Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome ortholog mutants of Saccharomyces cerevisiae
Deepali L. Kundnani,
Taehwan Yang,
Alli L. Gombolay,
Kuntal Mukherjee,
Gary Newnam,
Chance Meers,
Ishika Verma,
Kirti Chhatlani,
Zeel H. Mehta,
Celine Mouawad,
Francesca Storici
Affiliations
Deepali L. Kundnani
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Taehwan Yang
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Alli L. Gombolay
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
Kuntal Mukherjee
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Gary Newnam
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Chance Meers
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
Ishika Verma
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Kirti Chhatlani
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Zeel H. Mehta
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Celine Mouawad
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Francesca Storici
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Corresponding author
Summary: Ribonucleoside monophosphates (rNMPs) are abundantly found within genomic DNA of cells. The embedded rNMPs alter DNA properties and impact genome stability. Mutations in ribonuclease (RNase) H2, a key enzyme for rNMP removal, are associated with the Aicardi-Goutières syndrome (AGS), a severe neurological disorder. Here, we engineered orthologs of the human RNASEH2A-G37S and RNASEH2C-R69W AGS mutations in yeast Saccharomyces cerevisiae: rnh201-G42S and rnh203-K46W. Using the ribose-seq technique and the Ribose-Map bioinformatics toolkit, we unveiled rNMP abundance, composition, hotspots, and sequence context in these AGS-ortholog mutants. We found a high rNMP presence in the nuclear genome of rnh201-G42S-mutant cells, and an elevated rCMP content in both mutants, reflecting preferential cleavage of RNase H2 at rGMP. We discovered unique rNMP patterns in each mutant, showing differential activity of the AGS mutants on the leading or lagging replication strands. This study guides future research on rNMP characteristics in human genomes with AGS mutations.
