Graduation Year

2023

Document Type

Thesis

Degree

M.A.

Degree Name

Master of Arts (M.A.)

Degree Granting Department

Mathematics and Statistics

Major Professor

Nataša Jonoska, Ph.D.

Committee Member

Lu Lu, Ph.D.

Committee Member

Joel Rosenfeld, Ph.D.

Keywords

Bioconductor, exploratory analysis, genomics, R

Abstract

During the DNA replication process, ribonucleotides, the building blocks of RNA, may be occasionally incorporated in the newly synthesized DNA. DNA is primarily composed of deoxyribonucleotides and there exist cellular mechanisms for removing ribonucleotides from DNA, which may point towards ribonucleotide incorporation being a replication error. Further, an excess of these ribonucleotides in the genome has been known to lead to genomic instability and has been implicated in human diseases. However, there are also hypotheses that suggest that ribonucleotides may be beneficial in certain circumstances. In this study we examine ribonucleotide incorporation in the human genome in several human cell types. While ribonucleotide incorporation has been studied in yeast, there has yet to be a systematic study of this phenomenon in the human genome. We analyze data obtained through a sequencing protocol that detects the positions of ribonucleotide incorporation in genome samples. We use mathematical analysis to detect hotspots and sequence patterns, as well as biologically relevant regions where such ribonucleotide incorporation appears nonrandom. Our analysis shows that the phenomenon is most commonly seen in regions that are GC rich and may be correlated with some gene regulatory segments. Further study will be needed to ascertain whether ribonucleotide incorporation has a specific biological function in the human genome.

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