Arabidopsis 2010: Establishing Regulatory Networks in Arabidopsis: Integrating AGRIS with the Identification of Direct Targets for Transcription Factors

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Hierarchical arrangements (networks) of transcription factors (TFs) provide the information necessary to deploy genes with particular spatial and temporal patterns. The information for this is hardwired in the promoter regions formed by cis-regulatory elements that bind specific TFs. Direct target genes for a group of 31 selected TFs involved in regulatory networks associated with flower development and epidermal functions will be identified using chromatin immunoprecipitation followed by analysis of microarrays of promoter sequences (ChIP-CHIP). Identified direct target genes will be validated by in vitro DNA-binding experiments, and the TF binding sites will be determined using in vitro footprinting. The information obtained will be integrated into the established AGRIS databases, resulting in public resources that integrate TFs, their binding sites and the corresponding regulatory motifs. Results derived from this project will be made available at http://arabidopsis.med.ohio-state.edu/NSF2010Project. Materials developed in this research will be made readily available through the ABRC. The combination of experimental data and powerful computational tools will provide the first steps towards establishing the regulatory networks responsible for the expression of all Arabidopsis genes, one of the central objectives of the 2010 project.Broader Impact - Establishing the regulatory networks that control the expression of all plant genes provides a natural follow-up to the elucidation of the Arabidopsis genome and will significantly impact the research in Arabidopsis and other plants. This project integrates experimental biology, bioinformatics, statistics and mathematics, offering unique opportunities for interdisciplinary research training. The development of several databases available through the Web will continue to ensure that findings derived from this work will have the broadest possible dissemination. Tools and resources obtained from these studies will be applied for educational purposes in courses at California State University, San Marcos and Ohio State University.