title: Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure.
abstract: 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 tissue. In addition to providing reference data, unexpected behaviours included co-expression of PRR9 and ELF4, and regulation of PRR5 by GI. Absolute RNA quantification revealed low levels of PRR9 transcripts (peak approx. 50 copies cell(-1)) compared with other clock genes, and threefold higher levels of LHY RNA (more than 1500 copies cell(-1)) than of its close relative CCA1. The data are disseminated from BioDare, an online repository for focused timeseries data, which is expected to benefit mechanistic modelling. One data subset successfully constrained clock gene expression in a complex model, using publicly available software on parallel computers, without expert tuning or programming. We outline the empirical and mathematical justification for data aggregation in understanding highly interconnected, dynamic networks such as the clock, and the observed design constraints on the resources required to make this approach widely accessible.
authors.affiliation: Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany.
authors.forename: Anna
authors.initials: A
authors.lastname: Flis
authors.affiliation: SynthSys and School of Biological Sciences, University of Edinburgh, C.H. Waddington Building, Edinburgh EH9 3JD, UK.
authors.forename: Aurora Piñas
authors.initials: AP
authors.lastname: Fernández
authors.affiliation: SynthSys and School of Biological Sciences, University of Edinburgh, C.H. Waddington Building, Edinburgh EH9 3JD, UK.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Zielinski
authors.affiliation: Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany.
authors.forename: Virginie
authors.initials: V
authors.lastname: Mengin
authors.affiliation: Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany.
authors.forename: Ronan
authors.initials: R
authors.lastname: Sulpice
authors.affiliation: EPCC, University of Edinburgh, James Clerk Maxwell Building, Edinburgh EH9 3JZ, UK.
authors.forename: Kevin
authors.initials: K
authors.lastname: Stratford
authors.affiliation: SynthSys and School of Biological Sciences, University of Edinburgh, C.H. Waddington Building, Edinburgh EH9 3JD, UK EPCC, University of Edinburgh, James Clerk Maxwell Building, Edinburgh EH9 3JZ, UK.
authors.forename: Alastair
authors.initials: A
authors.lastname: Hume
authors.affiliation: SynthSys and School of Biological Sciences, University of Edinburgh, C.H. Waddington Building, Edinburgh EH9 3JD, UK Institute of Molecular Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Pokhilko
authors.affiliation: Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.
authors.forename: Megan M
authors.initials: MM
authors.lastname: Southern
authors.affiliation: SynthSys and School of Biological Sciences, University of Edinburgh, C.H. Waddington Building, Edinburgh EH9 3JD, UK.
authors.forename: Daniel D
authors.initials: DD
authors.lastname: Seaton
authors.affiliation: SynthSys and School of Biological Sciences, University of Edinburgh, C.H. Waddington Building, Edinburgh EH9 3JD, UK.
authors.forename: Harriet G
authors.initials: HG
authors.lastname: McWatters
authors.affiliation: Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany mstitt@mpimp-golm.mpg.de.
authors.forename: Mark
authors.initials: M
authors.lastname: Stitt
authors.affiliation: SynthSys and School of Biological Sciences, University of Edinburgh, C.H. Waddington Building, Edinburgh EH9 3JD, UK karen.halliday@ed.ac.uk.
authors.forename: Karen J
authors.initials: KJ
authors.lastname: Halliday
authors.affiliation: SynthSys and School of Biological Sciences, University of Edinburgh, C.H. Waddington Building, Edinburgh EH9 3JD, UK andrew.millar@ed.ac.uk.
authors.forename: Andrew J
authors.identifier: http://orcid.org/0000-0003-1756-3654
authors.initials: AJ
authors.lastname: Millar
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D029681:Arabidopsis Proteins / Q000096:biosynthesis / Q000235:genetics / Q000378:metabolism; D001683:Biological Clocks / Q000235:genetics; D056926:CLOCK Proteins / Q000235:genetics*; D002940:Circadian Rhythm / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D030541:Databases, Genetic; D025461:Feedback, Physiological; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D013395:Sucrose / Q000378:metabolism; D014157:Transcription Factors / Q000096:biosynthesis / Q000235:genetics / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D056926:CLOCK Proteins; D004268:DNA-Binding Proteins; D012333:RNA, Messenger; D013395:Sucrose; D014157:Transcription Factors; C114425:CCA1 protein, Arabidopsis; C432430:At2g25930 protein, Arabidopsis; C465973:ELF4 protein, Arabidopsis; C121183:GI protein, Arabidopsis; C113192:LHY protein, Arabidopsis; C504848:Lux Arrhythmo protein, Arabidopsis; C523307:PRR5 protein, Arabidopsis; C514751:PRR9 protein, Arabidopsis
keywords: biological clocks; circadian rhythms; data management; gene regulatory networks; model optimization; plant biology