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CC BY V4.0, Open Access
Dissertation
Protein-DNA Interactions Shape the Melanoma Genome by Modulating Rates of UV Photoproduct Formation
Washington State University
Doctor of Philosophy (PhD), Washington State University
2023
DOI:
https://doi.org/10.7273/000005370
Abstract
Cancer often develops from recurrent somatic mutations in coding regions of the genome, known as ‘driver’ mutations. It is becoming increasingly clear that recurrent mutations in non-coding DNA, such as transcription factor binding sites (TFBSs), are also abundant in skin cancer genomes. However, the molecular mechanism(s) that promote mutagenesis at TFBSs and other chromatin features (i.e. nucleosomes) in melanoma were previously unclear. Previous studies by our lab and others have suggested that molecular interactions between DNA-binding proteins and their binding sites may affect the rate of ultraviolet (UV) damage formation, resulting in recurrent damage ‘hotspots’. Other studies have suggested that the physical sequestration of the DNA by proteins inhibits accessibility to repair machinery, thereby increasing the lifespan of DNA damage and increasing the potential to induce mutations during replication. We show here that a TF known as CCCTC-binding factor (CTCF) induces cyclobutane pyrimidine dimer (CPD) hotspots within CTCF binding sites during binding. The major CPD hotspot correlates precisely with the major recurrent mutation hotspot observed at CTCF binding sites in skin cancers. We additionally show that inhibition of NER by CTCF binding occurs broadly throughout the CTCF binding site, and is not specific to the mutation hotspot. Finally, we elucidate the molecular mechanism by which CTCF binding causes CPDs to form at a higher rate at specific positions within the binding site. Likewise, nucleosomal DNA exhibits a pattern of recurrent mutagenesis with a precise periodicity in skin cancers, which correlates with positions with elevated UV damage, indicating that similar mechanisms may modulate UV damage formation at strongly positioned nucleosomes. Here, we investigate CPD formation rates at nucleosomes, and show that base flexibility correlates poorly with CPD enrichment, particularly in linker DNA. Finally, we show that nucleosomal CPD periodicity is induced by a molecular mechanism, in which the sharp twisting of the DNA around the histone octamer changes the structural conformation of the DNA in such a way that photochemistry becomes more favorable at positions where the minor groove of the DNA faces out from the histone octamer (minor-out position). Taken together, these studies reveal a molecular mechanism that can explain how protein binding modulates UV damage formation in cells, which can potentially account for a number of recurrent mutations in skin cancers such as melanoma.
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Details
- Title
- Protein-DNA Interactions Shape the Melanoma Genome by Modulating Rates of UV Photoproduct Formation
- Creators
- Bastian Stark
- Contributors
- John J Wyrick (Advisor)Steven A Roberts (Committee Member)Eric A Shelden (Committee Member)Cynthia A Haseltine (Committee Member)
- Awarding Institution
- Washington State University
- Academic Unit
- Molecular Biosciences, School of
- Theses and Dissertations
- Doctor of Philosophy (PhD), Washington State University
- Publisher
- Washington State University
- Number of pages
- 146
- Identifiers
- 99901031039001842
- Language
- English
- Resource Type
- Dissertation