Global Analysis of Functional Units in Plant Chromosomes: DNA Replication, Domain Structure, and Transcription

众所周知，高等生物，包括植物，开始在其基因组的许多不同位置复制它们的DNA的过程。然而，到目前为止，我们对这些起点(“复制起点”)是如何定义的，或者它们与其他染色体特征之间的关系知之甚少。来自三个领先研究机构的跨学科团队将集中他们的努力和专业知识来研究这个问题，并对影响基因组功能的空间和生化参数有更深入的了解。具体目标：(1)他们的研究项目的一个主要目标是构建具有代表性的植物染色体大范围复制起始区的图谱，以及构建和覆盖关键染色体特征的图谱，如基质附着区、富含修饰组蛋白或甲基化DNA的区域。(2)并行的工作将定位同一染色体区域在几种不同发育条件下的DNA复制活性和基因活性(转录)，这将有助于更好地理解染色体结构和功能的相互关系。成果：该项目完成后，将帮助科学家了解染色体功能是如何在结构和功能领域中进行空间组织和协调的，并有助于确定在这些功能中发挥关键作用的染色体特征。拟议的实验将把强大的基因组技术与分子、细胞和生化工具结合起来。该团队将专注于水稻1号染色体的短臂和拟南芥4号染色体的全长，从而为代表两大作物类别的模式生物提供广泛的数据。将这些植物物种的染色体特征与动物和其他生物的数据进行比较，将有助于确定足够重要的染色体特征，以便在进化中广泛保存，并突出可能是植物界独有的特征。将通过网络和传统出版物向科学界的其他成员提供新的基因组信息和工具(包括精心设计的一套序列，用作基因组微阵列上的测绘标志)。数据将提交到基因表达总览主页(http://www.ncbi.nlm.nih.gov/geo/))和公共存储库ArrayExpress(http://www.ebi.ac.uk/arrayexpress/).所有染色体元素的序列注释都将提交给GenBank。该项目产生的关于染色体结构的基本信息将有助于支持新一代基因工程技术，其中可能包括指导基因表达、靶向基因插入和构建人工染色体的新方法。此外，该项目还将提供最先进的功能基因组和生物信息学技术方面的培训。本科生、研究生和博士后将参与这项研究，并将为美国东南部的科学家组织研讨会，包括历史上的黑人和少数民族机构的教职员工和学生。该团队还将与当地教育工作者合作，开发有助于向高中生展示基因组学概念的教学工具。

It is well known that higher organisms, including plants, begin the process of replicating their DNA at many different places in their genomes. However, as yet we know very little about how these starting points ("replication origins") are defined, or how they relate to other chromosomal features. An interdisciplinary team from three leading research institutions will pool their efforts and expertise to investigate this question and attain a deeper understanding of spatial and biochemical parameters affecting genome function. Specific objectives:(1) A primary goal of their research project is to construct maps of replication origins in large regions of representative plant chromosomes, as well as to construct and overlay maps of key chromosomal features such as matrix attachment regions, regions enriched in modified histones or methylated DNA. (2) A parallel effort will map DNA replication activity and gene activity (transcription) in the same chromosomal regions under several different developmental conditions, which will lead to a better understanding of the interrelationship of chromosome structure and function. Outcomes:When completed, the project will help scientists understand how chromosome functions are spatially organized and coordinated in structural and functional domains, and help define chromosomal features that play key roles in these functions. The proposed experiments will combine powerful genomic technologies with molecular, cellular and biochemical tools. The team will focus on the short arm of rice chromosome 1 and the full length of Arabidopsis chromosome 4, thus providing extensive data for model organisms representing each of the two major groups of crop plants. Comparing chromosomal features for these plant species with data for animals and other organisms will help identify chromosomal features important enough to be broadly conserved in evolution, as well as highlight features that may be unique to the plant kingdom. New genomic information and tools that are generated (including the carefully designed set of sequences to be used as mapping landmarks on genomic microarrays) will be made available to other members of the scientific community via the web as well as through conventional publications. Data will be submitted to the Gene Expression Omnibus homepage (http://www.ncbi.nlm.nih.gov/geo/) and ArrayExpress, a public repository (http://www.ebi.ac.uk/arrayexpress/) . All sequence annotation for the chromosomal elements will be submitted to GenBank.The basic information on chromosome structure generated by this project will help support a new generation of genetic engineering technologies, which may include new methods for directing gene expression, targeted gene insertion, and construction of artificial chromosomes. In addition, the project will provide training in state-of-the-art functional genomic and bioinformatics techniques. Trainees at the undergraduate, graduate and postdoctoral levels will participate in the research, and workshops will be organized for scientists in the southeastern US, including faculty and students at historically black and minority institutions. The team will also work with local educators to develop teaching tools useful for presenting genomics concepts to high school students.