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

Sathya Balachander, Alli L. Gombolay, Taehwan Yang, Penghao Xu, Gary Newnam, Havva Keskin, Waleed M. M. El-Sayed, Anton V. Bryksin, Sijia Tao, Nicole E. Bowen, Raymond F. Schinazi, Baek Kim, Kyung Duk Koh, Fredrik O. Vannberg and Francesca Storici ()
Additional contact information
Sathya Balachander: Georgia Institute of Technology
Alli 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 F. 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

Nature Communications, 2020, vol. 11, issue 1, 1-14

Abstract: 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.

Date: 2020
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-020-16152-5 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16152-5

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-020-16152-5

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().