32415
doi
10.1098/rsob.150042
oai:zenodo.org:32415
user-eu
Piñas Fernández, Aurora
SynthSys and School of Biological Sciences, C.H. Waddington Building, University of Edinburgh, Edinburgh EH9 3JD, Scotland, UK
Zielinski, Tomasz
SynthSys and School of Biological Sciences, C.H. Waddington Building, University of Edinburgh, Edinburgh EH9 3JD, Scotland, UK
Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure
Flis, Anna
Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
url:http://www.research.ed.ac.uk/portal/en/datasets/data-code-and-models-for-flis-et-al-rs-open-biology-2015(fd297498-7d0d-4d57-9040-769af9c65212).html
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Systems biology
Arabidopsis thaliana
Gene regulatory networks
Biological clocks
Circadian rhythms
<p>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 <em>Arabidopsis thaliana</em> 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 <em>PRR9</em> and <em>ELF4</em>, and regulation of <em>PRR5</em> by <em>GI</em>. Absolute RNA quantification revealed low levels of <em>PRR9</em> transcripts (peak ~50 copies/cell) compared with other clock genes, and three-fold higher levels of <em>LHY</em> RNA (>1500 copies/cell) than of its close relative <em>CCA1</em>. The data are disseminated from BioDare, an online repository for focussed 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.</p>
Zenodo
2015-09-24
info:eu-repo/semantics/article
618373
user-eu
award_title=Linking the clock to metabolism; award_number=245143; award_identifiers_scheme=url; award_identifiers_identifier=https://cordis.europa.eu/projects/245143; funder_id=00k4n6c32; funder_name=European Commission;
1579540251.006307
5701183
md5:d03397007a36f3ab11fe6b136e12e29f
https://zenodo.org/records/32415/files/rsob_150042_all.pdf
public
http://www.research.ed.ac.uk/portal/en/datasets/data-code-and-models-for-flis-et-al-rs-open-biology-2015(fd297498-7d0d-4d57-9040-769af9c65212).html
Is part of
url
Royal Society Open Biology
2015-09-24