Ribonucleotide Incorporation in Yeast Genomic DNA Shows Preference for Cytosine and Guanosine Preceded by Deoxyadenosine

Overview

Journal Nat Commun

Specialty Biology

Date 2020 May 17

PMID 32415081

Citations 18

Authors

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

Francesca Storici

Affiliations

Soon will be listed here.

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.

Citing Articles

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rNMPID: a database for riboNucleoside MonoPhosphates in DNA.

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Detection of ribonucleotides embedded in DNA by Nanopore sequencing.

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Light-strand bias and enriched zones of embedded ribonucleotides are associated with DNA replication and transcription in the human-mitochondrial genome.

Xu P, Yang T, Kundnani D, Sun M, Marsili S, Gombolay A Nucleic Acids Res. 2023; 52(3):1207-1225.

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