Computing Regulatory DNA by Comparing Plant Genomes

主要人员：布莱恩·C·托马斯(加州大学伯克利分校)这是一个基于基因组的植物研究项目，将提供植物育种和研究界所需的调控DNA序列数据库、绘图工具和软件。主要的生物学研究活动是将高粱中的每个基因与其在水稻中的同源基因进行比对，评估外显子注释，然后定义和存储那些在进化过程中保守的非编码序列，称为CNSS。这些序列预计包括结合蛋白质的DNA位点和调节基因可获得性或表达的小RNA。当CNS发现完成时，植物群落应该有大约17万个短的(平均=31bps长)CNS，代表功能(保守的)非编码区，被分类到特定的基因。CNS之间非保守的非编码序列将被用作控制序列。许多以前未知的功能将被发现。CNSS将与基序、表达模式、甲基化状态等相关联，结果显示在项目网站(http://synteny.cnr.berkeley.edu/))上，并通过DAS服务器和PlantGDB向社区提供。植物研究界和这个项目都需要一个比较基因组学软件应用程序，它将使用静态和动态程序将任何染色体区域与任何植物的任何其他染色体区域进行比较。该项目包括这个新的软件系统COGE的设计和描述。所有结果、数据库、应用程序和代码都将在该项目的网站以及期刊和社区网站上公开提供(http://sourceforge.net；http://plantgdb.org.This项目具有更广泛的影响。高粱-水稻中枢神经系统发现项目产生了泛草图谱标记。没有序列数据库的草，以小米为例的孤儿草商品，应该是最直接受益的。至少有一名研究生和几名本科生是这项研究的主要参与者。这个项目包括为湾区高中学生的暑期实习，这些学生有天赋，没有得到充分的服务，并由他们的生物老师推荐给我们。

PI: Michael Freeling (UC Berkeley)Key personnel: Brian C. Thomas (UC Berkeley)This is a Genome-Enabled Plant Research project that will provide databases of regulatory DNA sequences, mapping tools and software needed by the plant breeding and research community. The primary biological research activity is to align each gene in sorghum with its orthologous gene in rice, evaluate exon annotations, and then define and store those noncoding sequences that have been conserved over evolutionary time, called "CNSs". These sequences are expected to comprise DNA sites that bind proteins and small RNAs that regulate gene availability or expression. When CNS discovery is complete, the plant community should have approximately 170,000 short (mean= 31 bps long) CNSs representing functional (conserved) noncoding regions sorted to particular genes. Noncoding sequences between CNSs that are not conserved will be used as control sequences. Many previously unknown functions will be discovered. CNSs will be associated with motifs, expression patterns, methylation status and the like, with results displayed on the project web site (http://synteny.cnr.berkeley.edu/) and available to the community through a DAS server and PlantGDB. Both the plant research community and this project need a comparative genomics software application that will compare - using static and on-the-fly procedures - any chromosomal region with any other from any plant. This project includes the design and description of this new software system, called CoGe. All results, databases, applications and code will be publicly available on this project's website, and in journal and community websites (http://sourceforge.net; http://plantgdb.org.This project has broader impacts. The sorghum-rice CNS-discovery project generates pan-grass mapping markers. Grasses without sequence databases, orphan grass commodities exemplified by foxtail millet, should benefit most directly. At least one graduate student and several undergraduate researchers are essential participants in this research. This project includes summer internships for Bay Area high school students who are talented, underserved, and recommended to us by their biology teachers.