Oxidative DNA damage modulates genome and epigenome integrity via base excision repair

Authors

Pawlos S. TsegayFollow

Document Type

Dissertation

Degree

Doctor of Philosophy (PhD)

Major/Program

Biochemistry

First Advisor's Name

Yuan Liu

First Advisor's Committee Title

committee chair

Second Advisor's Name

Lou Kim

Second Advisor's Committee Title

committee member

Third Advisor's Name

Yukching Tse Dinh

Third Advisor's Committee Title

committee member

Fourth Advisor's Name

Xiaotang Wang

Fourth Advisor's Committee Title

committee member

Keywords

oxidative DNA damage, cyclodeoxy purine, Base excision repair, microRNA, 8-oxoG, DNA polymerase β (pol β), DNA polymerase η (pol η), 8-oxoG DNA glycosylase 1 (OGG1).

Date of Defense

10-4-2021

Abstract

Oxidative DNA damage is one of the leading causes of genome instability, cell death, and diseases. It is repaired by DNA base excision repair (BER), during which repair and translesion DNA polymerases may incorporate damaged nucleotides and mediate RNA-guided DNA repair induced by DNA replication and gene transcription leading to the modulation of genome stability. On the other hand, oxidative DNA damage may result in cellular epigenetic responses to regulate DNA repair, altering genome stability and integrity. In this dissertation, we revealed the molecular mechanisms underlying the misincorporation of oxidized nucleotides, 5′,8-cyclo-2-cyclodeoxyadenosine (cdA) and RNA-guided base lesion repair mediated by repair and translesion DNA polymerases. We then explored how oxidative DNA damage induced cellular epigenetic responses by disrupting microRNA expression to regulate BER. We found that DNA polymerase β (pol β) and DNA polymerase η (pol η) incorporated cdA that basepaired with dC, resulting in an A:C mismatch. We further demonstrated that cdA lesions were readily extended and ligated in duplex DNA. We showed that the polymerases incorporated cdAs independent of their hydrogen bonding with a template nucleotide using molecular docking. Our study reveals a unique mechanism underlying the accumulation of cyclodeoxypurine lesions in the genome. We then explored the mechanisms by which DNA polymerases can utilize RNA as a template to synthesize DNA and repair a DNA base lesion. We found that translesion DNA polymerases, pol η, θ, and ν and repair DNA polymerases, pol β, λ and κ exhibited DNA synthesis activity, i.e., reverse transcriptase activity to mediate RNA-guided DNA base lesion repair. We further demonstrated that the completion of base lesion repair was accomplished by the RNA-guided translocation of a nick into duplex DNA via the strand displacement synthesis of the polymerases. We then explored the cellular mechanisms by which oxidative DNA damage modulates microRNA expression to regulate DNA repair. Our study revealed that oxidative DNA damage upregulated the expression of microRNA-499-5p (miR-499-5p) that subsequently downregulated the expression of the key BER enzyme, pol β, in human cells. Further analysis showed that the inhibition of 8-oxoG DNA glycosylase 1 (OGG1) activity significantly suppressed the upregulation of miR-499-5p, suggesting the epigenetic role of OGG1 in mediating the expression of miR-449-5p as cellular DNA damage response. Our study provides new insights into the crosstalk among oxidative DNA damage and repair, miRNAs, RNA-guided base lesion repair in modulating genome stability and integrity.

Identifier

FIDC010414

ORCID

https://orcid.org/0000-0003-3527-7053

Previously Published In

1. Qu F, Tsegay PS, Liu Y. (2021) N6-methyladenosine, DNA repair, and genome stability. Front. Mol. Biosci. (8):104.
2. Rubfiaro AS, Tsegay PS, Lai Y, Cabello E, Shaver M, Hutcheson J, Liu Y, and He J. (2021). Scanning Ion Conductance Microscopy Study Reveals the Disruption of the Integrity of the Human Cell Membrane Structure by Oxidative DNA Damage. ACS Appl. Bio Mater. 4 (2), 1632-1639.
3. Jiang Z, Lai Y, Beaver JM, Tsegay PS, Zhao ML, Horton JK, Zamora M, Rein HL, Miralles F, Shaver M, Hutcheson JD, Agoulnik I, Wilson SH, Liu Y. (2020) Oxidative DNA Damage Modulates DNA Methylation Pattern in Human Breast Cancer 1 (BRCA1) Gene via the Crosstalk between DNA Polymerase β and a de novo DNA Methyltransferase. Cells 9(1): 225.
4. Tsegay PS, Lai Y, Liu Y. (2019). Replication stress and consequential instability of the genome and epigenome. Molecules 24 (21), 3870.
5. Chatgilialoglu, C, Ferreri, C, Geacintov, E, Krokidis, M, Liu, Y, Masi, A, Shafirovich, V, Terzidis, M and Tsegay, PS. (2019). 5′,8-Cyclopurine Lesions in DNA Damage: Chemical, Analytical, Biological, and Diagnostic Significance. Cells 2019, 8, 513.

Recommended Citation

Tsegay, Pawlos S., "Oxidative DNA damage modulates genome and epigenome integrity via base excision repair" (2021). FIU Electronic Theses and Dissertations. 4902.
https://digitalcommons.fiu.edu/etd/4902