Author ORCID Identifier
0000-0002-3644-1284
Date of Graduation
12-2023
Document Type
Dissertation (PhD)
Program Affiliation
Genetics and Epigenetics
Degree Name
Doctor of Philosophy (PhD)
Advisor/Committee Chair
Wenbo Li
Committee Member
Francesca Cole
Committee Member
Jichao Chen
Committee Member
Ken Chen
Committee Member
Leng Han
Abstract
The human genome is intricately folded within the confines of a minuscule nucleus, maintaining critical activities, including transcription, replication, and DNA repair. These processes are orchestrated by the epigenome. Prior research has established that both the epigenome and its three-dimensional structure are highly instructive to gene regulation, underscoring the importance of investigating the 3D epigenome under various cellular and disease conditions.
In this dissertation, I perform an in-depth characterization of 3D epigenomes in two distinct pathological contexts: Trisomy 21 neural stem cells and cells acutely infected with SARS-CoV-2. For Trisomy 21 cells, I applied a cutting-edge, combinatorial indexing-based single-cell RNA sequencing approach to chart the developmental progression of trisomic brain organoids. This single-cell transcriptomic analysis uncovered impaired differentiation pathways in trisomic stem cells, leading to suboptimal development into neural progenitor cells and neurons. By employing chromatin conformation capture methodologies, I have detailed the 3D genome structures across different layers in Trisomy 21 neural stem cells.
Turning to SARS-CoV-2, I charted the three-dimensional chromatin structure and comprehensive epigenomes during acute infection. My research reveals pronounced disruptions in host chromatin organization, highlighted by the weakening of compartment A, increased intermingling of compartments A and B, reduced interactions within topologically associating domains (TADs). Notably, a targeted depletion of the cohesin complex within TADs points to a potential interference with loop extrusion processes by the infection. Accompanying these structural and epigenome disturbances is the compromising of interferon-stimulated genes and an increase of proinflammatory genes, paralleling a rise in H3K4me3 modifications at the promoters of pro-inflammatory genes. This investigation not only characterizes the impact of SARS-CoV-2 acute infection on host chromatin but also lays the groundwork for future work into the long-lasting epigenomic consequences of infection.
Keywords
3D genome, epigenetics, gene regulation