Arabidopsis 2010: Genomics Approaches to Finding Transcriptional Networks

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Transcription factor networks are the genetic blueprint by which plants and other organisms orchestrate the proper activation and timing of gene expression. A first step in deciphering transcriptional networks is to determine the expression pattern of all genes at cell-type resolution. To accomplish this goal, this research project will develop a new genomics approach, which involves sorting cells from transgenic lines in which a fluorescent protein is used as a cell-specific marker. The sorted cell populations will then be used as a source of RNA that is hybridized to microarrays. The project focuses on genes expressed in the Arabidopsis root, which is a tractable model because of its simple and highly organized structure. The gene networks in question will be primarily those that involve DNA-binding transcription factors. The regulatory regions of these genes will be fused to fluorescent proteins to determine the ability of these sequences to confer tissue-specific expression. In addition, translational fusions of the same DNA binding factors will be made, enabling an analysis of post-transcriptional events that affect protein localization. Bioinformatics tools will be developed that refine expression patterns based on multiple sources of data. These analysis tools will be made available through links at the Benfey lab website (http://www.biology.duke.edu/benfeylab/at2010.html) at Duke University. The list of all transcription factors with their root cell-type specific expression profiles will be made available in regular updates of this site. Thus, the research will determine the specific expression domains of a vast number of genes, which is an important first step in determining gene function. The research will also provide the input for emerging analysis tools that can decipher the controls of gene regulation based on detailed expression patterns. This will help establish the function of transcription factors in terms of how they affect the transcription of other genes. To harness the power of gene function discoveries, it is critical to find ways to gain greater control over the expression of genes. Targeted modification of gene expression is likely to be one of the most important ways to improve plant performance. This research will identify a large number of genes with highly specific expression patterns whose specific regulatory "code" will be of significant use in many areas of plant research and improvement. The detailed information on where and when many genes are expressed and the proteins that control their expression will help advance the understanding of how all plants control their growth and development. Another important part of the project will be to train the next generation of scientists to integrate computational approaches into plant biology. Graduate and undergraduate students will participate actively in the research. Duke and NYU have very diverse student populations with excellent representation of minority and women students. The PIs also will participate actively in outreach efforts such as programs for local high school teachers.