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

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