ArticleNature protocols2015
Genome-wide mapping of embedded ribonucleotides and other noncanonical nucleotides using emRiboSeq and EndoSeq.
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 37 papers.
What it found
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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.
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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.
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Who cites it
37 citing papers in PubMed, 48 citations in OpenAlex.
- Ribonucleotide errors, RNase HII, and ribonucleotide excision repair.Critical reviews in biochemistry and molecular biology · 2026Review
- High-throughput characterization of transcription factors that modulate UV damage formation and repair at single-nucleotide resolution.Nature communications · 2026Article
- Deciphering the Role of DNA Polymerase Eta on the Incorporation and Bypass of Inosine and Cell Cycle Arrest.International journal of molecular sciences · 2025Article
- High-throughput characterization of transcription factors that modulate UV damage formation and repair at single-nucleotide resolution.Research square · 2025Article
- Genome-wide ribonucleotide detection in Archaea.Nucleic acids research · 2025Article
- 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
- High UV damage and low repair, but not cytosine deamination, stimulate mutation hotspots at ETS binding sites in melanoma.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- rNMPID: a database for riboNucleoside MonoPhosphates in DNA.Bioinformatics advances · 2024Article
- Processing of matched and mismatched rNMPs in DNA by archaeal ribonucleotide excision repair.iScience · 2023Article
- Genome-wide maps of rare and atypical UV photoproducts reveal distinct patterns of damage formation and mutagenesis in yeast chromatin.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Mapping atypical UV photoproductsSTAR protocols · 2022Article
- High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors.eLife · 2022Article
- Article
- