Dataset Information

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

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.

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.

SUBMITTER: Dubos C

PROVIDER: S-EPMC4234446 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature

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Publications

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

Dubos Christian C Kelemen Zsolt Z Sebastian Alvaro A Bülow Lorenz L Huep Gunnar G Xu Wenjia W Grain Damaris D Salsac Fabien F Brousse Cecile C Lepiniec Loïc L Weisshaar Bernd B Contreras-Moreira Bruno B Hehl Reinhard R

BMC genomics 20140428

<h4>Background</h4>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 a ...[more]

PMID: 24773781

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Dataset Information

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

Background

Results

Conclusions

Publications

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

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