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Abstract
Despite the abundance of ribonucleoside monophosphates (rNMPs) in DNA, sites of rNMP incorporation remain poorly characterized. Here, by using ribose-seq and Ribose-Map techniques, we built and analyzed high-throughput sequencing libraries of rNMPs derived from mitochondrial and nuclear DNA of budding and fission yeast. We reveal both common and unique features of rNMP sites among yeast species and strains, and between wild type and different ribonuclease H-mutant genotypes. We demonstrate that the rNMPs are not randomly incorporated in DNA. We highlight signatures and patterns of rNMPs, including sites within trinucleotide-repeat tracts. Our results uncover that the deoxyribonucleotide immediately upstream of the rNMPs has a strong influence on rNMP distribution, suggesting a mechanism of rNMP accommodation by DNA polymerases as a driving force of rNMP incorporation. Consistently, we find deoxyadenosine upstream from the most abundant genomic rCMPs and rGMPs. This study establishes a framework to better understand mechanisms of rNMP incorporation in DNA.
Ribonucleoside monophosphates are incorporated by DNA polymerases into double-stranded DNA. Here, the authors use ribose-seq and Ribose-Map techniques to reveal that signatures and patterns of ribonucleotide incorporation in yeast mitochondrial and nuclear DNA show preference for cytosine and guanosine preceded by deoxyadenosine.
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1 Georgia Institute of Technology, School of Biological Sciences, Atlanta, USA (GRID:grid.213917.f) (ISNI:0000 0001 2097 4943)
2 Georgia Institute of Technology, School of Biological Sciences, Atlanta, USA (GRID:grid.213917.f) (ISNI:0000 0001 2097 4943); Omega Bio-tek, Norcross, USA (GRID:grid.213917.f)
3 Georgia Institute of Technology, School of Biological Sciences, Atlanta, USA (GRID:grid.213917.f) (ISNI:0000 0001 2097 4943); National Institute of Oceanography and Fisheries, Marine Microbiology Department, Red Sea, Egypt (GRID:grid.419615.e) (ISNI:0000 0004 0404 7762)
4 Georgia Institute of Technology, Molecular Evolution Core, Parker H. Petit Institute of Bioengineering and Bioscience, Atlanta, USA (GRID:grid.213917.f) (ISNI:0000 0001 2097 4943)
5 Emory University, Department of Pediatrics, School of Medicine, Atlanta, USA (GRID:grid.189967.8) (ISNI:0000 0001 0941 6502)
6 University of California San Francisco, Lung Biology Center, Department of Medicine, San Francisco, USA (GRID:grid.266102.1) (ISNI:0000 0001 2297 6811)