Computing Regulatory DNA by Comparing Plant Genomes

PI：Michael Freeling（UC Berkeley）关键人员：Brian C.托马斯（加州大学伯克利分校）这是一个基因组使能植物研究项目，将提供调控DNA序列的数据库，映射工具和植物育种和研究社区所需的软件。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直向同源基因进行比对，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”。 预计这些序列包含与调节基因可用性或表达的蛋白质和小RNA结合的DNA位点。当CNS发现完成时，植物群落应该有大约170，000个短的（平均= 31 bp长）CNS，代表分类到特定基因的功能（保守）非编码区。不保守的CNS之间的非编码序列将用作控制序列。许多以前未知的功能将被发现。 CNS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。 植物研究界和该项目都需要一个比较基因组学软件应用程序，该软件应用程序将使用静态和动态程序将任何植物的任何染色体区域与任何其他区域进行比较。该项目包括设计和描述这个新的软件系统，称为CoGe。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（http：sourceforge.net; http://plantgdb.org.This）上公开提供。高粱-水稻CNS-发现项目产生泛草作图标记。 没有序列数据库的草，孤儿草商品，如谷子，应该最直接受益。至少有一名研究生和几名本科生研究人员是这项研究的重要参与者。 该项目包括湾区高中学生的暑期实习，他们才华横溢，服务不足，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.