Simultaneous Integration of Combinatorial Histone Marks by the Atypical PHD-finger Protein EDM2 in Arabidopsis Thaliana

拟南芥中非典型 PHD 指蛋白 EDM2 的组合组蛋白标记的同时整合

• 批准号: 1330905
• 负责人: Thomas Eulgem
• 金额: $ 33.7万
• 依托单位: University of California-Riverside
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-09-01 至 2016-02-29
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1330905&HistoricalAwards=false
• 关键词: Simultaneous; Integration; Combinatorial; Histone; Marks

While the role of DNA in life processes is generally limited to the storage of genetic information, proteins have many structural roles and control nearly all biochemical processes in cells. Eukaryotic cells contain certain types of proteins, termed histones, which physically associate with DNA. Originally histones were found to be critical for the organized compaction of DNA that enables the DNA to fit into the nuclei of eukaryotic cells and to be faithfully transmitted (after duplication) to each of both daughter cells after cell divisions. During the past decade, a new type of biological code critical for the proper function of genes has emerged. This so-called histone or epigenetic code is manifested in certain chemical modifications of DNA and DNA-associated histone proteins. In contrast to the DNA code, which provides instructions for the synthesis of proteins, the histone code defines the activity states of genes and determines to what extent their genetic information is utilized. Numerous types of chemical modifications that can mark histone proteins at defined positions within their amino acid sequences have been identified. In some cases defined histone marks have been associated with enhanced or suppressed activity of genes. For example, the addition of an acetyl-tag to the 4th amino acid (a lysine) of the histone type H3 is often found in highly active genes, while methyl-tags at amino acid 9 (also a lysine) of H3 has been associated with suppressed genetic activity. It is also well established that certain proteins can ?read? this histone code and bind to these defined marks. When recruited to defined DNA regions by docking to their cognate histone marks, such histone binding proteins can alter activity levels of their respective target genes. Intellectual Merit-This project focuses on the characterization of a new type of histone binding protein in Arabidopsis plants. The EDM2 protein, which was originally identified as a critical regulator of plant immune responses, was found by the PI?s laboratory to specifically bind to the histone H3 protein bearing certain combinations of three different chemical marks. Responsible for this unusual property is a part of EDM2 related to the known-PHD finger domain. While conventional PHD-finger domains have been found previously to dock to either single or double histone marks, it is remarkable that the atypical PHD-finger domain of EDM2 appears to be unable to bind to single or double marks, but is only able to ?read? triple histone modifications. This novel mode of context-dependent histone binding behavior points to the existence of an additional, so far unknown, layer of the histone code, which is based on the combination of defined single marks. The PI proposes to perform a detailed analysis of histone-binding characteristics of the EDM2-type PHD finger domain. Besides biochemical experiments to understand how this type of ?histone reader? module distinguishes between different combinations of histone marks, studies will also be performed to identify which plant genes bear such ?higher-level of histone code words? that can be read by EDM2. If successful, this study will substantially advance our basic understanding of epigenetics, which is the biological discipline focused on the function of histone marks and chemical modifications of DNA. Broader Impacts-In addition to its scientific significance, this project will have broader societal impacts. An important component of the proposed project is an involvement of undergraduate students, mainly from minority groups. The project will be linked to classes on plant biochemistry, biotechnology and molecular biology taught by the PI and the ongoing NSF-REU Plant Cell Biology program within the Center for Plant Cell Biology at UC-Riverside. In addition, the proposed project will provide a strong platform for training of a postdoctoral scholar and a graduate student and prepare them for careers as senior researchers in academia or industry. The goals of the America COMPETES Act of 2007 that emphasize the importance of comprehensive professional training and awareness of the responsible and ethical conduct of research are a top priority of this project. By regulating an immune receptor gene, EDM2 has an important role in mediating resistance of plants against diseases. Therefore, the significance of this study goes beyond its impact on basic epigenetics and will likely benefit society by allowing new solutions in crop disease protection.

虽然DNA在生命过程中的作用通常仅限于存储遗传信息，但蛋白质具有许多结构作用，并控制细胞中几乎所有的生化过程。真核细胞含有某些类型的蛋白质，称为组蛋白，它们与DNA物理结合。最初发现组蛋白对于DNA的有组织压缩至关重要，使DNA能够适合真核细胞的细胞核，并在细胞分裂后忠实地传递（复制后）到两个子细胞中的每一个。在过去的十年中，出现了一种对基因的正常功能至关重要的新型生物密码。这种所谓的组蛋白或表观遗传密码表现在DNA和DNA相关组蛋白的某些化学修饰中。与提供蛋白质合成指令的DNA密码相反，组蛋白密码定义基因的活动状态，并决定基因信息的利用程度。已经鉴定了可以在组蛋白的氨基酸序列内的限定位置标记组蛋白的许多类型的化学修饰。在某些情况下，定义的组蛋白标记与基因活性的增强或抑制有关。例如，在组蛋白H3型的第4个氨基酸（赖氨酸）上添加乙酰基标签通常存在于高活性基因中，而H3的第9个氨基酸（也是赖氨酸）上的甲基标签与抑制的遗传活性有关。它也是公认的，某些蛋白质可以？阅读？这个组蛋白编码并结合到这些特定的标记上。当通过与其同源组蛋白标记对接而被招募到限定的DNA区域时，这样的组蛋白结合蛋白可以改变其各自靶基因的活性水平。学术成就-本计画著重于拟南芥中一种新型组蛋白结合蛋白的特性。EDM 2蛋白，这最初被确定为一个关键的调节植物免疫反应，发现了PI？该实验室专门结合到组蛋白H3蛋白轴承三种不同的化学标记的某些组合。负责这种不寻常的属性是EDM 2的一部分，与已知的PHD指域。虽然传统的PHD-指结构域已被发现以前对接到单或双组蛋白标记，值得注意的是，EDM 2的非典型PHD-指结构域似乎不能结合到单或双标记，但只能？阅读？三重组蛋白修饰这种依赖于上下文的组蛋白结合行为的新模式表明存在一个额外的、迄今为止未知的组蛋白密码层，该密码层基于定义的单个标记的组合。PI建议对EDM 2型PHD指结构域的组蛋白结合特征进行详细分析。除了生化实验，如何了解这类？组蛋白阅读器？模块区分不同组合的组蛋白标记，研究也将进行，以确定哪些植物基因承担这样的？更高层次的组蛋白编码词可以被EDM 2读取。如果成功，这项研究将大大推进我们对表观遗传学的基本理解，表观遗传学是一门专注于组蛋白标记功能和DNA化学修饰的生物学科。更广泛的影响-除了其科学意义，该项目将有更广泛的社会影响。拟议项目的一个重要组成部分是主要来自少数群体的本科生的参与。该项目将与PI教授的植物生物化学，生物技术和分子生物学课程以及UC-Riverside植物细胞生物学中心正在进行的NSF-REU植物细胞生物学课程相联系。此外，拟议的项目将为博士后学者和研究生的培训提供一个强大的平台，并为他们在学术界或工业界担任高级研究人员做好准备。2007年《美国竞争法》的目标强调了全面专业培训的重要性，以及对负责任和合乎道德的研究行为的认识，这是该项目的重中之重。EDM 2通过调节免疫受体基因，在介导植物抗病性中发挥重要作用。因此，这项研究的重要性超出了其对基础表观遗传学的影响，并可能通过提供作物病害保护的新解决方案而造福社会。