Ribonucleotide incorporation in yeast genomic DNA shows preference for cytosine and guanosine preceded by deoxyadenosine
Open Access
- 15 May 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Communications
- Vol. 11 (1), 1-14
- https://doi.org/10.1038/s41467-020-16152-5
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.Keywords
This publication has 57 references indexed in Scilit:
- RNase H2-Initiated Ribonucleotide Excision RepairMolecular Cell, 2012
- Frequent Incorporation of Ribonucleotides during HIV-1 Reverse Transcription and Their Attenuated Repair in MacrophagesPublished by Elsevier BV ,2012
- Ribonucleotide Discrimination and Reverse Transcription by the Human Mitochondrial DNA PolymerasePublished by Elsevier BV ,2011
- Genome instability due to ribonucleotide incorporation into DNANature Chemical Biology, 2010
- DNA Polymerase β Ribonucleotide Discrimination: INSERTION, MISINSERTION, EXTENSION, AND CODINGPublished by Elsevier BV ,2010
- Abundant ribonucleotide incorporation into DNA by yeast replicative polymerasesProceedings of the National Academy of Sciences of the United States of America, 2010
- Simultaneous Quantification of Intracellular Natural and Antiretroviral Nucleosides and Nucleotides by Liquid Chromatography−Tandem Mass SpectrometryAnalytical Chemistry, 2010
- Contributions of the two accessory subunits, RNASEH2B and RNASEH2C, to the activity and properties of the human RNase H2 complexNucleic Acids Research, 2008
- Bacterial Nonhomologous End Joining Ligases Preferentially Seal Breaks with a 3′-OH MonoribonucleotidePublished by Elsevier BV ,2008
- RNA-templated DNA repairNature, 2007