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In partial fulfillment of the requirements for the degree of
Doctor of Philosophy in Bioinformatics
in the School of Biological Sciences
Alli L. Gombolay
Defends her thesis:
Characterization of Biological Signatures of Ribonucleotides Incorporated into DNA using the Ribose-Map Bioinformatics Toolkit
Thursday, June 23, 2022
11:00 am Eastern Time
Zoom = https://gatech.zoom.us/j/92161044967
Thesis advisor:
Dr. Francesca Storici, School of Biological Sciences, Georgia Institute of Technology
Committee Members:
Dr. I. King Jordan, School of Biological Sciences, Georgia Institute of Technology
Dr. Mark Borodovsky, School of Biomedical Engineering and School of Computational Science and Engineering, Georgia Institute of Technology
Dr. Fredrik Vannberg, Department of Biology, Georgia State University
Dr. Soojin Yi, Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara
Abstract
The incorporation of ribonucleoside monophosphates (rNMPs) into DNA is one of the most frequently occurring errors during DNA synthesis. To maintain genome integrity, the ribonuclease (RNase) H enzymes efficiently remove rNMPs that are mistakenly incorporated into DNA during DNA replication or repair. However, if these enzymes fail to remove rNMPs from DNA, the 2’-hydroxyl group of the ribose sugar of rNMPs can attack the double-helix backbone of DNA, leading to genome instability, such as increased mutations, replication stress, single-strand breaks, double-strand breaks, and alterations in the structural and mechanical properties of DNA. Recently, five high-throughput rNMP sequencing techniques have been developed (ribose-seq, emRiboSeq, Alk-HydEn-seq, RHII-HydEn-seq, and Pu-seq) to map the locations of rNMPs in DNA to single-nucleotide resolution. Since the development of rNMP sequencing techniques is recent, the biological signatures of rNMP incorporation in DNA have yet to be thoroughly characterized. In addition, a standardized toolkit to characterize the biological signatures of rNMP incorporation in DNA is needed. To address this, I created the Ribose-Map bioinformatics toolkit. In addition, I applied Ribose-Map to characterize the biological signatures of rNMP incorporation in the DNA of different species, strains, and RNase H-relevant genotypes of yeast. This work serves as a foundational resource for the emerging field of rNMP mapping, leading to an improved understanding of the role of rNMPs in genome stability.
