ArticleNature protocols2015
Mapping ribonucleotides in genomic DNA and exploring replication dynamics by polymerase usage sequencing (Pu-seq).
Article in Nature protocols, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Response of the replisome to araA and araC suggests a mechanism for arabinosyl nucleoside tolerance.The EMBO journal · 2026Article
- Multiplexed TrAEL-seq captures DNA replication dynamics in mammalian cells.Nucleic acids research · 2026Article
- Article
- The fork protection complex generates DNA topological stress-induced DNA damage while ensuring full and faithful genome duplication.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Strategic targeting of Cas9 nickase induces large segmental duplications.Cell genomics · 2024Article
- SUMO protease and proteasome recruitment at the nuclear periphery differently affect replication dynamics at arrested forks.Nucleic acids research · 2024Article
- S-phase checkpoint prevents leading strand degradation from strand-associated nicks at stalled replication forks.Nucleic acids research · 2024Article
- Light-strand bias and enriched zones of embedded ribonucleotides are associated with DNA replication and transcription in the human-mitochondrial genome.Nucleic acids research · 2024Article
- Article
- Global landscape of replicative DNA polymerase usage in the human genome.Nature communications · 2022Article
- RESCOT: Restriction Enzyme Set and Combination Optimization Tools for rNMP Capture Techniques.Theoretical computer science · 2021Article
- Detection of Genomic Uracil Patterns.International journal of molecular sciences · 2021Review
- Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq.PLoS biology · 2021Article
- Replication dynamics of recombination-dependent replication forks.Nature communications · 2021Article
- Increased expression of Polδ does not alter the canonical replication programWellcome open research · 2021Article
- Capture of Ribonucleotides in Yeast Genomic DNA Using Ribose-Seq.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Simultaneous Mapping and Quantitation of Ribonucleotides in Human Mitochondrial DNA.Journal of visualized experiments : JoVE · 2017Article
- Set2 Methyltransferase Facilitates DNA Replication and Promotes Genotoxic Stress Responses through MBF-Dependent Transcription.Cell reports · 2017Article
- Ribonucleotide incorporation by human DNA polymerase η impacts translesion synthesis and RNase H2 activity.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
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 genome. Polymerase usage sequencing (Pu-seq) has been used to define, in unprecedented detail, replication dynamics in yeasts. Although other methods that examine replication dynamics provide direct measures of replication timing and indirect estimates of origin efficiency, Pu-seq directly ascertains origin efficiency. The Pu-seq protocol can be completed in 12-14 d.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.