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遗传信息的存储，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有物理联系。最初，组蛋白被发现对DNA的有组织压缩至关重要，使DNA能够适应真核细胞的细胞核，并在细胞分裂后忠实地（在复制后）传递给每一个子细胞。在过去的十年中，一种对基因正常功能至关重要的新型生物密码已经出现。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密码不同，组蛋白密码定义了基因的活性状态，并决定了它们的遗传信息在多大程度上被利用。许多类型的化学修饰可以标记组蛋白在其氨基酸序列的特定位置已经确定。在某些情况下，组蛋白标记与基因活性的增强或抑制有关。例如，在H3组蛋白类型的第4个氨基酸（赖氨酸）上添加乙酰标签通常在高活性基因中发现，而在H3组蛋白类型的第9个氨基酸（也是赖氨酸）上添加甲基标签则与抑制遗传活性有关。此外，某些蛋白质可以“读懂”也是公认的事实。这个组蛋白编码并结合到这些定义的标记上。当通过与同源组蛋白标记对接而被招募到特定的DNA区域时，这些组蛋白结合蛋白可以改变各自靶基因的活性水平。本项目主要研究拟南芥植物中一种新的组蛋白结合蛋白的特性。EDM2蛋白最初被认为是植物免疫反应的关键调节因子，是由PI？这是一种由三种不同化学标记组合而成的组蛋白H3。造成这种不寻常性质的是EDM2中与已知phd指域相关的部分。虽然传统的博士指结构域以前被发现与单或双组蛋白标记对接，但值得注意的是，EDM2的非典型博士指结构域似乎无法与单或双标记结合，而只能“读取”。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，组蛋白代码中存在一个迄今未知的额外层，该层基于已定义的单个标记的组合。PI建议对edm2型PHD手指结构域的组蛋白结合特性进行详细分析。除了生化实验如何理解这类？组蛋白的读者?模块区分不同组合的组蛋白标记，还将进行研究，以确定哪些植物基因承担这样的？更高水平的组蛋白编码？EDM2可以读取的数据。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化学修饰的生物学学科。更广泛的影响-除了其科学意义外，该项目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，主要来自少数民族。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植物细胞生物学项目相关联。此外，拟议的项目将为培养博士后学者和研究生提供一个强大的平台，为他们成为学术界或工业界的高级研究人员做好准备。2007年《美国竞争法案》强调了全面的专业培训的重要性，以及对负责任和合乎道德的研究行为的认识，这是本项目的首要任务。EDM2通过调节一个免疫受体基因，在介导植物抗病方面发挥重要作用。因此，这项研究的意义超越了其对基础表观遗传学的影响，并可能通过为作物病害保护提供新的解决方案而造福社会。

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.