Arabidopsis 2010: Expression Profiling of Plant Disease Resistance Pathways

该项目的目标是确定拟南芥防御反应信号网络中关键转录因子（TFs）的功能（见http://ausubellab）。Mgh.harvard.edu/nsf2010/查看目前正在研究的转录因子列表)。TFs是控制植物对病原体防御反应的关键开关，使用基因芯片（微阵列）进行表达谱分析是可用于高通量转录事件分析的最强大的基因组学方法。分析将在尚未充分研究的防御途径中确定候选tf，包括那些通常与植物和动物病原体相关的所谓“PAMP”分子诱导的tf。我们将评估TF突变体对疾病抗性的影响，以发现破坏基因及其功能是否会影响任何防御反应。用这种方法鉴定的TF将与绿色荧光蛋白连接，对表达TF基因的细胞进行标记和分选。转录谱分析将在这些细胞中进行，以识别表达模式与tf（即队列转录组）相对应的基因。tf也将被修改，这样它们进入细胞核的运输就可以通过实验控制，它们的靶基因也将被识别出来。总的来说，这些实验将提供目前缺乏的与防御相关的转录事件的空间、时间和层次信息，但需要建立相互作用的防御途径的转录网络模型。本项目获得的数据将存入IMDS（集成微阵列数据系统）（http://ausubellab.mgh.harvard.edu/imds），并及时向公众提供。IMDS是由该项目创建的一个公共网络微阵列数据库，用于促进微阵列数据集的存储、检索和分析。它存储实验描述、原始微阵列数据和规范化数据集。IMDS中的数据将通过输出到NCBI基因表达综合数据库和拟南芥信息资源而保存到2010年奖项的生命周期之后。这一多方研究者的努力对2010年总体项目目标的意义是多方面的。植物的防御反应涉及基因表达的全局变化（基因组的10%）。因此，识别tf是理解防御机制的关键。此外，对大型基因集的深入分析需要几个实验室的努力，该项目提供的协调避免了重复工作并降低了成本。最后，每一个添加到IMDS的新的分析实验都将增强科学界研究人员设计实验的能力，这些实验将进一步阐明植物防御反应的关键特征。本项目为本科生、博士生和博士后提供培养环境。参与者不仅将学习经典的遗传和植物病理学方法，还将学习尖端的基因组学和生物信息学技术。一个关键的培训组成部分是该项目的年度研讨会，学生和博士后在半正式的环境中展示他们的研究。基因组学和生物信息学的本科培训也是这个项目的一个重要方面。

The goal of this project is to determine the function of key transcription factors (TFs) in the plant Arabidopsis defense-response signaling network (see http://ausubellab. mgh.harvard.edu/nsf2010/ for the current list of transcription factors under study). TFs are key switches that control plant defense responses against pathogens, and expression profiling using Gene Chips (microarrays) is the most powerful genomics approach available for high through-put analysis of transcriptional events. Profiling will identify candidate TFs in understudied defense pathways, including those induced by so-called "PAMP" molecules that are commonly associated with pathogens of plants as well as animals. We will evaluate the TF mutants for their impact on disease resistance to find whether disrupting the genes and their functions will affect any defense response. The TFs identified in this way will be linked to green fluorescent protein to mark and sort the cells expressing the TF genes . Transcriptional profiling will be conducted in these cells to identify genes whose expression patterns mirror those of the TFs (i.e., cohort transcriptomes). The TFs will also be modified so their transport into the nucleus, where they function, can be controlled experimentally and their target genes will be identified. Collectively, these experiments will provide the spatial, temporal, and hierarchical information about defense-related transcriptional events which is currently lacking, but needed to build a model of the transcriptional network of interacting defense pathways. Data obtained in this project will be deposited in IMDS (integrated microarray data system) (http://ausubellab.mgh.harvard.edu/imds) and made available to the public in a timely manner. IMDS is a public web-accessible microarray database created by this project to facilitate storage, retrieval and analysis of microarray data sets. It stores experimental descriptions, raw microarray data and sets of normalized data. The data in IMDS will be maintained beyond the lifetime of the 2010 award by exporting it to the NCBI Gene Expression Omnibus and the Arabidopsis Information Resource. The significance of this multi-investigator effort to the overall 2010 project objectives is several-fold. Defense responses in plants involve global changes in gene expression (10% of the genome). Therefore, identifying TFs holds the key for understanding the mechanism of defense. Also, an in-depth analysis of large gene sets requires the efforts of several laboratories and coordination afforded by this project avoids duplication of efforts and cuts costs. Finally, each new profiling experiment added to IMDS will enhance the ability of researchers in the scientific community to design experiments that will further elucidate key features of the plant defense response. This project provides a training environment for undergraduates, doctoral students, and postdocs. Participants will learn not only classical genetic and phytopathology methods, but also cutting-edge genomics and bioinformatics technologies. A key training component is the project's annual workshop, where students and postdocs present their research in a semi-formal setting. Undergraduate training in genomics and bioinformatics is also a significant aspect of this project.