Dynamics and molecular mechanisms linking metabolism and the epigenome

项目摘要/摘要 细胞对可用的大量营养素和细胞外信号的反应依赖于细胞特有的表观遗传状态 细胞，由决定特定基因的基因组上方的一层生化信息定义 表情。表观基因组由依赖于DNA序列的蛋白质、非编码RNA、DNA 甲基化和组蛋白翻译后修饰(PTM)，如赖氨酸乙酰化和甲基化。这个 后两种机制是由酶催化的，酶必须‘解释’传入的信号，读作‘现有的’ 表观遗传景观，并做出适当的反应。修饰组蛋白和非组蛋白的酶 如甲基转移酶、去甲基酶、乙酰转移酶和脱乙酰酶等使用中枢代谢物(S- 腺苷甲硫氨酸；α-酮戊二酸，αKG；乙酰辅酶A和烟酰胺腺嘌呤二核苷酸， 分别)作为共基质。新的证据表明，这些表观代谢物的波动是由饮食引起的， 环境、微生物区系和遗传学可以驱动PTM动态，但相关机制仍然存在 大多数情况下都不清楚。表观代谢物的变化是通过信号通路还是通过底物水平来感知的？ 驱动催化还是两者兼而有之？此外，局部生产的表观代谢物是否能促进/加速基因表达？ 染色质的作用机制？ 非组蛋白乙酰化是一种主要的PTM，它可以调节细胞许多方面的功能并发生 在所有的细胞隔间里。但是，尽管对修改内容有广泛的了解，但最紧迫的挑战是 是理解如何、为什么和何时，这构成了这项提议的一个首要主题。一个 了解可逆蛋白质乙酰化作为调节PTM的研究的主要部分将涉及 了解特定途径的乙酰辅酶A(和其他乙酰辅酶A)的产生如何导致动态乙酰化 在细胞外刺激之后。此外，这项工作将集中在详细的分子机制，通过 核内依赖NAD的脱乙酰酶SIRT6/7(sirtuins 6和7)受到调控，以及这些酶如何发挥作用 如此精致的核小体脱乙酰化。将这两个项目联系在一起的这个提案的一个子主题是 了解PTM酶作用于染色质/核小体的基本原理。这 提案是唯一准备在这些突出问题上取得重大进展的国家。为了实现这些目标， 这些项目协同使用了体外生物化学/生物物理、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”传入的信号，并做出适当的反应。

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.