IDENTIFICATION AND VISUALIZATION OF REGULATORY ELEMENTS AND 3D GENOME STRUCTURE

Restricted (Penn State Only)
Author:
Wang, Yanli
Graduate Program:
Integrative Biosciences
Degree:
Doctor of Philosophy
Document Type:
Dissertation
Date of Defense:
May 26, 2017
Committee Members:
  • Feng Yue, Dissertation Advisor
  • James Riley Broach, Committee Chair
  • Ross Cameron Hardison, Committee Member
  • James Riley Broach, Committee Member
  • Jennifer Baccon, Outside Member
Keywords:
  • Genomcs
  • Genomic Structure
  • Hi-C
  • Genome Browser
  • Cis-Regulatory Elements
  • Enhancers
  • Promoters
Abstract:
The three-dimensional (3D) organization of vertebrate genomes is intricately linked to genome function, specifically gene regulation. At the DNA level, distal regulatory elements such as enhancers need to be in physical contact with their target genes. At a larger scale, topological associating domains (TADs) have been suggested to be the basic unit of genome organization. To gain a better understanding of the relationship between chromatin structure and function, we designed and implemented a widely-used online platform for visualizing the spatial organization of the genome, which is also integrated with thousands of genomic datasets such as ChIP-Seq and RNA-Seq. This system is currently visited by thousands of people each month, as it facilitate researchers to hypothesize the function of non-coding elements and disease-related variants. We employed zebrafish as a model organism to explore its cis-regulatory landscape and investigate how the structure of the vertebrate genome impact its function.