In partial fulfillment of the requirements for the degree of

Doctor of Philosophy in Biology
In the
School of Biological Sciences

Taehwan Yang

Will defend his dissertation

Revealing Unknown Features of Ribonucleotide Incorporation in Various Genomic DNA

June 24th, 2025
11:00 AM EDT
EBB Room# 5029

Thesis Advisor:
Francesca Storici, Ph.D.
School of Biological Sciences
Georgia Institute of Technology

Committee Members:
Kirill Lobachev, Ph.D.
School of Biological Sciences
Georgia Institute of Technology

Loren Williams, Ph.D.
School of Chemistry & Biochemistry
Georgia Institute of Technology

Nathan McDonald, Ph.D.
School of Biological Sciences
Georgia Institute of Technology

Dr. Eugene Kroll, Ph.D.
Okinawa Institute of Science and Technology

Abstract
Ribonucleotides, known as ribonucleoside monophosphates (rNMPs), are considered being the most plentiful non-canonical nucleotides easily found in genomic DNA. The presence of rNMPs was initially found in mitochondrial DNA from mice and HeLa cells in the 1970’s. Many studies have shown that the failure to prevent the incorporation and accumulation of cellular rNMPs in genomic DNA can lead to genome instability and, in mammals, contribute to the development of Aicardi-Goutières Syndrome (AGS). The efforts to unlock the secrets of rNMP incorporation have partially revealed which mechanisms and what genes are involved in. However, conducting deeper research to investigate the function/s of embedded rNMPs found in cellular genomic DNA has often encountered difficulties due to the activity of ribonucleotide excision repair (RER) pathway and the absence of appropriate mapping techniques. To map rNMPs in genomic DNA and broaden our understanding of their incorporation features in larger genomes, we upgraded the ribose-seq protocol, a technique developed in 2015 for capturing rNMPs, by integrating modern technical advances. We successfully extended our understanding of non-randomly incorporated rNMPs captured in various yeast genomes, both in the presence of active ribonucleotide excision repair (RER) and in two AGS-associated mutants modeled in yeast. In addition, advancing our techniques to study rNMPs in mammalian cells, enabled us to explore the specific signatures of rNMPs in both mitochondrial and nuclear DNA across a wide range of human cell types. These findings have revealed fundamental insights into the functional and structural impacts of rNMPs on genome metabolism, as well as potential clues to rNMP repair mechanisms relevant to human disease.