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CC BY V4.0, Open Access
Dissertation
A COMPUTATIONAL APPROACH TO EXPLORING THE IMPACT OF CHROMATIN ON DNA DAMAGE, REPAIR, AND MUTAGENESIS
Washington State University
Doctor of Philosophy (PhD), Washington State University
07/2024
DOI:
https://doi.org/10.7273/000006893
Abstract
Maintaining genome integrity is vital to the survival and proliferation of all life. DNA is constantly exposed to a variety of damaging agents, both endogenous (e.g., radical oxygen species) and exogenous (e.g., ultraviolet (UV) light from the sun or benzo[a]pyrene from cigarette smoke). Repair mechanisms such as mismatch repair (MMR) and nucleotide excision repair (NER) are responsible for fixing this damage which, left unrepaired, can lead to mutagenesis and cancer. While much is known about the interplay between DNA damage and repair that leads to mutations, the genomes of higher eukaryotes are highly dynamic and interact with a myriad of DNA-binding proteins such as histones and transcription factors. As a result, the extent to which DNA damage and repair vary throughout the genome is not fully understood. To elucidate the impact of nucleosomes on mutagenesis, we developed mutperiod, a software package which quantifies periodic trends about nucleosomes, and used it to link MMR activity to nucleosomal mutation patterns in esophageal cancer. We also leveraged this software to explore damage and repair patterns for UV-induced cyclobutane pyrimidine dimers (CPDs) in Drosophila cells, which revealed that nucleosome spacing varies across different chromatin domains, significantly impacting CPD repair. This analysis leveraged excision-repair sequencing (XR-seq) data which mapped NER activity throughout the genome, albeit without precise lesion positioning. To increase this precision, we developed an analysis pipeline utilizing heightened cytosine deamination rates in CPDs to locate damaged bases in XR-seq reads at single nucleotide resolution. By applying this pipeline to existing XR-seq data, we found evidence for an HYV (not guanine; pyrimidine; not thymine) sequence bias at the 5’ NER incision location and coupling between the two NER incision events during repair in eukaryotic cells. Finally, by analyzing repair and damage data for the primary DNA adduct in lung cancer, benzo[a]pyrene diol epoxide (BPDE), we showed that a preference for damage formation in unbound DNA establishes the unusual mutation enrichment at linker regions in lung cancer. Together, these results contribute to our understanding of how DNA damage and repair are modulated by chromatin and provide computational methods for the continued study of these interactions.
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Details
- Title
- A COMPUTATIONAL APPROACH TO EXPLORING THE IMPACT OF CHROMATIN ON DNA DAMAGE, REPAIR, AND MUTAGENESIS
- Creators
- Benjamin S. Morledge-Hampton
- Contributors
- John J. Wyrick (Chair)Ananth Kalyanaraman (Committee Member)Steven A. Roberts (Committee Member)Eric A. Shelden (Committee Member)
- Awarding Institution
- Washington State University
- Academic Unit
- School of Molecular Biosciences
- Theses and Dissertations
- Doctor of Philosophy (PhD), Washington State University
- Publisher
- Washington State University
- Number of pages
- 236
- Identifiers
- 99901152338601842
- Language
- English
- Resource Type
- Dissertation