Dynamics and molecular mechanisms linking metabolism and the epigenome

连接代谢和表观基因组的动力学和分子机制

• 批准号: 10624003
• 负责人: JOHN M DENU
• 金额: $ 66.93万
• 依托单位: UNIVERSITY OF WISCONSIN-MADISON
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-07-01 至 2028-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10624003
• 关键词: Acceleration; Acetyl Coenzyme A; Acetylation; Acetyltransferase; Animals; Biochemical; Biochemistry; Biophysics; Catalysis; Cell physiology; Cells; Chromatin; Communication; DNA Methylation; DNA Sequence; Deacetylase; Deacetylation; Diet; Disease; Environment; Enzymes; Epigenetic Process; Etiology; Foundations; Gene Expression; Genetic; Genome; Goals; Histones; Human body; In Vitro; Instruction; Investigation; Knowledge; Link; Lysine; Macronutrients Nutrition; Metabolism; Methylation; Methyltransferase; Modeling; Molecular; Molecular Machines; Nicotinamide adenine dinucleotide; Nuclear; Nucleosomes; Pathway interactions; Pharmacology; Post-Translational Protein Processing; Production; Protein Acetylation; Proteins; Research; S-Adenosylhomocysteine; S-Adenosylmethionine; Signal Pathway; Signal Transduction; Sirtuins; Untranslated RNA; Work; alpha ketoglutarate; cell type; drug development; epigenome; extracellular; insight; microbiota; non-histone protein; response

Project Summary/Abstract Cellular responses to available macronutrients and extra-cellular signals rely on the unique epigenetic state of the cell, defined by a layer of biochemical information above the genome that dictates specific gene expression. The epigenome consists of DNA sequence-dependent proteins, non-coding RNAs, DNA methylation and histone post-translation modifications (PTMs) such as lysine acetylation and methylation. The latter two mechanisms are catalyzed by enzymes that must ‘interpret’ incoming signals, ‘read’ the existing epigenetic landscape and ‘respond’ appropriately. Enzymes that modify histones and non-histone proteins such as methyltransferases, demethylases, acetyltransferases and deacetylases use central metabolites (S- adenosyl methionine, SAM; α-ketoglutarate, αKG; acetyl-CoA and nicotinamide adenine dinucleotide, NAD+, respectively) as co-substrates. New evidence suggests that fluctuation in such epi-metabolites caused by diet, environment, microbiota and genetics can drive PTM dynamics, however the relevant mechanisms remain unclear in most cases. Are changes in epi-metabolites sensed by signaling pathways or by substrate-level driven catalysis or both? Also, does local production of epi-metabolites enable/accelerate gene expression mechanisms on chromatin? Non-histone protein acetylation is a major PTM that can regulate many aspects of cellular function and occurs in all cellular compartments. But despite broad knowledge of what gets modified, the most pressing challenge is to understand the how, the why and the when, which constitutes an overarching theme of this proposal. A major portion of the research to understand reversible protein acetylation as a regulatory PTM will involve knowledge of how pathway-specific acetyl-CoA (and other acyl-CoAs) production leads to dynamic acetylation after extra-cellular stimulation. Also, this work will focus on the detailed molecular mechanisms by which nuclear NAD+-dependent deacetylases SIRT6/7 (Sirtuins 6 & 7) are regulated and how these enzymes perform such exquisite deacetylation of nucleosomes. A sub-theme of this proposal that connects these two projects is to understand the fundamental principles that govern PTM enzymes acting on chromatin/nucleosomes. This proposal is uniquely poised to make major advances to these salient questions. To accomplish these goals, the projects synergistically employ in vitro biochemistry/biophysics, complementary genetics and pharmacology, and cell- and animal-based models. Results from these investigations will provide i.) insight into the etiology of diseases resulting from the link between metabolism and the epigenome, ii.) foundations for drug development against the enzymes described here, and iii.) a fundamental understanding of how the cell ‘interprets’ incoming signals in the context of existing epigenetic information and ‘responds’ appropriately.

项目概要/摘要 细胞对可用大量营养素和细胞外信号的反应依赖于独特的表观遗传状态 细胞，由决定特定基因的基因组上方的一层生化信息定义 表达。表观基因组由 DNA 序列依赖性蛋白质、非编码 RNA、DNA 组成 甲基化和组蛋白翻译后修饰 (PTM)，例如赖氨酸乙酰化和甲基化。这 后两种机制是由酶催化的，这些酶必须“解释”传入的信号，“读取”现有的信号 表观遗传景观和适当的“反应”。修饰组蛋白和非组蛋白的酶 例如甲基转移酶、去甲基酶、乙酰转移酶和脱乙酰酶使用中心代谢物（S- 腺苷甲硫氨酸，SAM； α-酮戊二酸，αKG；乙酰辅酶A和烟酰胺腺嘌呤二核苷酸，NAD+， 分别）作为共底物。新证据表明，饮食引起的此类表观代谢物的波动， 环境、微生物群和遗传学可以驱动 PTM 动态，但相关机制仍然存在 大多数情况下不清楚。表观代谢物的变化是通过信号通路还是通过底物水平感知的 驱动催化还是两者兼而有之？此外，表观代谢物的本地产生是否能够/加速基因表达 染色质的机制？ 非组蛋白乙酰化是一种主要的 PTM，可以调节细胞功能的许多方面并发生 在所有细胞室中。但是，尽管对修改内容有了广泛的了解，但最紧迫的挑战 是了解如何、为何和何时，这构成了本提案的首要主题。一个 了解可逆蛋白质乙酰化作为监管 PTM 的研究的主要部分将涉及 了解途径特异性乙酰辅酶A（和其他酰基辅酶A）的产生如何导致动态乙酰化 细胞外刺激后。此外，这项工作将重点关注详细的分子机制 核 NAD+ 依赖性脱乙酰酶 SIRT6/7（Sirtuins 6 和 7）的调节以及这些酶的表现 如此精致的核小体脱乙酰作用。该提案连接这两个项目的一个子主题是 了解控制 PTM 酶作用于染色质/核小体的基本原理。这 该提案独特地准备在这些突出问题上取得重大进展。为了实现这些目标， 这些项目协同运用体外生物化学/生物物理学、互补遗传学和 药理学以及基于细胞和动物的模型。这些调查的结果将提供 i.) 洞察 由代谢和表观基因组之间的联系引起的疾病的病因学，ii.) 的基础 针对此处描述的酶的药物开发，以及 iii.) 对细胞如何 在现有表观遗传信息的背景下“解释”传入信号并适当地“响应”。