DNA Methylation: Structures, Functions, and Regulation

DNA 甲基化：结构、功能和调控

• 批准号: 8123687
• 负责人: Xiaodong Cheng
• 金额: $ 9.74万
• 依托单位: EMORY UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-27 至 2011-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8123687
• 关键词: Affect; Affinity; Ankyrin Repeat; Architecture; Base Pairing; Binding; Biochemical; C-terminal; Catalysis; Catalytic Domain; Chromatin; CpG dinucleotide; DNA; DNA Binding; DNA Binding Domain; DNA Methylation; DNA Methyltransferase; DNA Modification Methylases; Data; Defect; Detection; Enzymes; Epigenetic Process; Event; Excision; Fertility Disorders; Fertilization in Vitro; Filament; Gene Expression; Generations; Goals; Histone H3; Histones; Immune response; In Vitro; Infant; Length; Link; Lysine; Maintenance; Malignant Neoplasms; Mammalian Cell; Mammals; Maps; Mediating; Methylation; Methyltransferase; Modeling; Modification; N Domain; N-terminal; Nucleoproteins; Nucleosomes; Obesity; Pattern; Peptides; Periodicity; Phosphorylation; Plants; Positioning Attribute; Post-Translational Protein Processing; Proteins; Publishing; Reader; Recruitment Activity; Regulation; Signal Transduction; Site; Stretching; Structure; Study models; System; Tail; Testing; Therapeutic Agents; Work; dimer; homeodomain; human disease; imprint; in vivo; insight; method development; novel strategies; preference; public health relevance; research study; spatial relationship

DESCRIPTION (provided by applicant): One of the fundamental questions in control of gene expression in mammals is how epigenetic methylation patterns of DNA and histones are established, erased, and detected. Epigenetic regulation is a newly appreciated mechanism that profoundly influences chromatin function, which has direct relevance to a large number of human diseases from nine known imprinting-associated fertility disorders, obesity, immune response, to cancer. Mammalian DNA methylation at CpG dinucleotides is intricately connected to the methylation status of two lysine residues of histone H3: the unmodified lysine 4 (H3K4) and methylated lysine 9 (H3K9). Mammalian DNA methyltransferases, Dnmt1 and Dnmt3a, each contain a C-terminal catalytic domain and a largely uncharacterized N-terminal region including several distinct regulatory domains. Two protein lysine (K) methyltransferases (PKMTs) - G9a and Set7 - are believed to interact directly with Dnmts and modulate DNA methylation. Despite its importance, it is not known how Dnmts and PKMTs work in concert. We hypothesize that modification(s) of Dnmts themselves by PKMTs is a major component of epigenetic regulation, and may serve as a checkpoint for correct assembly of the machinery required to accurately methylate DNA. The central goal of this proposal is to determine how and where Dnmts are methylated, and how methylated Dnmts are recognized and recruited. Further, both de novo methylation of DNA CpGs by Dnmt3a, and maintenance methylation of hemimethylated DNA by Dnmt1, will be studied in parallel. I propose here four new specific aims that will determine (1) how the Set7-mediated lysine methylation marks on Dnmt1 are influenced by modifications at nearby residues, (2) how G9a-mediated methylation of Dnmt1 is recognized and recruited to the replication foci, (3) how Dnmt3a lysine methylation marks are created and recognized, and (4) the architecture of Dnmt3a-Dnmt3L heterotetramer, that is responsible for detecting both unmethylated H3K4 and CpG spacing. PUBLIC HEALTH RELEVANCE: One of the fundamental questions in control of gene expression in mammals is how epigenetic methylation patterns of DNA and histones are established, erased, and detected. Epigenetic regulation is a newly appreciated mechanism that profoundly influences chromatin function, which has direct relevance to a large number of human diseases. Serious human diseases, ranging from nine known imprinting-associated fertility disorders, obesity, immune response, to cancer, can result from defects in the "methyl marking" system. Alterations in this methylation can also profoundly affect infants conceived through in vitro fertilization. Thus, structural and biochemical studies directed against the emerging epigenetic regulatory enzymes may provide a method for the development of highly selective therapeutic agents that promise entirely novel approaches for the treatment of human diseases. In this proposal, we will explore questions of dynamic regulation (creating and recognizing) of DNA and histone lysine modifications and modification(s) of enzymes themselves, and biochemical crosstalk between modifications by two distinct classes of epigenetic regulators.

描述（由申请人提供）：哺乳动物中基因表达控制的基本问题之一是如何建立、消除和检测DNA和组蛋白的表观遗传甲基化模式。表观遗传调控是近年来发现的一种深刻影响染色质功能的机制，它与9种已知的印迹相关的生育障碍、肥胖、免疫反应和癌症等多种人类疾病有直接关系。哺乳动物DNA在CpG二核苷酸上的甲基化与组蛋白H3的两个赖氨酸残基的甲基化状态密切相关：未修饰的赖氨酸4（H3 K4）和甲基化的赖氨酸9（H3 K9）。哺乳动物DNA甲基转移酶，Dnmt 1和Dnmt 3a，每个都含有一个C-末端催化结构域和一个很大程度上未表征的N-末端区域，包括几个不同的调节结构域。两种蛋白质赖氨酸（K）甲基转移酶（PKMT）-G9 a和Set 7-被认为直接与Dnmts相互作用并调节DNA甲基化。尽管它的重要性，它是不知道如何Dnmts和PKMTs协同工作。我们假设PKMT对Dnmts本身的修饰是表观遗传调控的主要组成部分，并且可以作为正确组装精确甲基化DNA所需的机器的检查点。该提案的中心目标是确定Dnmts如何以及在何处被甲基化，以及甲基化的Dnmts如何被识别和招募。此外，将平行研究Dnmt 3a对DNA CpG的从头甲基化和Dnmt 1对半甲基化DNA的维持甲基化。我在这里提出了四个新的具体目标，将确定（1）Dnmt 1上Set 7介导的赖氨酸甲基化标记如何受到附近残基修饰的影响，（2）G9 a介导的Dnmt 1甲基化如何被识别并招募到复制灶，（3）Dnmt 3a赖氨酸甲基化标记如何被创建和识别，以及（4）Dnmt 3a-Dnmt 3L异源四聚体的结构，其负责检测未甲基化的H3 K4和CpG间隔。 公共卫生相关性：控制哺乳动物基因表达的基本问题之一是DNA和组蛋白的表观遗传甲基化模式是如何建立、消除和检测的。表观遗传调节是一种新发现的机制，它深刻影响染色质功能，与许多人类疾病直接相关。严重的人类疾病，从九种已知的与印记相关的生育障碍、肥胖、免疫反应到癌症，都可能是由“甲基标记”系统的缺陷引起的。这种甲基化的改变也会深刻地影响通过体外受精受孕的婴儿。因此，针对新兴的表观遗传调节酶的结构和生化研究可能提供一种方法，用于开发高度选择性的治疗剂，从而为治疗人类疾病提供全新的方法。在这个提议中，我们将探讨DNA和组蛋白赖氨酸修饰和酶本身修饰的动态调节（创建和识别）问题，以及两种不同类型的表观遗传调节剂修饰之间的生物化学串扰。