Characterization of biological signatures of ribonucleotides incorporated into DNA using the Ribose-Map bioinformatics toolkit

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Gombolay, Alli
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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.
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