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

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角色，并控制着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，这些蛋白质在物理上与DNA相关。最初，组蛋白被发现对DNA的有组织紧凑至关重要，使DNA能够适应真核细胞的核，并在细胞分裂后忠实地传递给(复制后)两个子细胞。在过去的十年里，出现了一种对基因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在DNA和DNA相关组蛋白的某些化学修饰中表现出来。与为蛋白质合成提供指令的DNA密码不同，组蛋白密码定义了基因的活动状态，并决定了基因信息的利用程度。已经确定了多种类型的化学修饰，它们可以在组蛋白的氨基酸序列中的特定位置标记组蛋白。在某些情况下，确定的组蛋白标记与基因活性增强或抑制有关。例如，在组蛋白类型H3的第4个氨基酸(赖氨酸)上添加乙酰标签通常在高活性基因中被发现，而H3的第9氨基酸(也是赖氨酸)上的甲基标签与遗传活性受到抑制有关。某些蛋白质可以阅读？这一点也得到了充分证实。这个组蛋白编码并结合到这些定义的标记上。当通过对接到它们的同源组蛋白标记而被招募到定义的DNA区域时，这种组蛋白结合蛋白可以改变它们各自目标基因的活性水平。智力价值-这个项目的重点是在拟南芥植物中描述一种新型的组蛋白结合蛋白。EDM2蛋白最初被认为是植物免疫反应的关键调节因子，由皮？S实验室发现，它特异性地与带有三种不同化学标志的特定组合的组蛋白H3结合。造成这种不寻常特性的是EDM2中与已知的PHD指状域相关的一部分。虽然以前已经发现常规的PhD-Finger结构域与单或双组蛋白标记对接，但值得注意的是，EDM2的非典型PhD-Finger结构域似乎不能与单或双标记结合，而只能阅读？三重组蛋白修饰。这种与上下文相关的组蛋白结合行为的新模式表明，存在另一层迄今未知的组蛋白密码层，该层基于已定义的单个标记的组合。PI建议对EDM2型PHD指状域的组蛋白结合特性进行详细分析。除了生化实验外，我们还需要了解这种类型的组蛋白阅读器是如何？模块区分不同的组蛋白标记组合，还将进行研究，以确定哪些植物基因携带这样的基因？更高水平的组蛋白密码字？可以由EDM2读取。如果成功，这项研究将极大地促进我们对表观遗传学的基本理解，表观遗传学是专注于组蛋白标记的功能和DNA的化学修饰的生物学学科。更广泛的影响--这个项目除了具有科学意义外，还将产生更广泛的社会影响。拟议项目的一个重要组成部分是本科生的参与，他们主要来自少数群体。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加州大学河滨分校植物细胞生物学中心正在进行的NSF-REU植物细胞生物学计划相联系。此外，拟议的项目将为培养一名博士后学者和一名研究生提供一个强有力的平台，并为他们作为学术界或工业界高级研究人员的职业生涯做好准备。2007年《美国竞争法》的目标强调综合专业培训的重要性，以及对负责任和合乎道德的研究行为的认识，是该项目的最优先事项。EDM2通过调节免疫受体基因，在植物抗病中发挥重要作用。因此，这项研究的意义超越了它对基本表观遗传学的影响，并可能通过在作物病害保护方面提供新的解决方案来造福社会。

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.