Nuclear Receptor DNA Binding in Human Physiology and Disease

人类生理和疾病中的核受体 DNA 结合

• 批准号: 8258935
• 负责人: FRANCES M. SLADEK
• 金额: $ 38万
• 依托单位: UNIVERSITY OF CALIFORNIA RIVERSIDE
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-03-05 至 2016-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8258935
• 关键词: Accounting; Adverse effects; Affect; Affinity; Alcohol consumption; Binding; Binding Sites; Biochemical; Bioinformatics; Biological Assay; Body Weight; Code; Custom; DNA; DNA Binding; DNA Sequence; Data; Data Set; Databases; Diabetes Mellitus; Disease; Disease susceptibility; Drug Delivery Systems; Ensure; Eye Color; Foundations; Gene Expression; Gene Targeting; Genes; Genetic; Genetic Polymorphism; Genome; Genomics; Genotype; Goals; Hair Color; Health Care Costs; Heart Diseases; Hormones; Human; Immunofluorescence Immunologic; In Vitro; Individual; Lead; Learning; Life; Ligands; Link; Location; Malignant Neoplasms; Mammalian Cell; Medicine; Mental disorders; Molecular; Monozygotic twins; Muscle Tonus; Mutation; Nuclear Receptors; Nucleic Acid Regulatory Sequences; Nucleotides; Online Systems; Pharmaceutical Preparations; Physiological; Physiology; Play; Predisposition; Protein Binding; Proteins; Quantitative Trait Loci; Reaction; Research; Response Elements; Role; Single Nucleotide Polymorphism; Specificity; Spottings; Technology; Tissues; United States National Institutes of Health; Variant; Vitamins; base; design; drug metabolism; genetic association; genome wide association study; genome-wide; kinetosome; new technology; novel; preference; protein function; receptor binding; research study; response; tool; transcription factor; web site

DESCRIPTION (provided by applicant): Nuclear receptors (NRs) are ligand-dependent transcription factors that regulate the expression of a wide variety of genes involved in nearly al aspects of human physiology and disease. They do so in large part by first binding specific DNA response elements (RE) in regulatory regions of genes. While the past 25+ years has led to a basic understanding of NR DNA binding, recent studies indicate that we have much more to learn about the NR-DNA interaction, and the factors that influence it. Furthermore, while NRs have been investigated heavily for their role in physiology and disease and are themselves targets of many successful drugs, we still do not have a complete understanding of their role in disease susceptibility nor in individual responses to drug treatments. Variability between individuals is determined at least partially by their genetic make-up and single nucleotide polymorphisms (SNPs) are thought to account for much that variability. While many SNPs in the coding portion of genes have been associated with altered protein function, recent genome-wide studies show that certain SNPs are associated with changes in levels of expression of nearby genes (eSNPs). However, what is lacking is a systematic, functional characterization of eSNPs. We propose that a significant proportion SNPs affect gene expression by altering the affinity of NRs for their DNA response elements. In this proposal, we will examine NR DNA binding specificity and how it is influenced by SNPs by integrating a range of biochemical, molecular, genomic and bioinformatics approaches in three Specific Aims: In Aim 1, we will exhaustively determine the DNA binding specificity of a select group of NRs using an integrated approach based on protein binding microarrays (PBMs). PBMs are a novel, high throughput (10- 100,000's reactions) in vitro DNA binding assay. The PBM results will be used to search the genome for potential NR target genes and then cross referenced with genome-wide location and expression analysis. In Aim 2, we will expand PBMs to 1 million reactions in order to identify affinity altering SNPs (aaSNPs) for NRs in regulatory regions of genes associated with disease and drug metabolism. The results from the SNP PBMs will be cross referenced with publicly available databases (GWAS, dbSNP, GTEx, etc.) in order identify aaSNPs that have effects on expression levels of genes relevant to disease and drug metabolism. In Aim 3, PBMs will be used to investigate the effect of a variety of factors on NR DNA binding, including different ligands, NR partners, co-regulatory molecules. All results will be made publically available on a website dedicated to the project, as well as other public databases, and web-based tools for motif finding and target gene prediction will be developed. They will advance the long term goal of fast tracking research linking NRs to disease and drug metabolism, and thereby help personalize medicine and ensure that drugs that target NRs can be used in a more effective fashion. PUBLIC HEALTH RELEVANCE: Aside from identical twins, no two individuals are completely identical genetically. Most differences between individuals are due to single nucleotide changes or polymorphisms (SNPs) in the genome. SNPs are being increasingly recognized as playing a major role in phenotypic variations (e.g., eye and hair color, basal body weight, muscle tone, responsiveness to alcohol consumption, etc.) as well as susceptibility to diseases such as cancer, diabetes, heart disease and mental disorders. There is also tremendous variability in individuals' response to drug treatments that makes some drugs life-saving for certain people but cause serious side effects for others. Many SNPs introduce structural or functional changes in the proteins encoded by genes; other SNPs, the vast majority, are in the regulatory regions of genes that determine the level of expression of genes. The ultimate goal of this proposal is to examine the effect of SNPs on a special class of proteins called nuclear receptors that bind DNA and regulate the expression of many important genes in response to hormones, vitamins and drugs. SNPs in the DNA sequences that the nuclear receptors bind will be identified using a very powerful new technology called protein binding microarrays. SNPs in the nuclear receptors themselves will also be examined for their effect on nuclear receptor DNA binding. The functional characterization of both types of SNPs will help predict disease susceptibility and response to drug treatments. This characterization will help lay the foundation for personalized medicine which will ultimately lead to more effective and hence less costly health care costs.

