In partial fulfillment of the requirements for the degree of
Doctor of Philosophy in Bioinformatics
in the School of Biological Sciences
Mo Sun
Defends his thesis:
When DNA meets RNA: Ribonucleotides Embedded in the Genome
October 29, 2026, 1PM EST
Physical Location = Engineered Biosystems Building (EBB), CHOA seminar room EBB 1005
Zoom Link
Thesis Advisor:
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. Joseph Lachance
School of Biological Sciences
Georgia Institute of Technology
Dr. Yuhong Fan
School of Biological Sciences
Georgia Institute of Technology
Dr. Bing Yao
Department of Human Genetics
Emory University School of Medicine
Abstract:
Ribonucleotides (rNMPs) are essential building blocks of RNA but can also be incorporated into DNA during replication and repair. Embedded rNMPs are the most abundant naturally occurring noncanonical nucleotides in genomic DNA. Although several pathways process or remove embedded rNMPs, their genomic distribution, biological consequences, and mechanisms of removal remain incompletely understood.
In this study, we developed rNMPID, a publicly accessible database that integrates rNMP-mapping datasets across species, genotypes, and sequencing techniques. rNMPID enables standardized analyses of rNMP composition, sequence context, strand bias, and enrichment across genomic features, providing a valuable resource for comparing rNMP landscapes across studies.
Second, we characterized the distribution of embedded rNMPs in human mitochondrial DNA across multiple cell types using ribose-seq. We found that rNMP distribution was non-random, with preferential enrichment on the light strand in most cell types, recurrent rNMP hotspots, and distinct patterns associated with mitochondrial DNA replication and transcription.
Finally, we investigated how RNase H1, RNase H2, and topoisomerase I (Top1) shape the genome-wide distribution of embedded rNMPs in budding yeast nuclear DNA. We found that RNase H2 and Top1 influence rNMP accumulation on the leading strand of DNA replication, whereas RNase H1 deficiency preferentially affects lagging-strand associated rNMP accumulation. We further identified pervasive transcription-associated rNMP strand asymmetry, characterized by preferential enrichment on the non-template strand of transcribed genes. This asymmetry was particularly pronounced at highly transcribed loci, including ribosomal RNA genes. Moreover, rNMP-enriched regions overlapped R-loop enriched regions, and RNase H1 overexpression attenuated non-template strand bias, supporting a connection between R-loop metabolism and the distribution of embedded rNMPs.
Overall, this work demonstrates that the genomic distribution of embedded rNMPs is non-random and reflects the combined influences of DNA replication, transcription, and rNMP-processing pathways. These findings, together with the development of rNMPID, provide a foundation for investigating the roles of embedded rNMPs in genome stability and human diseases associated with defective nucleic acid metabolism, including Aicardi-Goutières syndrome.