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.

说明（由申请人提供）：核受体（NR）是配体依赖性转录因子，其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。它们在很大程度上通过首先结合基因调控区中的特异性DNA反应元件（RE）来实现。虽然过去的25年多已经导致了对NR DNA结合的基本理解，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有更多的了解。此外，虽然NR在生理学和疾病中的作用已经得到了大量的研究，并且它们本身也是许多成功药物的靶点，我们仍然没有完全了解它们在疾病易感性或对药物治疗的个体反应中的作用。个体之间的变异性至少部分由其遗传组成决定，单核苷酸多态性（SNP）被认为是造成这种变异性的主要原因。虽然基因编码部分的许多SNP与蛋白质功能的改变有关，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，缺乏的是系统的，功能性的eSNPs表征。我们提出，一个显着的比例SNP影响基因表达，通过改变其DNA响应元件的NR的亲和力。 在这项提案中，我们将研究NR DNA结合特异性，以及它是如何通过整合一系列的生物化学，分子，基因组和生物信息学的方法在三个特定的目标SNP的影响：在目标1，我们将详尽地确定一组选择的NR的DNA结合特异性使用基于蛋白质结合微阵列（PBM）的集成方法。PBM是一种新型的、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参考。 在目标2中，我们将PBM扩展到100万个反应，以确定与疾病和药物代谢相关的基因调控区中NR的亲和力改变SNP（aaSNP）。SNP PBM的结果将与公开可用的数据库（GWAS、dbSNP、GTEx等）交叉引用。以鉴定对疾病和药物代谢相关基因的表达水平具有影响的aaSNPs。 目的3：利用PBMs研究多种因素对NR DNA结合的影响，包括不同配体、NR配偶体、共调节分子等。 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，并将开发基于网络的基序发现和靶基因预测工具。他们将推进快速跟踪研究的长期目标，将NR与疾病和药物代谢联系起来，从而帮助个性化医疗，并确保靶向NR的药物可以更有效地使用。 公共卫生相关性：除了同卵双胞胎，没有两个人是完全相同的基因。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）。SNP越来越多地被认为在表型变异中起主要作用（例如，眼睛和头发的颜色、基础体重、肌肉张力、对酒精消耗的反应性等）以及易患癌症、糖尿病、心脏病和精神障碍等疾病。个体对药物治疗的反应也存在巨大的差异，这使得一些药物对某些人来说可以挽救生命，但对其他人却会产生严重的副作用。许多SNPs在基因编码的蛋白质中引入结构或功能变化;其他SNPs，绝大多数，位于决定基因表达水平的基因调控区。该提案的最终目标是研究SNP对一类特殊蛋白质的影响，这些蛋白质称为核受体，它们结合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称为蛋白质结合微阵列的新技术进行鉴定。核受体自身中的SNP也将检查其对核受体DNA结合的影响。这两种类型的SNPs的功能特征将有助于预测疾病的易感性和对药物治疗的反应。这一特征将有助于为个性化医疗奠定基础，这将最终导致更有效，从而降低医疗保健成本。