Arabidopsis2010: Determining Genome-wide Transcription Networks of TGA Factors

拟南芥完整的基因组序列编码了至少1533个转录调控因子，其中大多数预计与DNA结合。这些dna结合蛋白和同源启动子序列之间的相互作用是建立影响体内平衡、发育和适应的基因电池空间和时间表达模式的主要决定因素。然而，我们目前对靶基因和调控网络的了解，除了少数植物转录因子外，最多还停留在初级阶段。考虑到未来的挑战，到2010年，为这种高等植物相对大量的未表征转录因子分配基因调控功能的努力将受益于更多的全球和高通量方法。在这方面，2010年的项目奖将利用一个互补和综合的策略，包括高通量植物染色质免疫沉淀（pChIP）和基因表达分析，绘制拟南芥的转录调控网络。计划进行其他平行实验以评估研究结果的功能有效性。研究的重点是TGA家族的基本/亮氨酸拉链蛋白，这是一个复杂的转录系统，在发育和防御中具有重要的调节功能。这里需要回答的一个关键问题是主要靶基因及其相关网络的身份。该项目的数据将定期发布在TIGR （http://www.tigr.org/tdb/e2k1/ath1/）和CAB （http://www.umbi.umd.edu/~cab/）网站上建立的链接下。根据该合同开发的方法和工具将包括高通量pChIP技术和基因间序列的部分基因组阵列，这些将在该项目的3年时间线上线时公开提供。除了为了解拟南芥转录控制机制建立一个新的范例外，该项目还将促进美国国家科学基金会鼓励的教育和培训任务。2010年项目奖的目标是识别和分类发生在dna结合蛋白子集和它们在活植物中控制的基因之间的基因调控相互作用。这些基因的表达与植物对感染和毒素的防御反应有关。因此，这项工作不仅将为基因调控的机制基础提供重要的新信息，而且可能通过引导新的环境友好策略来遗传增强作物植物的天然保护基因，从而造福农业。

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 (http://www.tigr.org/tdb/e2k1/ath1/) and CAB (http://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.