Revealing unknown features of ribonucleotide incorporation in various genomic DNA
Author(s)
Yang, Taehwan
Advisor(s)
Editor(s)
Collections
Supplementary to:
Permanent Link
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.
Sponsor
Date
2025-07-31
Extent
Resource Type
Text
Resource Subtype
Dissertation