Systematic Mapping of the Functional Common Noncoding Variants in the TNFAIP3 Locus

TNFAIP3 基因座功能性常见非编码变异的系统作图

基本信息

批准号：
9258074
负责人：
John Philip Ray
金额：
$ 5.71万
依托单位：
BROAD INSTITUTE, INC.
依托单位国家：
美国
项目类别：
财政年份：
2017
资助国家：
美国
起止时间：
2017-02-01 至 2020-01-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9258074
关键词：
A20 protein Affect Alleles Animal Disease Models Autoimmune Diseases Autoimmune Process Autoimmunity B-Lymphocytes Binding Biochemical Biological Assay CRISPR/Cas technology Cells Chromatin Complex Data Diagnostic Factor Disease Disease model Enhancers Environment Epigenetic Process Future Gene Expression Gene Expression Profile Genes Genetic Genetic Engineering Genetic Predisposition to Disease Genetic Variation Genome Genome engineering Genomics Goals Haplotypes Heritability Human Human Genetics Immune Knowledge Learning Linkage Disequilibrium Maps Methods Mus Mutation Nature Nucleic Acid Regulatory Sequences Pathogenesis Pathogenicity Patients Population Protein Isoforms RNA Splicing Regulation Regulator Genes Reporter Research Risk Site Syndrome Systemic Lupus Erythematosus T-Lymphocyte Testing Therapeutic United States Variant Woman Work base cell type epigenetic variation genetic variant genome wide association study genome-wide genotyped patients histone modification improved in vivo insight monocyte mouse model new therapeutic target personalized medicine repaired trait transcription factor transcriptomics

项目摘要

Project Summary/Abstract The mechanisms for induction of autoimmunity remain enigmatic, in part due to the unconfirmed activity of many autoimmune-associated noncoding common genetic variants. To dissect the specific mechanisms of how all common and disease-associated noncoding variation modulates gene expression, I propose to employ scalable assays in three cell types that will assess 2708 noncoding common variants for gene-modulatory function in an important autoimmune-associated locus containing the negative regulatory gene TNFAIP3/A20. One assay will test ~2700 variants for their effects on reporter expression pre- and post-stimulation. A second assay will evaluate ~43,000 systematic locus-wide deletions in the genome to determine regulatory regions (and potentially active variants within) in cell types. I will then map the active disease-associated variants from these assays to the open chromatin of autoimmune patient cell types to create a ranked list of those that putatively operate in disease. I will then determine the mechanism of action for these active, open chromatin localized variants through genetically engineering risk and non-risk alleles using CRISPR-Cas9 homology directed repair and performing biochemical assays. This method is scalable to study many loci in future work, which will contribute to our knowledge of disease gene networks, accurate animal disease models, and more efficacious therapeutics.

项目摘要/摘要自身免疫性诱导的机制仍然神秘，部分原因是许多人的活性未经证实自身免疫相关的非编码常见遗传变异。剖析如何所有人的特定机制常见和与疾病相关的非编码变异调节基因表达，我建议采用可扩展的三种细胞类型的测定将评估2708个非编码常见变体，用于基因调节功能重要的自身免疫相关基因座，其中包含负调节基因TNFAIP3/A20。一个测定法测试〜2700种变体对记者表达前和刺激后的影响。第二种测定将评估基因组中的〜43,000个全系统缺失，以确定调节区域（并且潜在的活性在细胞类型中的变体。然后，我将从这些测定中绘制与活动相关的活性相关变体自身免疫性患者细胞类型的染色质，以创建在疾病中起作用的排名列表。我会然后确定通过遗传的这些活性开放的染色质局部变体的作用机理使用CRISPR-CAS9同源性维修和执行生化的工程风险和非风险等位基因测定。这种方法可扩展研究以后的工作中的许多基因座，这将有助于我们的了解疾病基因网络，准确的动物疾病模型和更有效的治疗学。