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.