Epigenome Dynamics During DNA Replication

PI：William F.汤普森（北卡罗来纳州州立大学）CoPIs：乔治C。艾伦和琳达汉利鲍登（北卡罗来纳州州立大学），罗伯特马汀森（冷泉港实验室）和马修W。Vaughn（德克萨斯大学奥斯汀分校，德克萨斯州高级计算中心）。 高级人员：Pete E. Pascuzzi（北卡罗来纳州州立大学）和大卫A. Micklos（冷泉港实验室）表观遗传学，研究染色体的结构或化学修饰如何影响遗传性状的表达，是生物学的一个令人兴奋的新领域。然而，人们对通过多轮DNA复制和细胞分裂来传递这些结构或化学修饰的过程（称为“表观遗传标记”）知之甚少，而这些DNA复制和细胞分裂是制造植物或动物所必需的。理解这种细胞间的传递需要理解仅在DNA合成的细胞周期的一小部分（“S期”）发生的事件。在这个项目中，从以前的NSF支持的项目的工具和知识将被用来研究在两个重要的模式系统-玉米和拟南芥的表观遗传标记通过S期的传输。预计这些结果将与大多数植物和动物有关。数以百万计的植物细胞核将被分离出来，然后根据它们含有多少DNA使用一种称为流式细胞术的技术进行分类。这种分选技术将为DNA复制过程中几个阶段的表观遗传标记的全基因组分析提供材料。研究复制周期中的事件顺序将有助于理解导致染色体沿着不同位置形成活性或非活性结构的分子机制。类似的技术应用于已知染色体结构或功能缺陷的突变植物，可能有助于突出更微妙的控制机制。这些结果有望更好地了解基因如何受到DNA及其所在染色体的结构和化学修饰的影响。了解这些表观遗传影响将对基础和应用植物生物学产生深远的影响。例如，许多作物是无性繁殖的，偶尔出现的“运动”（表观遗传变异）会影响产量和质量。另一个例子涉及通过基因转移工程改造的作物，这些作物通常经历所转移基因的意外失活或“沉默”。沉默使获得商业上可行的植物系的过程大大复杂化。该项目将有助于提高预测和控制基因沉默的能力，这将具有相当大的应用价值，该项目将汇集具有生物化学、分子生物学、遗传学、基因组学和生物信息学专门知识的研究人员，并支持两个主要研究机构之间的富有成效的合作。将为研究生和博士后学生提供良好的培训环境，选定的本科生将参与研究的各个方面。将开展两项主要的外联工作。在以前的PGRP项目期间为中学创建的一个成功的遗传学“手提箱中的科学”单元将得到更新，教师讲习班将扩大到包括更多的教师和学生。此外，一个表观遗传学项目将在多兰DNA学习中心开幕。该计划将针对高级高中学生和两年制和农业大学的教师，并将为表观遗传学教学提供宝贵的资源。将创建网络材料和播客以及实验资源的组合。将通过项目网站（www.plantreplication.net）、GEO（http：//www.ncbi.nlm.nih.gov/geo/）、NCBI的SRA（http：//www.ncbi.nlm.nih.gov/sra）、Gramene（http：//www.gramene.org/）、MaizeGDB（http：//www.maizegdb.org/）和TAIR（http：//www.arabidopsis.org/）向公众提供关于该项目的信息，包括与原始数据的链接。

PI: William F. Thompson (North Carolina State University)CoPIs: George C. Allen and Linda Hanley-Bowdoin (North Carolina State University), Robert Martienssen (Cold Spring Harbor Laboratory) and Matthew W. Vaughn (University of Texas at Austin, the Texas Advanced Computing Center). Senior Personnel: Pete E. Pascuzzi (North Carolina State University) and David A. Micklos (Cold Spring Harbor Laboratory)Epigenetics, the study of structural or chemical modifications of chromosomes that affect how genetic traits are expressed, is an exciting new area of biology. However, very little is yet known about the processes that transmit these structural or chemical modifications - known as "epigenetic marks" - through the multiple rounds of DNA replication and cell division that are required to make a plant or animal. Understanding this cell-to-cell transmission requires understanding events occurring only during the small part of the cell cycle in which DNA is synthesized ("S-phase"). In this project, the tools and knowledge from a previous NSF-supported project will be used to study transmission of epigenetic marks through S phase in two important model systems - maize and Arabidopsis. The results are expected to be relevant to most plants and animals. Millions of plant cell nuclei will be isolated and then sorted into groups depending on how much DNA they contain using a technique called flow cytometry . This sorting technique will provide material for a genome-wide analysis of epigenetic marks at each of several stages in the DNA replication process. Studying the sequence of events through the replication cycle will help to understand the molecular mechanisms that lead to formation active or inactive structures at different places along a chromosome. Similar techniques applied to mutant plants with known defects in chromosome structure or function may help highlight even more subtle control mechanisms. The results are expected to provide a better understanding of how genes are affected by structural and chemical modifications of DNA and the chromosomes in which it is housed. Understanding these epigenetic influences will have a profound impact on both basic and applied plant biology. For example, many crops are propagated clonally, and the occasional occurrence of "sports" (epigenetic variants) can impact both yield and quality. Another example involves crops engineered by gene transfer, which often experience unexpected inactivation, or "silencing", of the transferred gene. Silencing greatly complicates the process of obtaining commercially viable plant lines. This project will contribute to the ability to predict, and perhaps to control, gene silencing, which will be of considerable value for a wide variety of applications.The project will bring together investigators with expertise in biochemistry, molecular biology, genetics, genomics and bioinformatics, and support a productive collaboration between two major research institutions. An excellent training environment for graduate and postdoctoral students will be provided, and selected undergraduates will participate in various aspects of the research. There will be two principal outreach efforts. A successful "Science in a Suitcase" unit on Genetics for middle schools, created during a previous PGRP project, will be updated, and teacher workshops will be extended to include many more teachers and students. In addition, a program in epigenetics will be inaugurated at the Dolan DNA Learning Center. This program will target advanced high school students and faculty at two year and agricultural colleges, and will provide valuable resources for teaching about epigenetics. A combination of web materials and podcasts, as well as resources for experiments, will be created. Public access to information about this project, including links to primary data, will be provided through the project website (www.plantreplication.net), GEO (http://www.ncbi.nlm.nih.gov/geo/), the NCBI's SRA (http://www.ncbi.nlm.nih.gov/sra), Gramene (http://www.gramene.org/), MaizeGDB (http://www.maizegdb.org/), and TAIR (http://www.arabidopsis.org/).