Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure
Identifieur interne : 000124 ( Main/Exploration ); précédent : 000123; suivant : 000125Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure
Auteurs : Anna Flis [Allemagne] ; Aurora Pi As Fernández [Royaume-Uni] ; Tomasz Zielinski [Royaume-Uni] ; Virginie Mengin [Allemagne] ; Ronan Sulpice [Allemagne] ; Kevin Stratford [Royaume-Uni] ; Alastair Hume [Royaume-Uni] ; Alexandra Pokhilko [Royaume-Uni] ; Megan M. Southern [Royaume-Uni] ; Daniel D. Seaton [Royaume-Uni] ; Harriet G. Mcwatters [Royaume-Uni] ; Mark Stitt [Allemagne] ; Karen J. Halliday [Royaume-Uni] ; Andrew J. Millar [Royaume-Uni]Source :
- Open Biology [ 2046-2441 ] ; 2015.
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
Url:
DOI: 10.1098/rsob.150042
PubMed: 26468131
PubMed Central: 4632509
Affiliations:
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Waddington Building, Edinburgh EH9 3JD</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af4"><addr-line>Institute of Molecular Cell and Systems Biology</addr-line>,<institution>University of Glasgow</institution>,<addr-line>Bower Building, Glasgow G12 8QQ</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Southern, Megan M" sort="Southern, Megan M" uniqKey="Southern M" first="Megan M." last="Southern">Megan M. Southern</name><affiliation wicri:level="1"><nlm:aff id="af5"><addr-line>Department of Biological Sciences</addr-line>,<institution>University of Warwick</institution>,<addr-line>Coventry CV4 7AL</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Seaton, Daniel D" sort="Seaton, Daniel D" uniqKey="Seaton D" first="Daniel D." last="Seaton">Daniel D. Seaton</name><affiliation wicri:level="1"><nlm:aff id="af2"><addr-line>SynthSys and School of Biological Sciences</addr-line>,<institution>University of Edinburgh</institution>,<addr-line>C.H. 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Waddington Building, Edinburgh EH9 3JD</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Zielinski, Tomasz" sort="Zielinski, Tomasz" uniqKey="Zielinski T" first="Tomasz" last="Zielinski">Tomasz Zielinski</name><affiliation wicri:level="1"><nlm:aff id="af2"><addr-line>SynthSys and School of Biological Sciences</addr-line>,<institution>University of Edinburgh</institution>,<addr-line>C.H. Waddington Building, Edinburgh EH9 3JD</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Mengin, Virginie" sort="Mengin, Virginie" uniqKey="Mengin V" first="Virginie" last="Mengin">Virginie Mengin</name><affiliation wicri:level="1"><nlm:aff id="af1"><institution>Max Planck Institute of Molecular Plant Physiology</institution>,<addr-line>Am Muehlenberg 1, 14476 Potsdam-Golm</addr-line>,<country>Germany</country></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Sulpice, Ronan" sort="Sulpice, Ronan" uniqKey="Sulpice R" first="Ronan" last="Sulpice">Ronan Sulpice</name><affiliation wicri:level="1"><nlm:aff id="af1"><institution>Max Planck Institute of Molecular Plant Physiology</institution>,<addr-line>Am Muehlenberg 1, 14476 Potsdam-Golm</addr-line>,<country>Germany</country></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Stratford, Kevin" sort="Stratford, Kevin" uniqKey="Stratford K" first="Kevin" last="Stratford">Kevin Stratford</name><affiliation wicri:level="1"><nlm:aff id="af3"><addr-line>EPCC</addr-line>,<institution>University of Edinburgh</institution>,<addr-line>James Clerk Maxwell Building, Edinburgh EH9 3JZ</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Hume, Alastair" sort="Hume, Alastair" uniqKey="Hume A" first="Alastair" last="Hume">Alastair Hume</name><affiliation wicri:level="1"><nlm:aff id="af2"><addr-line>SynthSys and School of Biological Sciences</addr-line>,<institution>University of Edinburgh</institution>,<addr-line>C.H. Waddington Building, Edinburgh EH9 3JD</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af3"><addr-line>EPCC</addr-line>,<institution>University of Edinburgh</institution>,<addr-line>James Clerk Maxwell Building, Edinburgh EH9 3JZ</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Pokhilko, Alexandra" sort="Pokhilko, Alexandra" uniqKey="Pokhilko A" first="Alexandra" last="Pokhilko">Alexandra Pokhilko</name><affiliation wicri:level="1"><nlm:aff id="af2"><addr-line>SynthSys and School of Biological Sciences</addr-line>,<institution>University of Edinburgh</institution>,<addr-line>C.H. Waddington Building, Edinburgh EH9 3JD</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af4"><addr-line>Institute of Molecular Cell and Systems Biology</addr-line>,<institution>University of Glasgow</institution>,<addr-line>Bower Building, Glasgow G12 8QQ</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Southern, Megan M" sort="Southern, Megan M" uniqKey="Southern M" first="Megan M." last="Southern">Megan M. Southern</name><affiliation wicri:level="1"><nlm:aff id="af5"><addr-line>Department of Biological Sciences</addr-line>,<institution>University of Warwick</institution>,<addr-line>Coventry CV4 7AL</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Seaton, Daniel D" sort="Seaton, Daniel D" uniqKey="Seaton D" first="Daniel D." last="Seaton">Daniel