Title:
Characterization of biological signatures of ribonucleotides incorporated into DNA using the Ribose-Map bioinformatics toolkit
Characterization of biological signatures of ribonucleotides incorporated into DNA using the Ribose-Map bioinformatics toolkit
dc.contributor.author | Gombolay, Alli | |
dc.contributor.department | Biology | |
dc.date.accessioned | 2022-08-25T13:38:29Z | |
dc.date.available | 2022-08-25T13:38:29Z | |
dc.date.created | 2022-08 | |
dc.date.issued | 2022-07-30 | |
dc.date.submitted | August 2022 | |
dc.date.updated | 2022-08-25T13:38:29Z | |
dc.description.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 (OH) group of the ribose sugar of rNMPs can attack the double-helix backbone of DNA, resulting in several types of genome instability, including SSBs, DSBs, short deletion mutations, replication stress, cell cycle checkpoint activation, aberrant recombination, formation of protein-DNA crosslinks, and alterations in the structural properties of DNA. Recently, five high-throughput rNMP sequencing (rNMP-seq) 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-seq is recent, the biological signatures of rNMPs have yet to be thoroughly characterized. In addition, a standardized bioinformatics toolkit to characterize the biological signatures of rNMPs is needed. To address this, I created the Ribose-Map bioinformatics toolkit. In addition, I applied Ribose-Map to characterize the biological signatures of rNMPs in the DNA of different species, strains, and RNase H genotypes (wild type and mutant) of the yeast, S. cerevisiae, S. pombe, and S. paradoxus. 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. | |
dc.description.degree | Ph.D. | |
dc.format.mimetype | application/pdf | |
dc.identifier.uri | http://hdl.handle.net/1853/67299 | |
dc.language.iso | en_US | |
dc.publisher | Georgia Institute of Technology | |
dc.subject | bioinformatics | |
dc.subject | ribonucleotides | |
dc.subject | ribose-seq | |
dc.subject | ribonucleotide mapping | |
dc.title | Characterization of biological signatures of ribonucleotides incorporated into DNA using the Ribose-Map bioinformatics toolkit | |
dc.type | Text | |
dc.type.genre | Dissertation | |
dspace.entity.type | Publication | |
local.contributor.corporatename | College of Sciences | |
local.contributor.corporatename | School of Biological Sciences | |
relation.isOrgUnitOfPublication | 85042be6-2d68-4e07-b384-e1f908fae48a | |
relation.isOrgUnitOfPublication | c8b3bd08-9989-40d3-afe3-e0ad8d5c72b5 | |
thesis.degree.level | Doctoral |