Functional assessment of distal regulatory SNPs associated with type 1 diabetes.

 描述(申请人提供)：1型糖尿病(T1D)是一种自身免疫性疾病，导致胰岛素产生细胞的丧失。遗传学研究，包括双胞胎的研究，表明这种疾病有很强的遗传基础。全基因组关联研究(GWAS)产生了大量与T1D相关的单核苷酸多态(SNPs)，但往往无法确定致病突变。这可能是由于疾病的复杂性；或者部分原因是许多相关的SNP位于基因编码区之外。最近对GWASs的评估表明，45%的疾病或性状相关SNPs位于内含子，而43%位于基因间隔区。全球确定染色质状态的方法已经表明，相关的SNP可以重叠远端调控区域，如增强子。我们已经构建了基于H3K4me1在分离的人T细胞中定位的增强子图。我们分析了来自NHGRI Gwas目录的与T1D相关的SNP是否与我们的全球T辅助细胞增强子预测重叠。利用1000个基因组数据，我们确定了额外的连锁不平衡SNP，以扩大增强子元件上与T1D相关的SNP的数量。目标：我们的目标是从功能上验证与T1D相关的rSNP。我们将使用一系列高通量分析和系统评估来确定功能最相关的rSNP。我们还将确定与T1D SNPs重叠的增强子的靶基因，以确定在T1D发病机制中重要的新基因。我们将通过以下具体目标做到这一点。具体目的1.确定T1D rSNPs对增强子活性的影响。特定目的2.确定T1D相关增强子SNPs上的TF结合是否被破坏。特定目的3.识别含有相关SNPs的增强子的靶基因。

 DESCRIPTION (provided by applicant): Type 1 diabetes (T1D) is an autoimmune disease resulting in the loss of insulin- producing cells. Genetic studies, including those in twins, sugget a strong genetic basis for this disease. Genome-wide association studies (GWASs) have produced large numbers of T1D-associated single-nucleotide polymorphisms (SNPs), but often fail to determine a causative mutation. 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 distal regulatory regions such as enhancers. We have constructed enhancer maps based H3K4me1 localization in isolated, human T cells. We analyzed the T1D-associated SNPs from the NHGRI GWAS catalog for overlap with our global T helper cell enhancer predictions. Using 1000 Genomes data we identified additional SNPs in linkage disequilibrium to expand the number of T1D-associated SNPs at enhancer elements. Goal: Our goal is to functionally validate T1D-associated rSNPs. We will use a series of high- throughput assays and systematic evaluation to determine the most functionally relevant rSNPs. We will also determine the target genes of enhancers overlapping T1D SNPs in order to identify new genes important in the etiology of T1D pathogenesis. We will do so through the following specific aims. Specific Aim 1. Determine the effect of T1D rSNPs on enhancer activity. Specific Aim 2. Determine if TF binding is disrupted at T1D-associated enhancer SNPs. Specific Aim 3. Identification of target genes for enhancers harboring associated SNPs.