Ribonucleotide incorporation in yeast genomic DNA shows preference for cytosine and guanosine preceded by deoxyadenosine

• Type of Material: Article
• Authors: Sathya Balachander, Georgia Institute of Technology; Ali L. Gombolay, Georgia Institute of Technology; Taehwan Yang, Georgia Institute of Technology; Penghao Xu, Georgia Institute of Technology; Gary Newnam, Georgia Institute of Technology; Havva Keskin, Georgia Institute of Technology; Waleed M. M. El-Sayed, Georgia Institute of Technology; Anton V. Bryksin, Georgia Institute of Technology; Sijia Tao, Emory University; Nicole E. Bowen, Emory University; Raymond Schinazi, Emory University; Baek Kim, Emory University; Kyung Duk Koh, University of California San Francisco; Fredrik O. Vannberg, Georgia Institute of Technology; Francesca Storici, Georgia Institute of Technology
• Language: English
• Date: 2020-05-15
• Publisher: Nature Publishing Group
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2020.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1038/s41467-020-16152-5
• Title of Journal or Parent Work: Nature Communications
• Volume: 11
• Issue: 1
• Start Page: 2447
• End Page: 2447
• Grant/Funding Information: We acknowledge funding from the National Institutes of Health, NIH AI136581 (to B.K.), AI150451 (to B.K.), MH116695 (to R.F.S.), R01ES026243 (to F.S.), the Parker H. Petit Institute for Bioengineering and Bioscience at Georgia Institute of Technology 12456H2 (to F.S.), and the Howard Hughes Medical Institute Faculty Scholar grant 55108574 (to F.S.) for supporting this work.
• Keywords: Excision; Recombination; Science & Technology - Other Topics; Strains; Replication; Repair; Discrimination; Saccharomyces cerevisiae; Science & Technology; In-vivo; Multidisciplinary Sciences; Reverse transcription; Polymerase
• Research Categories: Biology, Genetics; Biology, Microbiology; Engineering, Biomedical; Chemistry, Biochemistry

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.