title: Model selection reveals control of cold signalling by evening-phased components of the plant circadian clock.
abstract: Circadian clocks confer advantages by restricting biological processes to certain times of day through the control of specific phased outputs. Control of temperature signalling is an important function of the plant oscillator, but the architecture of the gene network controlling cold signalling by the clock is not well understood. Here we use a model ensemble fitted to time-series data and a corrected Akaike Information Criterion (AICc) analysis to extend a dynamic model to include the control of the key cold-regulated transcription factors C-REPEAT BINDING FACTORs 1-3 (CBF1, CBF2, CBF3). AICc was combined with in silico analysis of genetic perturbations in the model ensemble, and selected a model that predicted mutant phenotypes and connections between evening-phased circadian clock components and CBF3 transcriptional control, but these connections were not shared by CBF1 and CBF2. In addition, our model predicted the correct gating of CBF transcription by cold only when the cold signal originated from the clock mechanism itself, suggesting that the clock has an important role in temperature signal transduction. Our data shows that model selection could be a useful method for the expansion of gene network models.
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
authors.forename: Jack
authors.initials: J
authors.lastname: Keily
authors.forename: Dana R
authors.initials: DR
authors.lastname: MacGregor
authors.forename: Robert W
authors.initials: RW
authors.lastname: Smith
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Millar
authors.forename: Karen J
authors.initials: KJ
authors.lastname: Halliday
authors.forename: Steven
authors.initials: S
authors.lastname: Penfield
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000502:physiology; D029681:Arabidopsis Proteins / Q000235:genetics / Q000502:physiology*; D056926:CLOCK Proteins / Q000502:physiology; D057906:Circadian Clocks; D003080:Cold Temperature; D004268:DNA-Binding Proteins / Q000235:genetics / Q000502:physiology; D018506:Gene Expression Regulation, Plant; D008954:Models, Biological; D009154:Mutation; D010641:Phenotype; D015398:Signal Transduction; D014157:Transcription Factors / Q000235:genetics / Q000502:physiology*
chemical_list: D029681:Arabidopsis Proteins; C114425:CCA1 protein, Arabidopsis; D004268:DNA-Binding Proteins; C114578:DREB1A protein, Arabidopsis; C113192:LHY protein, Arabidopsis; C411822:TOC1 protein, Arabidopsis; D014157:Transcription Factors; D056926:CLOCK Proteins
keywords: Arabidopsis; circadian clock; cold acclimation; gene network model; temperature
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