High throughput interrogation of non-coding variants and 3D genome organization

项目摘要/摘要 最近的大规模努力，如ENCODE和Eigenome路线图项目，预测了数百万人 人类基因组中潜在的非编码调控元件。然而，目前还不清楚其中有多少人 真正起作用的，因为这些预测主要基于高通量基因组分析，如DNA酶- 组蛋白修饰和转录因子的SEQ或CHIP-SEQ。目前的大多数研究都是间接的 通过转基因报告试验测量增强子的活性，因此不能提供对 天然染色质状态。幸运的是，高通量筛选方法的最新进展是基于 CRISPR/Cas9基因组编辑技术使这种功能表征成为可能。另一项重要的 基因调控层是3D基因组组织，它将远端的增强子与其靶标连接起来 基因。基于染色质构象捕获(3C)的高通量方法已经出现。 C、Chia-PET、HiChIP和Capture Hi-C)，并为研究更高阶提供了前所未有的机会 染色质结构全基因组。尽管最近取得了进展，但染色质之间的复杂关系 相互作用和基因调控才刚刚开始解体。CTCF和粘附素复合体已被证明 在染色质环和拓扑相关结构域(TADS)的形成中起关键作用，但我们知道的很少 是否有其他重要的调节因子对这种染色质相互作用很重要。 鉴于上述挑战和我独特的多学科训练，我的长期目标是 使用高通量基因组实验、计算建模和功能分析的组合来 解决以下两个基本问题：1)通过高吞吐量确定功能增强剂 分析和研究基因变异如何影响它们的功能；2)确定形成的新调节因子 3D基因组的组织特征。拟议的工作将加深我们对基因如何 变异体有助于基因调控、3D基因组组织和人类潜在的分子机制 疾病。

PROJECT SUMMARY / ABSTRACT Recent large-scale efforts such as the ENCODE and Epigenome Roadmap projects have predicted millions of potential non-coding regulatory elements in the human genome. However, it is not clear how many of them are truly functional, as the predictions were mainly based on high-throughput genomics assays such as DNase- Seq or ChIP-Seq for histone modifications and transcription factors. Most of the current studies indirectly measure enhancer activity through transgenic reporter assays and therefore do not provide insights into the native chromatin state. Fortunately, recent advances in high-throughput screening methods based on CRISPR/Cas9 genome editing technology make such functional characterization possible. Another important layer of gene regulation is the 3D genome organization, which can link the distal enhancers with their target genes. High-throughput methods based on Chromatin Conformation Capture (3C) have emerged (such as Hi- C, ChIA-PET, HiChIP, and Capture Hi-C) and present an unprecedented opportunity to study higher-order chromatin structure genome-wide. Despite the recent advances, the complex relationship between chromatin interactions and gene regulation has just begun to unravel. CTCF and cohesin complex have been shown to be critical in the formation of chromatin loops and topologically associating domains (TADs), but we know little of whether there are other important regulators are important for such chromatin interactions. Given the aforementioned challenges and my unique multi-disciplinary training, my long-term goal is to use a combination of high throughput genomic experiments, computational modeling, and functional assays to address the following two fundamental questions: 1) Identify functional enhancers through high-throughput assays and study how genetic variants can affect their functions; 2) Identify novel regulators for the formation of 3D genome organization features. The proposed work will deepen our understanding on how genetic variants contribute to gene regulation, 3D genome organization, and molecular mechanisms underlying human diseases.