000061488 001__ 61488
000061488 005__ 20170612112602.0
000061488 0247_ $$2doi$$a10.1186/1471-2164-15-317
000061488 0248_ $$2sideral$$a98823
000061488 037__ $$aART-2014-98823
000061488 041__ $$aeng
000061488 100__ $$aDubos, C.
000061488 245__ $$aIntegrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes
000061488 260__ $$c2014
000061488 5060_ $$aAccess copy available to the general public$$fUnrestricted
000061488 5203_ $$aBackground: 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.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.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.
000061488 540__ $$9info:eu-repo/semantics/openAccess$$aby$$uhttp://creativecommons.org/licenses/by/3.0/es/
000061488 590__ $$a3.986$$b2014
000061488 591__ $$aGENETICS & HEREDITY$$b39 / 166 = 0.235$$c2014$$dQ1$$eT1
000061488 591__ $$aBIOTECHNOLOGY & APPLIED MICROBIOLOGY$$b26 / 163 = 0.16$$c2014$$dQ1$$eT1
000061488 655_4 $$ainfo:eu-repo/semantics/article$$vinfo:eu-repo/semantics/publishedVersion
000061488 700__ $$aKelemen, Z.
000061488 700__ $$aSebastian, A.
000061488 700__ $$aBülow, L.
000061488 700__ $$aHuep, G.
000061488 700__ $$aXu, W.
000061488 700__ $$aGrain, D.
000061488 700__ $$aSalsac, F.
000061488 700__ $$aBrousse, C.
000061488 700__ $$aLepiniec, L.
000061488 700__ $$aWeisshaar, B.
000061488 700__ $$0(orcid)0000-0002-5462-907X$$aContreras-Moreira, B.
000061488 700__ $$aHehl, R.
000061488 773__ $$g15, 1 (2014), 317 [17 pp]$$pBMC genomics$$tBMC Genomics$$x1471-2164
000061488 8564_ $$s784060$$uhttps://zaguan.unizar.es/record/61488/files/texto_completo.pdf$$yVersión publicada
000061488 8564_ $$s100786$$uhttps://zaguan.unizar.es/record/61488/files/texto_completo.jpg?subformat=icon$$xicon$$yVersión publicada
000061488 909CO $$ooai:zaguan.unizar.es:61488$$particulos$$pdriver
000061488 951__ $$a2017-06-12-09:40:00
000061488 980__ $$aARTICLE