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.
Type 1 diabetes is an autoimmune disease with a strong genetic basis; however many associated variants have proved uninformative due to their non-genic locations. Using genome-wide approaches to map regulatory elements in human T cells, we identified enhancers that overlap type 1 diabetes-associated SNPs. We will functionally validate enhancer SNPs by several high-throughput methods to determine enhancer gene targets, and to tests for SNP disruption of transcription factor binding and enhancer activity.
