Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes

Dubos C, Kelemen Z, Sebastian A, Bülow L, Huep G, Xu W, Grain D, Salsac F, Brousse C, Lepiniec L, Weisshaar B, et al. (2014)
BMC genomics 15(1): 317.

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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. 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.
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Dubos C, Kelemen Z, Sebastian A, et al. Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes. BMC genomics. 2014;15(1): 317.
Dubos, C., Kelemen, Z., Sebastian, A., Bülow, L., Huep, G., Xu, W., Grain, D., et al. (2014). Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes. BMC genomics, 15(1): 317.
Dubos, C., Kelemen, Z., Sebastian, A., Bülow, L., Huep, G., Xu, W., Grain, D., Salsac, F., Brousse, C., Lepiniec, L., et al. (2014). Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes. BMC genomics 15:317.
Dubos, C., et al., 2014. Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes. BMC genomics, 15(1): 317.
C. Dubos, et al., “Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes”, BMC genomics, vol. 15, 2014, : 317.
Dubos, C., Kelemen, Z., Sebastian, A., Bülow, L., Huep, G., Xu, W., Grain, D., Salsac, F., Brousse, C., Lepiniec, L., Weisshaar, B., Contreras-Moreira, B., Hehl, R.: Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes. BMC genomics. 15, : 317 (2014).
Dubos, Christian, Kelemen, Zsolt, Sebastian, Alvaro, Bülow, Lorenz, Huep, Gunnar, Xu, Wenjia, Grain, Damaris, Salsac, Fabien, Brousse, Cecile, Lepiniec, Loïc, Weisshaar, Bernd, Contreras-Moreira, Bruno, and Hehl, Reinhard. “Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes”. BMC genomics 15.1 (2014): 317.
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