ABSTRACT Ribonucleotides are frequently misincorporated into DNA during replication, and they are rapidly repaired by ribonucleotide excision repair (RER). Although ribonucleotides in

template DNA perturb replicative polymerases and can be considered as DNA damage, they also serve positive biological functions, including directing the orientation of mismatch repair. Here

we describe a method for ribonucleotide identification by high-throughput sequencing that allows mapping of the location of ribonucleotides across the genome. When combined with specific

mutations in the replicative polymerases that incorporate ribonucleotides at elevated frequencies, our ribonucleotide identification method was adapted to map polymerase usage across the

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support SIMILAR CONTENT BEING VIEWED BY OTHERS GENOME-WIDE MEASUREMENT OF DNA REPLICATION FORK DIRECTIONALITY AND QUANTIFICATION OF DNA REPLICATION INITIATION AND TERMINATION WITH OKAZAKI

FRAGMENT SEQUENCING Article 18 January 2023 MAPPING RIBONUCLEOTIDES EMBEDDED IN GENOMIC DNA TO SINGLE-NUCLEOTIDE RESOLUTION USING RIBOSE-MAP Article 04 June 2021 MONITORING GENOME-WIDE

REPLICATION FORK DIRECTIONALITY BY OKAZAKI FRAGMENT SEQUENCING IN MAMMALIAN CELLS Article 13 January 2021 REFERENCES * Nick McElhinny, S.A. et al. Abundant ribonucleotide incorporation into

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acknowledges UK Medical Research Council (MRC) grant no. G1100074 and European Research Council (ERC) grant no. 268788-SMI-DDR. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Genome Damage

and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK Andrea Keszthelyi, Yasukazu Daigaku, Katie Ptasińska, Izumi Miyabe & Antony M Carr * Frontier Research

Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan Yasukazu Daigaku Authors * Andrea Keszthelyi View author publications You can also search for this author inPubMed 

Google Scholar * Yasukazu Daigaku View author publications You can also search for this author inPubMed Google Scholar * Katie Ptasińska View author publications You can also search for this

author inPubMed Google Scholar * Izumi Miyabe View author publications You can also search for this author inPubMed Google Scholar * Antony M Carr View author publications You can also

search for this author inPubMed Google Scholar CONTRIBUTIONS A.K., Y.D., K.P. and I.M. performed the experiments. A.K. and Y.D. designed the protocol and analytical methods. A.K., Y.D.,

A.M.C. and K.P. wrote the manuscript. CORRESPONDING AUTHOR Correspondence to Antony M Carr. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing financial interests.

RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Keszthelyi, A., Daigaku, Y., Ptasińska, K. _et al._ Mapping ribonucleotides in genomic DNA and exploring

replication dynamics by polymerase usage sequencing (Pu-seq). _Nat Protoc_ 10, 1786–1801 (2015). https://doi.org/10.1038/nprot.2015.116 Download citation * Published: 15 October 2015 * Issue

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