D. Seaton</name><affiliation wicri:level="1"><nlm:aff id="af2"><addr-line>SynthSys and School of Biological Sciences</addr-line>,<institution>University of Edinburgh</institution>,<addr-line>C.H. Waddington Building, Edinburgh EH9 3JD</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Mcwatters, Harriet G" sort="Mcwatters, Harriet G" uniqKey="Mcwatters H" first="Harriet G." last="Mcwatters">Harriet G. Mcwatters</name><affiliation wicri:level="1"><nlm:aff id="af2"><addr-line>SynthSys and School of Biological Sciences</addr-line>,<institution>University of Edinburgh</institution>,<addr-line>C.H. Waddington Building, Edinburgh EH9 3JD</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Stitt, Mark" sort="Stitt, Mark" uniqKey="Stitt M" first="Mark" last="Stitt">Mark Stitt</name><affiliation wicri:level="1"><nlm:aff id="af1"><institution>Max Planck Institute of Molecular Plant Physiology</institution>,<addr-line>Am Muehlenberg 1, 14476 Potsdam-Golm</addr-line>,<country>Germany</country></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Halliday, Karen J" sort="Halliday, Karen J" uniqKey="Halliday K" first="Karen J." last="Halliday">Karen J. Halliday</name><affiliation wicri:level="1"><nlm:aff id="af2"><addr-line>SynthSys and School of Biological Sciences</addr-line>,<institution>University of Edinburgh</institution>,<addr-line>C.H. Waddington Building, Edinburgh EH9 3JD</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Millar, Andrew J" sort="Millar, Andrew J" uniqKey="Millar A" first="Andrew J." last="Millar">Andrew J. Millar</name><affiliation wicri:level="1"><nlm:aff id="af2"><addr-line>SynthSys and School of Biological Sciences</addr-line>,<institution>University of Edinburgh</institution>,<addr-line>C.H. Waddington Building, Edinburgh EH9 3JD</addr-line>,<country>UK</country></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Open Biology</title><idno type="eISSN">2046-2441</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><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 <italic>Arabidopsis thaliana</italic> 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 <italic>PRR9</italic> and <italic>ELF4</italic>, and regulation of <italic>PRR5</italic> by <italic>GI</italic>. Absolute RNA quantification revealed low levels of <italic>PRR9</italic> transcripts (peak approx. 50 copies cell<sup>−1</sup>) compared with other clock genes, and threefold higher levels of <italic>LHY</italic> RNA (more than 1500 copies cell<sup>−1</sup>) than of its close relative <italic>CCA1</italic>. 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.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Zhang, Ee" uniqKey="Zhang E">EE Zhang</name></author><author><name sortKey="Kay, Sa" uniqKey="Kay S">SA Kay</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dong, G" uniqKey="Dong G">G Dong</name></author><author><name sortKey="Golden, Ss" uniqKey="Golden S">SS Golden</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dodd, An" uniqKey="Dodd A">AN Dodd</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ouyang, Y" uniqKey="Ouyang Y">Y Ouyang</name></author><author><name sortKey="Andersson, Cr" uniqKey="Andersson C">CR 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Stitt</name><name sortKey="Sulpice, Ronan" sort="Sulpice, Ronan" uniqKey="Sulpice R" first="Ronan" last="Sulpice">Ronan Sulpice</name></country><country name="Royaume-Uni"><noRegion><name sortKey="Fernandez, Aurora Pi As" sort="Fernandez, Aurora Pi As" uniqKey="Fernandez A" first="Aurora Pi As" last="Fernández">Aurora Pi As Fernández</name></noRegion><name sortKey="Halliday, Karen J" sort="Halliday, Karen J" uniqKey="Halliday K" first="Karen J." last="Halliday">Karen J. Halliday</name><name sortKey="Hume, Alastair" sort="Hume, Alastair" uniqKey="Hume A" first="Alastair" last="Hume">Alastair Hume</name><name sortKey="Hume, Alastair" sort="Hume, Alastair" uniqKey="Hume A" first="Alastair" last="Hume">Alastair Hume</name><name sortKey="Mcwatters, Harriet G" sort="Mcwatters, Harriet G" uniqKey="Mcwatters H" first="Harriet G." last="Mcwatters">Harriet G. Mcwatters</name><name sortKey="Millar, Andrew J" sort="Millar, Andrew J" uniqKey="Millar A" first="Andrew J." last="Millar">Andrew J. Millar</name><name sortKey="Pokhilko, Alexandra" sort="Pokhilko, Alexandra" uniqKey="Pokhilko A" first="Alexandra" last="Pokhilko">Alexandra Pokhilko</name><name sortKey="Pokhilko, Alexandra" sort="Pokhilko, Alexandra" uniqKey="Pokhilko A" first="Alexandra" last="Pokhilko">Alexandra Pokhilko</name><name sortKey="Seaton, Daniel D" sort="Seaton, Daniel D" uniqKey="Seaton D" first="Daniel D." last="Seaton">Daniel D. Seaton</name><name sortKey="Southern, Megan M" sort="Southern, Megan M" uniqKey="Southern M" first="Megan M." last="Southern">Megan M. Southern</name><name sortKey="Stratford, Kevin" sort="Stratford, Kevin" uniqKey="Stratford K" first="Kevin" last="Stratford">Kevin Stratford</name><name sortKey="Zielinski, Tomasz" sort="Zielinski, Tomasz" uniqKey="Zielinski T" first="Tomasz" last="Zielinski">Tomasz Zielinski</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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