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dc.contributor.author
Michael, Todd P.
dc.contributor.author
Mockler, Todd C.
dc.contributor.author
Breton, Ghislain
dc.contributor.author
McEntee, Connor
dc.contributor.author
Byer, Amanda
dc.contributor.author
Trout, Jonathan D.
dc.contributor.author
Hazen, Samuel P.
dc.contributor.author
Shen, Rongkun
dc.contributor.author
Priest, Henry D.
dc.contributor.author
Sullivan, Christopher M.
dc.contributor.author
Givan, Scott A.
dc.contributor.author
Yanovsky, Marcelo Javier
dc.contributor.author
Hong, Fangxin
dc.contributor.author
Kay, Steve A.
dc.contributor.author
Chory, Joanne
dc.date.available
2017-08-18T19:39:48Z
dc.date.issued
2008-02
dc.identifier.citation
Michael, Todd P.; Mockler, Todd C.; Breton, Ghislain; McEntee, Connor; Byer, Amanda; et al.; Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules; Public Library of Science; Plos Genetics; 4; 2; 2-2008; 1-17
dc.identifier.issn
1553-7390
dc.identifier.uri
http://hdl.handle.net/11336/22700
dc.description.abstract
Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase-specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module, by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover, we show that the three transcription modules are conserved across Arabidopsis, poplar, and rice. These results confirm the complex interplay between thermocycles, photocycles, and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
Public Library of Science
dc.rights
info:eu-repo/semantics/openAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject.classification
Bioquímica y Biología Molecular
dc.subject.classification
Ciencias Biológicas
dc.subject.classification
CIENCIAS NATURALES Y EXACTAS
dc.title
Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2017-07-18T14:50:35Z
dc.identifier.eissn
1553-7404
dc.journal.volume
4
dc.journal.number
2
dc.journal.pagination
1-17
dc.journal.pais
Estados Unidos
dc.journal.ciudad
San Francisco
dc.description.fil
Fil: Michael, Todd P.. Salk Institute for Biological Studies; Estados Unidos
dc.description.fil
Fil: Mockler, Todd C.. Salk Institute for Biological Studies; Estados Unidos
dc.description.fil
Fil: Breton, Ghislain. University of California at San Diego; Estados Unidos
dc.description.fil
Fil: McEntee, Connor. Salk Institute for Biological Studies; Estados Unidos
dc.description.fil
Fil: Byer, Amanda. Salk Institute for Biological Studies; Estados Unidos
dc.description.fil
Fil: Trout, Jonathan D.. Salk Institute for Biological Studies; Estados Unidos
dc.description.fil
Fil: Hazen, Samuel P.. University of California at San Diego; Estados Unidos
dc.description.fil
Fil: Shen, Rongkun. State University of Oregon; Estados Unidos
dc.description.fil
Fil: Priest, Henry D.. State University of Oregon; Estados Unidos
dc.description.fil
Fil: Sullivan, Christopher M.. State University of Oregon; Estados Unidos
dc.description.fil
Fil: Givan, Scott A.. State University of Oregon; Estados Unidos
dc.description.fil
Fil: Yanovsky, Marcelo Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. University of California at San Diego; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; Argentina
dc.description.fil
Fil: Hong, Fangxin. Salk Institute for Biological Studies; Estados Unidos
dc.description.fil
Fil: Kay, Steve A.. University of California at San Diego; Estados Unidos
dc.description.fil
Fil: Chory, Joanne. Salk Institute for Biological Studies; Estados Unidos
dc.journal.title
Plos Genetics
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0040014
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.plos.org/10.1371/journal.pgen.0040014
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