Biophysical and functional characterization of immune-related regulatory elements and noncoding variants

项目摘要 对各种免疫疾病的易感性与基因差异有关，这些差异影响 基因表达。了解这些遗传差异导致疾病的机制 一直是基因组工作的中心目标，旨在描述疾病机制和识别 治疗的靶点。虽然大规模的研究已经确定了数千种基因 与免疫疾病相关的差异，在大多数情况下，不知道哪些变异是 因果关系和非因果关系的乘客变体。对于许多人来说，这是一个相当大的问题 存在于基因组非编码区的变异体，其功能难以预测。因此， 迫切需要高通量的实验方法来表征该功能 以及与免疫疾病相关的许多非编码变体的机制。来解决这个问题 挑战，我们将使用两种互补的高通量方法来研究基因 免疫基因表达的变异。我们将使用MPRAS(大规模并行记者评估)来 研究基因变异对基因表达的影响。我们将使用我们最近开发的 CASCADE(DNA元件复杂装配的综合评估)方法，in 结合基于质谱学的研究，描述遗传变异对转铁蛋白- 辅因子复合体结合。我们将使用这些方法来描述(1)基因的影响 ~30个免疫基因调控元件上的变异；(2)~5000个遗传变异 与免疫疾病或基因表达改变有关。将这些方法结合起来将 解决细胞和刺激特异的遗传变异的功能和生物物理机制 举止。此外，由于许多调节辅因子可以被药物抑制，因此表征Tf- 结合在基因变异体上的辅因子复合体提供了一种识别治疗 抵消它们的影响。总之，通过集成互补性、高吞吐量的方法 直接考虑细胞类型和细胞刺激的影响，拟议的研究将确定 非编码变异影响基因表达和免疫疾病的机制。 此外，这些研究将为将大规模基因研究转化为 治疗免疫性疾病的治疗方法。

Project Summary Susceptibility to diverse immune diseases has been associated with genetic differences that affect gene expression. Understanding the mechanisms by which these genetic differences lead to disease has been a central goal of genomic efforts aimed at describing disease mechanisms and identifying targets for therapeutic treatments. While large-scale studies have identified thousands of genetic differences associated with immune diseases, in most cases, it is not known which variants are causal and which are non-causal passenger variants. This is a considerable problem for the many variants that exists in non-coding regions of the genome for which function is difficult to predict. Thus, there is a critical need for the high-throughput experimental approaches to characterize the function and mechanism of the many non-coding variants associated with immune diseases. To tackle this challenge, we will use two complementary high-throughput approaches to study the impact of genetic variants on immune gene expression. We will use MPRAs (Massively Parallel Reporter Assays) to study the impact of genetic variants on gene expression. We will use our recently developed CASCADE (Comprehensive Assessment of Complex Assembly at DNA Elements) approach, in conjunction with mass spectrometry-based studies, to profile the impact of genetic variants on TF- cofactor complex binding. We will use these approaches to characterize (1) the impact of genetic variants on ~30 immune gene regulatory elements, and (2) ~5000 genetic variants found to be associated with immune disease or altered gene expression. Combining these approaches will address both function and biophysical mechanism of genetic variants in a cell- and stimulus-specific manner. Furthermore, as many regulatory cofactors can be inhibited with drugs, characterizing TF- cofactor complexes bound at genetic variants provides an opportunity to identify therapeutics to counteract their effects. Altogether, by integrating complementary, high-throughput approaches that directly account for effects of cell type and cell stimulation, the proposed studies will identify the mechanisms by which non-coding variants affect gene expression and immune diseases. Furthermore, these studies will lay a foundation for translating large-scale genetic studies into therapeutic approaches to treat for immune diseases.