Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions

46 pages, 4 tables, 6 figures, 3 additinoal files.

Bibliographic Details
Authors: Carrera, Javier, Rodrigo, Guillermo, Jaramillo, Alfonso, Elena, Santiago F.
Format: article
Status:Published version
Publication Date:2009
Country:España
Institution:Consejo Superior de Investigaciones Científicas (CSIC)
Repository:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/17468
Online Access:http://hdl.handle.net/10261/17468
Access Level:Open access
Keyword:Arabidopsis thaliana
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spelling Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditionsCarrera, JavierRodrigo, GuillermoJaramillo, AlfonsoElena, Santiago F.Arabidopsis thaliana46 pages, 4 tables, 6 figures, 3 additinoal files.[Background] Understanding the molecular mechanisms plants have evolved to adapt their biological activities to a constantly changing environment is an intriguing question and one that requires a systems biology approach. Here we present a network analysis of genome-wide expression data combined with reverse-engineering network modelling to dissect the transcriptional control of A. thaliana. The regulatory network is inferred by using an assembly of microarray data containing steady-state RNA expression levels from several growth conditions, developmental stages, biotic and abiotic stresses, and a variety of mutant genotypes.[Results] We show that A. thaliana regulatory network has the characteristic properties of hierarchical networks. We successfully applied our quantitative network model to predict the full transcriptome of the plant for a set of microarray experiments not included in the training dataset. We also used our model to analyze the robustness in expression levels conferred by network motifs such as the coherent feedforward loop. In addition, the meta-analysis presented here has allowed us to identify regulatory and robust genetic structures.[Conclusions] These data suggest that A. thaliana has evolved a high connectivity in terms of transcriptional regulations among cellular functions involved in response and adaptation to changing environments; while gene networks constitutively expressed or less related to stress response are characterized by a lower connectivity. Taken together, these findings suggest conserved regulatory strategies that have been selected during the evolutionary history of this Eukaryote.This work was supported by grants BFU2006-14819-C02-01/BMC and TIN2006-12860 from the Spanish Ministerio de Ciencia e Innovación to S.F.E and A.J., respectively; FP6-NESTs 043340 (BioModularH2) and 043338 (Emergence), FP7-KBBE-212894 (Tarpol), the Structural Funds of the European Regional Development Fund (ERDF), the 91-A3405-ATIGE Genopole/UEVE and the MIT-France grants to A.J. J.C, G.R. and A.J. acknowledge the HPC-Europa program (RII3-CT-2003-506079). G.R. was supported by a graduate fellowship from the Generalitat Valenciana and an EMBO Short-term fellowship (ref. ASTF-343.00-2007). S.F.E. also acknowledges support from the Santa Fe Institute.Peer reviewedBioMed Central200920092009info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersion4231406 bytesapplication/pdfhttp://hdl.handle.net/10261/17468reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttp://dx.doi.org/10.1186/gb-2009-10-9-r96info:eu-repo/semantics/openAccessoai:digital.csic.es:10261/174682026-05-22T06:33:51Z
dc.title.none.fl_str_mv Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions
title Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions
spellingShingle Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions
Carrera, Javier
Arabidopsis thaliana
title_short Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions
title_full Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions
title_fullStr Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions
title_full_unstemmed Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions
title_sort Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions
dc.creator.none.fl_str_mv Carrera, Javier
Rodrigo, Guillermo
Jaramillo, Alfonso
Elena, Santiago F.
author Carrera, Javier
author_facet Carrera, Javier
Rodrigo, Guillermo
Jaramillo, Alfonso
Elena, Santiago F.
author_role author
author2 Rodrigo, Guillermo
Jaramillo, Alfonso
Elena, Santiago F.
author2_role author
author
author
dc.subject.none.fl_str_mv Arabidopsis thaliana
topic Arabidopsis thaliana
description 46 pages, 4 tables, 6 figures, 3 additinoal files.
publishDate 2009
dc.date.none.fl_str_mv 2009
2009
2009
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/17468
url http://hdl.handle.net/10261/17468
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://dx.doi.org/10.1186/gb-2009-10-9-r96
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 4231406 bytes
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
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