The completed genome sequence of Arabidopsis thaliana codes for at least 1,533 transcriptional regulators, of which the majority are predicted to bind DNA. Interactions between these DNA-binding proteins and cognate promoter sequences are primary determinants in establishing spatial and temporal expression patterns of batteries of genes that effect homeostasis, development and adaptation. However, our present knowledge of target genes and regulatory networks for all but a few plant transcription factors remains rudimentary at best. Considering the challenge ahead, efforts to assign gene-regulatory functions to the relatively large number of uncharacterized transcription factors of this higher plant by 2010 will strongly benefit from more global and high-throughput approaches. In this regard, this 2010 Project award will make use of a complementary and integrated strategy, involving high-throughput plant chromatin immunoprecipitation (pChIP) and gene expression analysis, for mapping transcriptional regulatory networks of Arabidopsis. Additional parallel experiments are planned to assess the functional validity of findings. The focus of study is the TGA family of basic/leucine-zipper proteins, which comprise a complex transcriptional system with important regulatory functions in development and defense. A key question to be answered here is the identity of primary target genes and their associated networks. Data from this project will be posted periodically under links to be established on TIGR (www.tigr.org/tdb/e2k1/ath1/) and CAB (www.umbi.umd.edu/~cab/) websites. Methodologies and tools to be developed under this award will include a high-throughput pChIP technology and partial genome array of intergenic sequences, which will be made publicly available as they come on line during the 3 year time-line of this project. In addition to developing a new paradigm for understanding transcriptional control mechanisms in Arabidopsis, this project will promote education and training missions that are encouraged by NSF. The goal of this 2010 project award is to identify and categorize gene-regulatory interactions that occur between a subset of DNA-binding proteins and the genes that they govern in the living plant. Expression of these genes is implicated in defense responses by plants to infection and toxins. Thus, this work will not only provide important new information on the mechanistic basis of how genes are regulated, but also may benefit agriculture by leading to new environmentally-friendly strategies for genetically enhancing natural protective genes of crop plants.
