic. This means that genes identified as cold-responsive are dependent on the time of day the experiment was performed and that a control at normal temperature will not correct for this effect, as was postulated up to now. Time of day also affects the number and strength of expression changes for a large number of transcription factors, and this likely further contributes to experimental differences. This reveals that interactions between cold and diurnal regulation are major factors in shaping the cold-responsive transcriptome and thus will be an important consideration in future experiments to dissect transcriptional regulatory networks controlling cold acclimation. In addition, our data revealed differential effects of cold on circadian output genes and a unique regulation of an oscillator component, suggesting that cold treatment could also be an important tool to probe circadian and diurnal regulatory mechanisms.
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