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其DNA的过程。 然而，到目前为止，我们对这些起始点（“复制起点”）是如何定义的，或者它们与其他染色体特征的关系知之甚少。 来自三个领先研究机构的跨学科团队将汇集他们的努力和专业知识来研究这个问题，并深入了解影响基因组功能的空间和生物化学参数。 具体目标：（1）他们研究项目的主要目标是构建代表性植物染色体大区域的复制起点图谱，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)一个平行的努力将映射DNA复制活动和基因活性（转录）在相同的染色体区域在几个不同的发育条件下，这将导致更好地了解染色体结构和功能的相互关系。 成果：完成后，该项目将帮助科学家了解染色体功能如何在结构和功能域中进行空间组织和协调，并帮助定义在这些功能中发挥关键作用的染色体特征。 拟议的实验将联合收割机强大的基因组技术与分子，细胞和生物化学工具。 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群体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体的数据进行比较，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守，并突出可能是植物王国独有的特征。 所产生的新的基因组信息和工具（包括精心设计的一套序列，用作基因组微阵列的定位标志）将通过网络和传统出版物提供给科学界的其他成员。 将数据提交至基因表达综合主页（http：//www.ncbi.nlm.nih.gov/geo/）和ArrayExpress（公共储存库）（http：//www.ebi.ac.uk/arrayexpress/）。 所有染色体元件的序列注释将提交到GenBank，本项目产生的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，包括指导基因表达的新方法、靶向基因插入和人工染色体的构建。 此外，该项目还将提供最先进的功能基因组学和生物信息学技术方面的培训。 本科生，研究生和博士后级别的受训人员将参加研究，并将为美国东南部的科学家组织研讨会，包括历史上黑人和少数民族机构的教师和学生。 该团队还将与当地教育工作者合作，开发有助于向高中生介绍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.