Bioinformatics and microgenomics integration for discovering cell specific gene regulation in a complex plant genome

功能有机体的蓝图指令由其基因组编码，由快速发展的基因组学（分子方法）和生物信息学（计算方法）研究。迄今为止，已经完成了11个高等植物基因组的测序。其中，基因的平均数量约为40，000个，从Arabidospis（一种小型“模式植物”）的25，000个到大豆（世界上经济上最重要的豆类作物植物）的66，000个不等。基因序列本身并不能为功能性植物提供足够的信息-基因需要侧翼序列，启动子（有时称为“基因开关”），它调节基因何时何地表达。这些启动子含有基因调节蛋白、转录因子可以结合的特定序列基序。基本的基因组在所有植物中可能大体上是相同的，但正是基因的调节使每个物种都是独特的。基因在何时何地开启和关闭，更有趣的是如何开启和关闭，即使在模式生物中也不是一个简单的预测问题，需要实验和计算分析方法来大规模解决这个问题。这项研究的独特之处在于它将高速计算（生物信息学）与分子技术（微基因组学）相结合，以找到细胞特异性基因调控背后的分子机制。我们的模型系统是大豆，它长期以来一直处于功能基因组学研究的前沿，基因组序列最近公布，还有许多其他遗传和基因组资源可用。我们将确定哪些启动子基序负责大豆基因的子集在几种不同的细胞类型中特异性表达。结果将在一个在线数据库中提供，在该数据库中可以在细胞特异性转录调节的分子机制和所产生的细胞类型之间建立联系。这项研究通过增加我们对植物发育和功能的基本知识，通过在生物技术和作物改良战略方面取得进展，以及通过在这个令人兴奋和迅速扩大的领域培养高素质的研究生，产生了宝贵的影响。

The blue print instructions for a functional organism are encoded by its genome, studied by the fast growing fields of genomics (molecular methods) and bioinformatics (computational methods). To date an amazing eleven higher plant genomes have been sequenced. Among these, the average number of genes is about 40,000, ranging from 25,000 in Arabidospis (a small 'model plant') to 66,000 in soybean (the economically most important legume crop plant in the world). Gene sequences alone do not provide sufficient information for a functional plant - the genes need flanking sequences, promoters (sometimes called "gene switches"), which regulate when and where the gene will be expressed. These promoters contain specific sequence motifs to which gene regulating proteins, transcription factors, can bind. The basic set of genes may by and large be the same in all plants, but it is the regulation of the genes that make each species unique. Where and when genes are switched on and off, and more interestingly how, is still not a matter of simple prediction even in model organisms, and both experimental and computational analysis methods are needed to address the problem at a large scale. The proposed research is unique in that it integrates high speed computing (bioinformatics) with molecular techniques (micro-genomics) to find the molecular mechanisms behind cell specific gene regulation. Our model system is soybean, which has long been in the forefront of functional genomics research, with the genome sequence recently released and a multitude of other genetic and genomic resources available. We will identify which promoter motifs are responsible for subsets of soybean genes being specifically expressed in several different cell types. The results will be available in an online database where links can be made between the molecular mechanism of cell specific transcriptional regulation and the resulting cell type. This research has invaluable impact by increasing our basic knowledge of plant development and function, by making progress for biotechnology and crop improvement strategies and by training highly qualified graduate students in this exciting and rapidly expanding field.