ArticleNature methods2015
Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA.
Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 79 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
79 citing papers in PubMed.
- DNA polymerase I and DnaE mediate RNA-templated DNA synthesis over embedded ribonucleotides.Nucleic acids research · 2026Article
- Ribonucleotide errors, RNase HII, and ribonucleotide excision repair.Critical reviews in biochemistry and molecular biology · 2026Review
- DNA polymerase I is an efficient reverse transcriptase that mediates RNA-templated DNA repair synthesis.bioRxiv : the preprint server for biology · 2025Article
- Emerging roles of RNA:DNA hybrid regulation by mammalian ribonuclease H2 in replication stress and cancer.Journal of cell science · 2025Review
- Genome-wide ribonucleotide detection in Archaea.Nucleic acids research · 2025Article
- Evidence that transient replication errors initiate nuclear genome mutations.Nucleic acids research · 2025Article
- Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method.Journal of visualized experiments : JoVE · 2025Article
- Uridine Embedded within DNA is Repaired by Uracil DNA Glycosylase via a Mechanism Distinct from That of Ribonuclease H2.Journal of the American Chemical Society · 2025Article
- The double life of mammalian DNA replication origins.Genes & development · 2025Review
- A tale of two strands: Decoding chromatin replication through strand-specific sequencing.Molecular cell · 2025Review
- MADDD-seq, a novel massively parallel sequencing tool for simultaneous detection of DNA damage and mutations.Nucleic acids research · 2024Article
- Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome ortholog mutants ofiScience · 2024Article
- Monitoring and quantifying replication fork dynamics with high-throughput methods.Communications biology · 2024Review
- S-phase checkpoint prevents leading strand degradation from strand-associated nicks at stalled replication forks.Nucleic acids research · 2024Article
- Detection of ribonucleotides embedded in DNA by Nanopore sequencing.Communications biology · 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
- DNA Damage Atlas: an atlas of DNA damage and repair.Nucleic acids research · 2024Article
- rNMPID: a database for riboNucleoside MonoPhosphates in DNA.Bioinformatics advances · 2024Article
- A sensor complements the steric gate when DNA polymerase ϵ discriminates ribonucleotides.Nucleic acids research · 2023Article
- Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome (AGS)-ortholog mutants ofbioRxiv : the preprint server for biology · 2023Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
Abstract
Abundant ribonucleotide incorporation in DNA during replication and repair has profound consequences for genome stability, but the global distribution of ribonucleotide incorporation is unknown. We developed ribose-seq, a method for capturing unique products generated by alkaline cleavage of DNA at embedded ribonucleotides. High-throughput sequencing of these fragments in DNA from the yeast Saccharomyces cerevisiae revealed widespread ribonucleotide distribution, with a strong preference for cytidine and guanosine, and identified hotspots of ribonucleotide incorporation in nuclear and mitochondrial DNA. Ribonucleotides were primarily incorporated on the newly synthesized leading strand of nuclear DNA and were present upstream of (G+C)-rich tracts in the mitochondrial genome. Ribose-seq is a powerful tool for the systematic profiling of ribonucleotide incorporation in genomic DNA.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.