Arabidopsis2010: Determining Genome-wide Transcription Networks of TGA Factors

拟南芥的完整基因组序列至少编码1,533个转录调控因子，其中大多数被预测与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动态平衡、发育和适应的一系列基因的时空表达模式的主要决定因素。然而，我们目前对目标基因和调控网络的了解，除了少数几个植物转录因子外，充其量仍然是初级的。考虑到未来的挑战，到2010年将基因调控功能分配给这种高等植物的相对大量的未鉴定转录因子的努力将从更全球化和高通量的方法中受益匪浅。在这方面，2010年的项目奖将利用一个补充和综合的战略，涉及高通量植物染色质免疫沉淀(PChIP)和基因表达分析，以绘制拟南芥转录调控网络。还计划进行更多的平行实验，以评估研究结果的功能有效性。研究的重点是TGA碱性/亮氨酸拉链蛋白家族，它们组成了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。这里要回答的一个关键问题是主要目标基因及其相关网络的身份。该项目的数据将定期张贴在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。根据该奖项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，它们将在该项目的3年时间线上公开提供。除了开发一种新的范式来理解拟南芥的转录控制机制外，这个项目还将促进由NSF鼓励的教育和培训任务。这个2010年项目奖的目标是识别和分类在DNA结合蛋白的子集和它们在活植物中控制的基因之间发生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，而且还可能通过导致从基因上增强作物天然保护基因的新的环境友好型策略而使农业受益。

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.