Comparative genomic analysis of diurnal and circadian gene expression regulation

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Comparative genomic analysis of diurnal and circadian gene expression regulationPI: Todd Mockler, Oregon State UniversityCoPI: Joanne Chory, The Salk Institute for Biological StudiesCoP: Steve Kay,The Scripps Research InstituteThe ability to phase gene expression to the correct time of day or night is critical to plant growth, confers improved fitness and ultimately allows a plant to survive. This project will explore how specific regulatory DNA elements confer phase-specific gene expression appropriate to the external light/temperature environment. Experiments are underway to describe these regulatory networks in Arabidopsis. Both computational and experimental approaches will be used to identify equivalent promoter elements and the proteins that bind to them in rice and poplar. The major aims of this work are (1) conducting diurnal/circadian microarray timecourse experiments in rice and poplar; (2) identification of known and predicted TF binding sites in the promoter sequences of cycling genes and comparisons of promoter sequences between species; and (3) initial biological validations of these promoter element predictions. Specific outcomes will include: 1) Databases of diurnal and circadian cycling genes in rice and poplar; 2) An improved ELEMENT algorithm for prediction of transcription factor binding sites in the promoters of co-expressed genes; 3) Databases of known and predicted transcription factor binding sites in the upstream regulatory regions of rice and poplar genes; 4) A web-interface for cross-species promoter architecture comparisons; and 5) A yeast one-hybrid library enriched for diurnal/circadian cycling transcription factors. Software tools will be made available to the scientific community through open-source software agreements. Biological resources generated in this project will be distributed by the Mockler lab during the project period and deposited at appropriate stock centers at the end of the project period. The project will provide training opportunities for high-school, undergraduate, and graduate students bridging diverse fields including plant biology, genomics, bioinformatics, computer science, and mathematics. The PI and coPIs will actively recruit underrepresented students through outreach mechanisms at their respective institutions. Topics directly relating to this project will be integrated by the PI into genomics and bioinformatics curricula at Oregon State University.Access to project outcomes: Project data will be disseminated via a project website http://diurnal.cgrb.oregonstate.edu. Microarray data will also be deposited into public databases including NCBI GEO (http://www.ncbi.nlm.nih.gov/geo/), PLEXdb (http://www.plexdb.org/), and ArrayExpress (http://www.ebi.ac.uk/arrayexpress/).