Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development
By Michael F. Covington, Julin N. Maloof, Martin Straume, Steve A. Kay, S. Harmer. Genome Biology, 2008
729 citations recorded by the source corpus.
BackgroundAs nonmotile organisms, plants must rapidly adapt to ever-changing environmental conditions, including those caused by daily light/dark cycles. One important mechanism for anticipating and preparing for such predictable changes is the circadian clock. Nearly all organisms have circadian oscillators that, when they are in phase with the Earth's rotation, provide a competitive advantage. In order to understand how circadian clocks benefit plants, it is necessary to identify the pathways and processes that are clock controlled.ResultsWe have integrated information from multiple circadian microarray experiments performed on Arabidopsis thaliana in order to better estimate the fraction of the plant transcriptome that is circadian regulated. Analyzing the promoters of clock-controlled genes, we identified circadian clock regulatory elements correlated with phase-specific transcript accumulation. We have also identified several physiological pathways enriched for clock-regulated changes in transcript abundance, suggesting they may be modulated by the circadian clock.ConclusionOur analysis suggests that transcript abundance of roughly one-third of expressed A. thaliana genes is circadian regulated. We found four promoter elements, enriched in the promoters of genes with four discrete phases, which may contribute to the time-of-day specific changes in the transcript abundance of these genes. Clock-regulated genes are over-represented among all of the classical plant hormone and multiple stress response pathways, suggesting that all of these pathways are influenced by the circadian clock. Further exploration of the links between the clock and these pathways will lead to a better understanding of how the circadian clock affects plant growth and leads to improved fitness.
Subfields: Endocrine and Autonomic Systems, Plant Science
View Paper: https://www.semanticscholar.org/paper/7dda376a56671982e77dcadc455ce9bf6e9ddf2d
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In Endocrine and Autonomic Systems
In Plant Science
- Huapeng Zhou
- Mingyue Liu
- Qikun Zhang
- Satchidananda Panda
- J. Doyle
- Changle Ma
- Pingping Wang
- Z. J. Chen
Citations in the corpus
- Polyploidy, the Nucleotype, and Novelty: The Impact of Genome Doubling on the Biology of the Cell (2019, background): “Since one-third of the Arabidopsis genome is under circadian control (Covington et al. 2008) and allopolyploidy is known to affect circadian behavior in Arabidopsis (Ni et al. 2009), such chromatin modifications could play a role in differences between diploids and autopolyploids.”
- Molecular mechanisms of polyploidy and hybrid vigor (2010, background): “At least ∼15% of genes, including those involved in photosynthesis and starch metabolism [96,97], and up to 90% of transcriptome [98] are affected by the circadian clock regulators.”
- Regulation of Plant Responses to Salt Stress (2021, background): “Several proteins that maintain the circadian clock play key roles in regulating salt stress tolerance [44,45].”
- Time of feeding and the intrinsic circadian clock drive rhythms in hepatic gene expression (2009, background): “In plants, up to 30% of the transcriptome, including several enzymes and regulators for nutrient production and metabolism, shows rhythmic expression under constant light when photosynthesis persists (31, 32).”