Identifying Gene Regulatory Networks in Arabidopsis by In Silico Prediction, Yeast-1-Hybrid, and Inducible Gene Profiling Assays
A system-wide understanding of gene regulation will provide deep insights into plant development and physiology. In this chapter we describe a threefold approach to identify the gene regulatory networks in Arabidopsis thaliana that function in a specific tissue or biological process. Since no single method is sufficient to establish comprehensive and high-confidence gene regulatory networks, we focus on the integration of three approaches. First, we describe an in silico prediction method of transcription factor–DNA binding, then an in vivo assay of transcription factor–DNA binding by yeast-1-hybrid and lastly the identification of co-expression clusters by transcription factor induction in planta. Each of these methods provides a unique tool to advance our understanding of gene regulation, and together provide a robust model for the generation of gene regulatory networks.
Key wordsGene regulatory networks Transcription factor–DNA binding In silico prediction Yeast-1-hybrid Inducible gene expression
We gratefully acknowledge members of the Benfey lab for their comments on this chapter and Siobhan Brady for instruction on yeast-1-hybrid assays. Research in the Benfey lab is supported by funding from the National Institutes of Health, the National Science Foundation, and the Gordon and Betty Moore Foundation.
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