Analysis of DNA Motifs Around Ribonucleoside Monophosphates in Human Cells

BACKGROUND AND QUESTION 
Ribonucleotides are RNA precursors incorporated during replication. They are embedded in the form of rNMPs (ribonucleoside monophosphate) and are the most frequent form of DNA aberrations, as shown in Figure 1. There are approximately two misincorporated rNMPs/kb in a DNA strand (Huang, Ghosh, & Pommier, 2015). However, there are mechanisms of removing these rNMPs misincorporated in the genomic DNA. A prominent pathway is known as Ribonucleotide Excision Repair (RER) by Ribonuclease (RNase) H2 (Cornelio et al., 2017). Due to lack of RNase H2 function, rNMP incorporation increases in genomic DNA. There are few effects of rNMPs some being positive. For example, rNMPs help mating type switching in fission yeast, thus aiding reproduction during its life-cycle (Yao et al., 2013). However, there are also effects deemed harmful. In humans, a mutation in RNase H2 has been associated with Aicardi-Goutières syndrome, which is a severe childhood neuroinflammatory autoimmune disorder (Uehara et al., 2018). It is characterized by abnormal development or destruction of the white matter that affects the brain, spinal cord, and immune system.

Although there is an abundance of rNMPs in DNA, the sites of the rNMP incorporation are still poorly characterized in the human genome (Balachander et al., 2020). Last fall, my project was directed towards finding: What consensus sequences, or motifs, are around the ribonucleotides in both the wildtype (WT) and knock-out (KO) cell lines in Saccaromyces cerevisiae libraries? In addition, I found transcription factor (TF) sites near rNMPs in both the wildtype (WT) and knock-out (KO) libraries. However, the code could be improved to accommodate for more motifs among the cell lines and the position of the motifs with respect to the rNMP site. This project will help us better understand rNMP incorporation in the human genome. Once we know what motifs are present, we can better predict the locations that are more prone to rNMP incorporation and thus potentially more prone to damage.