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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Abstract / Bemerkung
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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BMC genomics
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15
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1
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317
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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. doi:10.1186/1471-2164-15-317
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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