Graduation Date

Spring 5-7-2022

Document Type

Thesis

Degree Name

Master of Science (MS)

Programs

Molecular Genetics & Cell Biology

First Advisor

Dr. Kishor Bhakat

Abstract

Endogenous DNA damage can occur throughout the genome and is resolved through the Base Excision Repair (BER) pathway. The apurinic/apyrimidinic sites that result from endogenous DNA damage, called AP-sites, are created by DNA glycosylases removing oxidized or modified bases. These AP-sites are primarily repaired by AP endonuclease 1 (APE1) through the BER pathway. Modification of APE1 by acetylation of specific lysine residues in the proteins’ unstructured, N-terminal tail, have been shown to increase the residence time of APE1 (AcAPE1) at the AP-sites. It is unknown where AcAPE1 is binding to chromatin in the genome. Here, we are testing the hypothesis that DNA damage influences the genomic locations of AcAPE1 binding. By using ChIP-seq with a specific antibody for AcAPE1 we can accurately map the chromatin regions that are bound by AcAPE1. Our AcAPE1 ChIP-seq data shows a high localization of AcAPE1 in promoter regions of genes. Correlating our AcAPE1 ChIP-seq data with publicly available histone markers and ATAC-seq data confirmed our finding that AcAPE1 has preferential binding for open chromatin regions that are near genes. When introducing oxidative DNA damage by hydrogen peroxide treatment (H2O2), we see no noticeable changes in AcAPE1 binding. These results have been replicated in multiple cell lines. We have found that AcAPE1 has a strong preferential for binding to the promoter regions of genes. While we can accurately map AcAPE1 to gene-rich regions, we have yet to determine the reason for this preferential binding. It was expected that with oxidative DNA damage the distribution of AcAPE1 would change but this does not seem to be the case. In the future we would like to use ChIP-seq data for other proteins known to play a role in the BER pathway to help determine if the role of the AcAPE1 is related to DNA damage or some other function.

Available for download on Wednesday, October 26, 2022

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