描述（由申请人提供）：核受体（NR）是配体依赖性转录因子，调节涉及人类生理学和疾病的几乎所有方面的多种基因的表达。它们在很大程度上是通过首先结合基因调控区域中的特定 DNA 反应元件 (RE) 来实现这一点的。虽然过去 25 年多的时间人们对 NR DNA 结合有了基本的了解，但最近的研究表明，我们对 NR-DNA 相互作用以及影响它的因素还有更多需要了解。此外，尽管 NR 在生理学和疾病中的作用已被广泛研究，并且它们本身也是许多成功药物的靶标，但我们仍然没有完全了解它们在疾病易感性或个体对药物治疗的反应中的作用。个体之间的变异至少部分是由他们的基因组成决定的，单核苷酸多态性（SNP）被认为是造成这种变异的主要原因。虽然基因编码部分中的许多 SNP 与蛋白质功能改变有关，但最近的全基因组研究表明，某些 SNP 与附近基因 (eSNP) 表达水平的变化有关。然而，缺乏的是 eSNP 的系统性、功能性表征。我们认为，很大一部分 SNP 通过改变 NR 与其 DNA 反应元件的亲和力来影响基因表达。 在本提案中，我们将通过在三个具体目标中整合一系列生化、分子、基因组和生物信息学方法来检查 NR DNA 结合特异性以及它如何受到 SNP 的影响：在目标 1 中，我们将详尽地确定 NR DNA 结合特异性使用基于蛋白质结合微阵列 (PBM) 的集成方法选择 NR 组。 PBM 是一种新型、高通量（10-100,000 次反应）的体外 DNA 结合测定。 PBM 结果将用于在基因组中搜索潜在的 NR 靶基因，然后与全基因组定位和表达分析交叉引用。 在目标 2 中，我们将 PBM 扩展到 100 万个反应，以便识别与疾病和药物代谢相关的基因调控区域中 NR 的亲和力改变 SNP (aaSNP)。 SNP PBM 的结果将与公开数据库（GWAS、dbSNP、GTEx 等）交叉引用，以确定对疾病和药物代谢相关基因的表达水平有影响的 aaSNP。 在目标 3 中，PBM 将用于研究多种因素对 NR DNA 结合的影响，包括不同的配体、NR 伴侣、共调节分子。 所有结果将在该项目专用网站以及其他公共数据库上公开发布，并将开发基于网络的基序发现和目标基因预测工具。他们将推进将 NR 与疾病和药物代谢联系起来的快速追踪研究的长期目标，从而帮助个性化医疗并确保针对 NR 的药物能够以更有效的方式使用。 公共卫生相关性：除了同卵双胞胎之外，没有两个人的基因完全相同。个体之间的大多数差异是由于基因组中的单核苷酸变化或多态性（SNP）造成的。人们越来越认识到，SNP 在表型变异（例如眼睛和头发颜色、基础体重、肌肉张力、对饮酒的反应性等）以及对癌症、糖尿病、心脏病等疾病的易感性方面发挥着重要作用和精神障碍。个体对药物治疗的反应也存在巨大差异，这使得某些药物对某些人来说可以挽救生命，但对其他人来说却会产生严重的副作用。许多 SNP 会导致基因编码的蛋白质发生结构或功能变化；其他 SNP 绝大多数位于决定基因表达水平的基因调控区域。该提案的最终目标是检查 SNP 对一类特殊蛋白质（称为核受体）的影响，这种蛋白质结合 DNA 并调节许多重要基因的表达，以响应激素、维生素和药物。核受体结合的 DNA 序列中的 SNP 将使用一种非常强大的新技术（称为蛋白质结合微阵列）进行鉴定。核受体本身的 SNP 也将检查其对核受体 DNA 结合的影响。两种类型 SNP 的功能表征将有助于预测疾病易感性和对药物治疗的反应。这种特征将有助于为个性化医疗奠定基础，最终将带来更有效的结果，从而降低医疗保健成本。