Arabidopsis clock model P2011.3.1 - PLM_1041, version 1, SUBMITTED
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ABSTRACT:
SUBMITTER: BioData SynthSys
PROVIDER: 380 | FAIRDOMHub | 2019-12-20
REPOSITORIES: FAIRDOMHub
Publications
Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure.
Flis Anna A Fernández Aurora Piñas AP Zielinski Tomasz T Mengin Virginie V Sulpice Ronan R Stratford Kevin K Hume Alastair A Pokhilko Alexandra A Southern Megan M MM Seaton Daniel D DD McWatters Harriet G HG Stitt Mark M Halliday Karen J KJ Millar Andrew J AJ
Open biology 20151001 10
Our understanding of the complex, transcriptional feedback loops in the circadian clock mechanism has depended upon quantitative, timeseries data from disparate sources. We measure clock gene RNA profiles in Arabidopsis thaliana seedlings, grown with or without exogenous sucrose, or in soil-grown plants and in wild-type and mutant backgrounds. The RNA profiles were strikingly robust across the experimental conditions, so current mathematical models are likely to be broadly applicable in leaf tis ...[more]
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SBML files were verified using COPASI 4.24 (Build 197) software. The full process is described in Urquiza and Millar, In Silico Plants, 2021.
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Project description:Model U2020.3.
This model of the clock gene circuit in the plant Arabidopsis thaliana is inspired by the P2011 model, published in Pokhilko et al Mol Syst Biol 2012. The U2019 version uses very similar interactions to P2011, where the combined LHY/CCA1 component indirectly activates the wave of PRR gene expression, whereas the U2020 version uses both indirect activation and inter-PRR repression. The .3 versions of each model are scaled to match the absolute RNA level data from the TiMet project, in Flis et al. 2015.
SBML files were verified using COPASI 4.24 (Build 197) software. The full process is described in Urquiza and Millar, In Silico Plants, 2021.
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