Please use this identifier to cite or link to this item: http://hdl.handle.net/10261/96106
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dc.contributor.authorDubos, Christian-
dc.contributor.authorKelemen, Zsolt-
dc.contributor.authorSebastián Yagüe, Álvaro-
dc.contributor.authorBülow, Lorenz-
dc.contributor.authorHuep, Gunnar-
dc.contributor.authorXu, Wenjia-
dc.contributor.authorGrain, Damaris-
dc.contributor.authorSalsac, Fabien-
dc.contributor.authorBrousse, Cecile-
dc.contributor.authorLepiniec, Löic-
dc.contributor.authorWeisshaar, Bernd-
dc.contributor.authorContreras-Moreira, Bruno-
dc.contributor.authorHehl, Reinhard-
dc.date.issued2014-04-28-
dc.identifier.citationBMC Genomics 15(1): 317 (2014)-
dc.identifier.issn1471-2164-
dc.identifier.urihttp://hdl.handle.net/10261/96106-
dc.descriptionThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.-
dc.description.abstract[Background] Using motif detection programs it is fairly straightforward to identify conserved cis-sequences in promoters of co-regulated genes. In contrast, the identification of the transcription factors (TFs) interacting with these cis-sequences is much more elaborate. To facilitate this, we explore the possibility of using several bioinformatic and experimental approaches for TF identification. This starts with the selection of co-regulated gene sets and leads first to the prediction and then to the experimental validation of TFs interacting with cis-sequences conserved in the promoters of these co-regulated genes.-
dc.description.abstract[Results] Using the PathoPlant database, 32 up-regulated gene groups were identified with microarray data for drought-responsive gene expression from Arabidopsis thaliana. Application of the binding site estimation suite of tools (BEST) discovered 179 conserved sequence motifs within the corresponding promoters. Using the STAMP web-server, 49 sequence motifs were classified into 7 motif families for which similarities with known cis-regulatory sequences were identified. All motifs were subjected to a footprintDB analysis to predict interacting DNA binding domains from plant TF families. Predictions were confirmed by using a yeast-one-hybrid approach to select interacting TFs belonging to the predicted TF families. TF-DNA interactions were further experimentally validated in yeast and with a Physcomitrella patens transient expression system, leading to the discovery of several novel TF-DNA interactions.-
dc.description.abstract[Conclusions] The present work demonstrates the successful integration of several bioinformatic resources with experimental approaches to predict and validate TFs interacting with conserved sequence motifs in co-regulated genes.-
dc.description.sponsorshipThe work of Z.K., G.H., A.S., F.S., C.B., and L.B. was supported by the STREG project. W.X.’s work was supported by the China Scholarship Council (CSC). The authors would like to acknowledge the support of Jasmin Huebner and Nina Schmidt in the generation and analysis of transgenic A. thaliana.-
dc.publisherBioMed Central-
dc.relation.isversionofPublisher’s version-
dc.rightsopenAccess-
dc.subjectDatabases-
dc.subjectArabidopsis thaliana-
dc.subjectPhyscomitrella patens-
dc.subjectYeast one-hybrid-
dc.subjectMicroarray-
dc.subjectTranscription factor-
dc.subjectcis-element-
dc.titleIntegrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes-
dc.typeartículo-
dc.identifier.doi10.1186/1471-2164-15-317-
dc.relation.publisherversionhttp://dx.doi.org/10.1186/1471-2164-15-317-
dc.date.updated2014-04-30T23:11:17Z-
dc.description.versionPeer Reviewed-
dc.language.rfc3066en-
dc.rights.holderChristian Dubos et al.; licensee BioMed Central Ltd.-
dc.rights.licensehttp://creativecommons.org/licenses/by/2.0-
dc.contributor.funderChina Scholarship Council-
dc.relation.csic-
dc.identifier.funderhttp://dx.doi.org/10.13039/501100004543es_ES
item.fulltextWith Fulltext-
item.openairetypeartículo-
item.cerifentitytypePublications-
item.openairecristypehttp://purl.org/coar/resource_type/c_18cf-
item.grantfulltextopen-
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