title: Identifying Gene Regulatory Networks in Arabidopsis by In Silico Prediction, Yeast-1-Hybrid, and Inducible Gene Profiling Assays.
abstract: 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.
authors.affiliation: Department of Biology, Duke University, Durham, NC, USA.
authors.forename: Erin E
authors.initials: EE
authors.lastname: Sparks
authors.affiliation: Department of Biology, Duke University, Durham, NC, USA. philip.benfey@duke.edu.|Howard Hughes Medical Institute, Duke University, 124 Science Drive, Box 90338, Durham, NC, 27708, USA. philip.benfey@duke.edu.
authors.forename: Philip N
authors.initials: PN
authors.lastname: Benfey
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D003198:Computer Simulation; D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D020798:Two-Hybrid System Techniques
chemical_list: D029681:Arabidopsis Proteins; D018744:DNA, Plant; D014157:Transcription Factors
keywords: Gene regulatory networks; In silico prediction; Inducible gene expression; Transcription factor–DNA binding; Yeast-1-hybrid