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Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure

Flis, Anna; Fernandez, Aurora Pinas; Zielinski, Tomasz; Mengin, Virginie; Sulpice, Ronan; Stratford, Kevin; Hume, Alastair; Pokhilko, Alexandra; Southern, Megan M; Seaton, Daniel D; McWatters, Harriet G.; Stitt, Mark

Description

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...[Show more]

dc.contributor.authorFlis, Anna
dc.contributor.authorFernandez, Aurora Pinas
dc.contributor.authorZielinski, Tomasz
dc.contributor.authorMengin, Virginie
dc.contributor.authorSulpice, Ronan
dc.contributor.authorStratford, Kevin
dc.contributor.authorHume, Alastair
dc.contributor.authorPokhilko, Alexandra
dc.contributor.authorSouthern, Megan M
dc.contributor.authorSeaton, Daniel D
dc.contributor.authorMcWatters, Harriet G.
dc.contributor.authorStitt, Mark
dc.date.accessioned2018-11-29T22:57:00Z
dc.date.available2018-11-29T22:57:00Z
dc.identifier.issn2046-2441
dc.identifier.urihttp://hdl.handle.net/1885/153704
dc.description.abstractOur 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
dc.format.mimetypeapplication/pdf
dc.publisherRoyal Society Publishing
dc.sourceOpen Biology
dc.titleDefining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume5
dc.date.issued2015
local.identifier.absfor060705 - Plant Physiology
local.identifier.ariespublicationU3488905xPUB16699
local.type.statusPublished Version
local.contributor.affiliationFlis, Anna, College of Science, ANU
local.contributor.affiliationFernandez, Aurora Pinas, University of Edinburgh
local.contributor.affiliationZielinski, Tomasz, University of Edinburgh
local.contributor.affiliationMengin, Virginie, Max Planck Institute of Molecular Plant Physiology
local.contributor.affiliationSulpice, Ronan, Max Planck Institute of Molecular Plant Physiology
local.contributor.affiliationStratford, Kevin, University of Edinburgh
local.contributor.affiliationHume, Alastair, University of Edinburgh
local.contributor.affiliationPokhilko, Alexandra, University of Aberdeen
local.contributor.affiliationSouthern, Megan M, University of Edinburgh
local.contributor.affiliationSeaton, Daniel D , University of Edinburgh,
local.contributor.affiliationMcWatters, Harriet G., University of Edinburgh,
local.contributor.affiliationStitt, Mark, Max Planck Institute of Molecular Plant Physiology
local.bibliographicCitation.issue10
local.bibliographicCitation.startpage150042
local.bibliographicCitation.lastpage150042
local.identifier.doi10.1098/rsob.150042
local.identifier.absseo970106 - Expanding Knowledge in the Biological Sciences
dc.date.updated2018-11-29T08:15:00Z
local.identifier.scopusID2-s2.0-84946924658
local.identifier.thomsonID000365030400001
dcterms.accessRightsOpen Access
CollectionsANU Research Publications

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