Functional validation of Rheumatoid Arthritis-associated distal regulatory SNPs i

类风湿关节炎相关远端调节 SNP 的功能验证 i

• 批准号: 8810054
• 负责人: Raymond David Hawkins
• 金额: $ 43.63万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-03-01 至 2019-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8810054
• 关键词: Address; Asthma; Autoimmune Diseases; Autoimmune Process; Automobile Driving; Binding; Biological Assay; CD4 Positive T Lymphocytes; Cataloging; Catalogs; Categories; Cells; ChIP-seq; Chromatin; Code; Crohn' s disease; Disease; Distal; Enhancers; Equilibrium; Etiology; Evaluation; Gene Expression; Gene Targeting; Genes; Genetic Risk; Goals; Health; Helper-Inducer T-Lymphocyte; Human; Immune system; Insulin-Dependent Diabetes Mellitus; Intercistronic Region; Introns; Light; Maps; Mediating; Methods; Multiple Sclerosis; Mutation; National Human Genome Research Institute; Nucleic Acid Regulatory Sequences; Pathogenesis; Play; Process; Psoriasis; Regulation; Regulatory Element; Reporter; Research; Rheumatoid Arthritis; Role; Series; Single Nucleotide Polymorphism; T cell differentiation; T cell regulation; T-Lymphocyte; Technology; Testing; Time; Twin Studies; Ulcerative Colitis; Validation; base; cell type; epigenomics; genome wide association study; genome-wide; high throughput screening; innovation; next generation sequencing; risk variant; trait; transcription factor

 DESCRIPTION (provided by applicant): Genome-wide association studies (GWASs) have produced large numbers of disease associated single-nucleotide polymorphisms (SNPs). However, many of these studies have failed to identify causative mutations. This may be due to the complexity of the disease; or in part, due to many associated SNPs lying outside of gene coding regions. A recent assessment of GWASs illustrated that 45% of disease or trait associated SNPs fell in introns, while 43% lie in intergenic regions. Global methods for determining chromatin states have shown that associated SNPs can overlap regulatory regions. We have constructed enhancer maps based H3K4me1 localization in isolated, human T cells, which were activated, or polarized toward Th1 or Th2 lineages. We focused on an early time point of polarization to determine the cis-regulome of early T cell differentiation and regulation f T cell fate commitment. To determine if rheumatoid arthritis-associated SNPs are potentially rSNPs, we analyzed the vicinities of associated SNPs from the NHGRI GWAS catalog for overlap with our global T helper cell enhancer predictions. Goal: Having identified 440 potential regulatory SNPs within enhancers driving early T cell fates, our goal is to functionally validate RA-associated rSNPs through a series of high-throughput assays and systematic evaluation to determine the most functionally relevant rSNPs. Through this process we will also determine the target genes of enhancers harboring rSNPs in order to identify new genes important in the etiology of RA pathogenesis. We will do so through the following specific aims. Specific Aim 1. Determine the effect of rSNPs on enhancer activity. Specific Aim 2. Identification of TFs and their disrupted binding at enhancer SNPs. Specific Aim 3. Identification of target genes for enhancers harboring associated SNPs

 描述（由申请人提供）：全基因组关联研究（GWAS）产生了大量与疾病相关的单核苷酸多态性（SNP）。然而，这些研究中有许多未能确定致病突变。这可能是由于疾病的复杂性;或者部分是由于许多相关的SNP位于基因编码区之外。最近对GWAS的评估表明，45%的疾病或性状相关SNP位于内含子中，而43%位于基因间区域。用于确定染色质状态的全局方法已经表明，相关的SNP可以与调控区域重叠。我们已经构建了增强子地图的基础上H3 K4 me 1在孤立的，人类T细胞，这是激活，或极化向Th 1或Th 2谱系定位。我们专注于极化的早期时间点，以确定早期T细胞分化和T细胞命运定型调节的顺式调节组。为了确定类风湿性关节炎相关的SNP是否是潜在的rSNP，我们分析了NHGRI GWAS目录中相关SNP的邻近区域，以与我们的全球T辅助细胞增强子预测重叠。目标：在驱动早期T细胞命运的增强子内鉴定了440个潜在的调节性SNP后，我们的目标是通过一系列高通量测定和系统评价来功能性地验证RA相关的rSNP，以确定功能上最相关的rSNP。通过这一过程，我们还将确定携带rSNPs的增强子的靶基因，以鉴定在RA发病机制中重要的新基因。我们将通过以下具体目标这样做。具体目标1.确定rSNP对增强子活性的影响。具体目标2。TF的鉴定及其在增强子SNP处被破坏的结合。具体目标3。携带相关SNP的增强子的靶基因的鉴定