ArticlePLoS computational biology2014
Rethinking transcriptional activation in the Arabidopsis circadian clock.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
- Temperature compensation of the Arabidopsis circadian clock.Npj biological timing and sleep · 2025Review
- 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
- Abundant clock proteins point to missing molecular regulation in the plant circadian clock.Molecular systems biology · 2025Article
- Recent advances in designing synthetic plant regulatory modules.Frontiers in plant science · 2025Review
- Integrating temperature into the Arabidopsis circadian system.Npj biological timing and sleep · 2025Review
- Nature's Master of Ceremony: TheNpj biological timing and sleep · 2025Article
- Decoding the plant clock: a review of mathematical models for the circadian regulatory network.Plant molecular biology · 2024Review
- The seasons within: a theoretical perspective on photoperiodic entrainment and encoding.Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology · 2024Review
- Unlocking allelic variation in circadian clock genes to develop environmentally robust and productive crops.Planta · 2024Review
- Diurnal Rhythms in the Red Seaweed Gracilariopsis chorda are Characterized by Unique Regulatory Networks of Carbon Metabolism.Molecular biology and evolution · 2024Article
- The Roles of theInternational journal of molecular sciences · 2023Article
- Genome-wide circadian gating of a cold temperature response in bread wheat.PLoS genetics · 2023Article
- Red Light Resets the Expression Pattern, Phase, and Period of the Circadian Clock in Plants: A Computational Approach.Biology · 2022Article
- Circadian entrainment in Arabidopsis.Plant physiology · 2022Article
- The circadian clock mutant lhy cca1 elf3 paces starch mobilization to dawn despite severely disrupted circadian clock function.Plant physiology · 2022Article
- A spatial model of the plant circadian clock reveals design principles for coordinated timing.Molecular systems biology · 2022Article
- Restoring circadian gene profiles in clock networks using synthetic feedback control.NPJ systems biology and applications · 2022Article
- The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues.The Plant journal : for cell and molecular biology · 2022Review
- A crosstalk of circadian clock and alternative splicing under abiotic stresses in the plants.Frontiers in plant science · 2022Review
- LUX ARRHYTHMO Interacts With ELF3a and ELF4a to Coordinate Vegetative Growth and Photoperiodic Flowering in Rice.Frontiers in plant science · 2022Article
11 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Circadian clocks are biological timekeepers that allow living cells to time their activity in anticipation of predictable daily changes in light and other environmental factors. The complexity of the circadian clock in higher plants makes it difficult to understand the role of individual genes or molecular interactions, and mathematical modelling has been useful in guiding clock research in model organisms such as Arabidopsis thaliana. We present a model of the circadian clock in Arabidopsis, based on a large corpus of published time course data. It appears from experimental evidence in the literature that most interactions in the clock are repressive. Hence, we remove all transcriptional activation found in previous models of this system, and instead extend the system by including two new components, the morning-expressed activator RVE8 and the nightly repressor/activator NOX. Our modelling results demonstrate that the clock does not need a large number of activators in order to reproduce the observed gene expression patterns. For example, the sequential expression of the PRR genes does not require the genes to be connected as a series of activators. In the presented model, transcriptional activation is exclusively the task of RVE8. Predictions of how strongly RVE8 affects its targets are found to agree with earlier interpretations of the experimental data, but generally we find that the many negative feedbacks in the system should discourage intuitive interpretations of mutant phenotypes. The dynamics of the clock are difficult to predict without mathematical modelling, and the clock is better viewed as a tangled web than as a series of loops.
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