Functional validation of Rheumatoid Arthritis-associated distal regulatory SNPs i

 描述(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(SNPs)。然而，这些研究中的许多都未能确定致病突变。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可以重叠调控区域。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，这些T细胞被激活或极化为Th1或Th2谱系。我们专注于早期的极化时间点，以确定早期T细胞分化的顺式调节组和调节T细胞命运的承诺。为了确定类风湿性关节炎相关的SNPs是否可能是rSNPs，我们分析了NHGRI Gwas目录中相关SNPs的邻近区域，以与我们的全球T辅助细胞增强子预测重叠。目的：在早期T细胞命运的增强子中确定了440个潜在的调控SNP，我们的目标是通过一系列高通量分析和系统评估从功能上验证与RA相关的rSNPs，以确定功能上最相关的rSNPs。通过这一过程，我们还将确定含有rSNPs的增强子的靶基因，以确定在RA发病机制中重要的新基因。我们将通过以下具体目标做到这一点。具体目的1.确定rSNPs对增强子活性的影响。特定目的2.鉴定转录因子及其在增强子SNPs上的破坏结合。特定目的3.识别含有相关SNPs的增强子的靶基因

 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