Comparative genomic analysis of diurnal and circadian gene expression regulation

昼夜节律基因表达调控的比较基因组分析PI：托德·莫克勒，俄勒冈州立大学CoPI：Joanne Chory，索尔克生物研究所CoP：Steve Kay，斯克里普斯研究所基因表达相适应到白天或晚上的正确时间的能力对植物生长至关重要，提供更好的适合性，并最终允许植物存活。这个项目将探索特定的调控DNA元件如何赋予特定阶段的基因表达适合外部光/温度环境。目前正在进行实验，以描述拟南芥中的这些调控网络。计算和实验方法都将被用来识别水稻和杨树中等量的启动子元件和与它们结合的蛋白质。这项工作的主要目的是(1)在水稻和杨树上进行昼夜/昼夜微阵列时间过程实验；(2)鉴定循环基因启动子序列中已知和预测的Tf结合位点，并比较物种间的启动子序列；(3)对这些启动子元件预测的初步生物学验证。具体成果将包括：1)水稻和杨树昼夜循环基因数据库；2)用于预测共表达基因启动子中转录因子结合位点的改进的元件算法；3)水稻和杨树基因上游调控区已知和预测的转录因子结合位点数据库；4)用于跨物种启动子结构比较的网络界面；以及5)丰富的昼夜循环转录因子的酵母单杂交文库。将通过开放源码软件协议向科学界提供软件工具。该项目产生的生物资源将由莫克勒实验室在项目期间分配，并在项目结束时存放在适当的库存中心。该项目将为高中生、本科生和研究生提供培训机会，跨越植物生物学、基因组学、生物信息学、计算机科学和数学等不同领域。国际和平协会和COPIS将通过各自机构的外联机制积极招收任职人数偏低的学生。与该项目直接相关的主题将由公共投资纳入俄勒冈州立大学的基因组学和生物信息学课程。获取项目成果：项目数据将通过项目网站http://diurnal.cgrb.oregonstate.edu.传播微阵列数据还将存入公共数据库，包括NCBI GEO(http://www.ncbi.nlm.nih.gov/geo/)，PLEXdb(http://www.plexdb.org/)，和ArrayExpress(http://www.ebi.ac.uk/arrayexpress/).

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/).