Understanding gene regulation and genetic variation through the lens of three-dimensional genome architecture [electronic resource]

The three-dimensional organization of the genome defines a complex network of physical and functional interactions between distal regulatory elements, non-coding genetic variants they harbor and their target genes. In this thesis, I present a combination of computational and experimental techniques to explore the role of 3D genome architecture in gene regulation and disease. Chromosome conformation capture techniques such as Hi-C have revolutionized our ability to obtain genome-wide maps of 3D chromatin contacts. However, robust estimation of data quality and systematic comparison of these contact maps is challenging due to the multi-scale organization of the genome and the resulting esoteric properties of experimental noise affecting Hi-C data. To address these issues, I introduce new statistical measures based on a graph diffusion framework for multi-scale comparisons of 3D contact maps. I use our framework for estimating Hi-C data quality by evaluating reproducibility across replicate experiments and for robustly identifying differential contacts between cell types. Next, I present one of the first efforts to understand how non-coding genetic variation can affect diverse molecular phenotypes through 3D chromatin contacts. In this study, we integrated chromatin profiling experiments for three regulatory histone marks in lymphoblastoid cell lines (LCLs) from 75 sequenced individuals with LCL-specific 3D chromatin contact maps to uncover one of the largest collections of local and distal histone quantitative trait loci (hQTLs). We found that distal hQTLs are enriched within insulated topologically associated domains and exhibit largely concordant variation of chromatin state coordinated by proximal and distal non-coding genetic variants. hQTLs were also enriched for common variants associated with autoimmune diseases and enabled identification of regulatory elements and genes that are putative downstream targets of disease-associated variants from genome-wide association studies. I continue by presenting an ongoing project to understand the effects of perturbing 3D genome architecture on gene regulation by using different types (activation, inhibition and knockout) of CRISPR-Cas9 competitive growth screens targeting thousands of binding sites of the CTCF transcription factor at critical 3D chromatin loops. We found that 3%-5% of the tested sites exhibit a significant effect on cellular growth across the screen and investigate models that can explain the effects based on genomic, regulatory and 3D properties of the loci. We validated a subset of loci. Finally, I present a method I have been working on for creating ectopic chromatin contacts using the CRISPR system coupled to a synthetic dimerization system. Together, these studies expand our understanding of gene regulation and genetic variation through the lens of 3D genome architecture.

Keywords: Genetics.
Advisor: Kundaje Anshul
Snyder Michael
Bassik Michael advisor. Thesis advisor
Chang Howard Y. (Howard Yuan-Hao)
Pritchard Jonathan (Jonathan K.) advisor. Thesis advisor