Access Conditions The author retains rights to his/her dissertation, thesis or other graduate work according to U.S. copyright law. Electronic access is being provided by the USC Libraries in agreement with the a...

Repository Name University of Southern California Digital Library

Repository Location USC Digital Library, University of Southern California, University Park Campus MC 2810, 3434 South Grand Avenue, 2nd Floor, Los Angeles, California 90089-2810, USA

Abstract (if available)

Abstract Investigation into the organization of cell nucleus has been a longstanding topic of intense interests. With the development of microscopy and genomics technology, it has been shown that three-dimensional genome architecture within nucleus tremendously affects gene function and cell property. The underlying component of genome architecture is chromatin interactions that occur at the genome-wide scale. The specific long-range genomic segments contacts are achieved by chromatin looping and mostly are between enhancer and promoter, leading to well-regulated gene expression patterns. With the development of high throughput sequencing technologies, the priority of nuclear organization study has transitioned from microscopy to genomic approaches, and a couple of schemes have been developed to map the genome-wide chromatin interactions. ❧ In the dissertation, I introduce the analysis of circularized chromosome conformation capture coupled with next-generation sequencing (4C-Seq), which is developed to assess the long-range DNA-DNA interactions where one of the DNA segments is the locus of interest. I present a computational pipeline to analyze 4C-Seq data in an automated and user-friendly way. In addition, 4C-Seq is applied to interrogate functional interactions with a risk enhancer at 8q24 locus in human prostate cancer, and to identify high-fidelity interactions with a distal enhancer of Oct4 that is a key pluripotent gene in mouse pluripotent stem cells. Furthermore, 4C-Seq and an emerging approach named capture-C are employed to study significant genome architecture mediated by a long non-coding RNA, 5430416N02Rik. Besides, the analysis of other techniques based on next-generation sequencing is shown throughout the dissertation. These methods include ChIP-Seq to identify DNA-protein interactions, RIP-Seq to study RNA-protein interactions, RNA-Seq to examine gene expression levels, and Hi-C to assess DNA-DNA interactions between each pair of genomic regions across genome. These methods combine to provide us with a comprehensive map as to how physical interactions underlying genome architecture affect biological properties. ❧ The dissertation focuses on presenting the computational methods for analyzing datasets of 4C-Seq and other next-generation sequencing techniques. Meanwhile, the dissertation shows results of projects aimed to study genomic interactions with some functional element implicated in a phenotype, such as pluripotency or cancer. The methodologies and applications might provide insight into unveiling hidden signatures behind genome architecture.