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Thesis
Transcription factor binding enhances UV DNA Damage at specific loci within their binding sites
University of Iowa
Master of Science (MS), University of Iowa
Summer 2025
DOI: 10.25820/etd.008079
Abstract
Transcription factors (TFs) bind to specific sequences throughout the genome to regulate associated genes. Though thought to be well conserved, sites where TFs are bound (TFBSs) have high frequencies of sequence variation. This suggests that TF binding is inherently mutagenic. There is evidence for two models for how this can occur: 1) enhanced damage; 2) occlusion of repair. Both lead to an accumulation of damage and eventual mutation. The focus of this study is on whether, and to what extent, TFs enhance DNA damage using UV as a source of damage. We studied two different TFs, Ets1 and GR. Six different variations of the Ets1 consensus sequence and nine different variations of the GR consensus sequence were synthesized to test for enhancement of damage of specific di-pyrimidines in specific positions under different sequence contexts. Purified recombinant Ets1 and GR were bound to their respective sequences. These sequences were irradiated with UVC light and incubated with UVE1, an endonuclease that nicks 5’ to DNA damage. Nicked sequences were separated on a urea denaturing gel and DNA damage was quantified. Our results showed that the frequency of DNA damage is altered upon TF binding. In the Ets1 binding sites, TC (-4, -3) had a ~16-fold change in damage while other positions had a ~2-fold change of enhancement. When the identity of this di-pyrimidine was changed, enhanced damage was still observed indicating that the position of di-pyrimidine is what leads to DNA damage enhancement. At GR binding sites, damage enhancement was observed but was markedly lower. The enhancement of damage was influenced by position and sequence context. Damage patterns of both TFs were compared to predicted structures, but no significant correlations were found with any of the measured parameters. This work shows that more than one TF can enhance damage of DNA, though some have more modest effects.
Details
- Title: Subtitle
- Transcription factor binding enhances UV DNA Damage at specific loci within their binding sites
- Creators
- Jordan C. Riley
- Contributors
- Miles Pufall (Advisor)Todd Washington (Committee Member)Sheila Baker (Committee Member)Maria Spies (Committee Member)
- Resource Type
- Thesis
- Degree Awarded
- Master of Science (MS), University of Iowa
- Degree in
- Biochemistry and Molecular Biology
- Date degree season
- Summer 2025
- DOI
- 10.25820/etd.008079
- Publisher
- University of Iowa
- Number of pages
- xi, 93 pages
- Copyright
- Copyright 2025 Jordan C. Riley
- Language
- English
- Date submitted
- 07/15/2025
- Description illustrations
- Illustrations, tables, graphs, charts
- Description bibliographic
- Includes bibliographical references (pages 71-75).
- Public Abstract (ETD)
The human genome is made up of DNA, which acts like an instruction manual for life. DNA consists of four chemical building blocks called nucleotides: adenine, cytosine, guanine, and thymine. Changes in the order of these nucleotides, known as mutations, can sometimes lead to disease or even death.
Transcription factors (TFs) are proteins that bind to DNA to help it function properly. Surprisingly, they can also make DNA more likely to become damaged. To investigate this, we studied how TFs interact with DNA after exposure to ultraviolet (UV) light, a known cause of DNA damage.
We found that when one of the TFs was bound to DNA, it increased the vulnerability to UV damage, while another TF had also increased the vulnerability to UV damage, but to a lesser extent. Additionally, both the sequence and position of nucleotides within the DNA appeared to influence whether damage formed when the TF was bound.
This kind of damage, left unrepaired, can lead to mutations. These findings help us better understand how TF binding contributes to mutations that arise in our genome that may lead to disease.
- Academic Unit
- Biochemistry and Molecular Biology
- Record Identifier
- 9984948238602771
Metrics
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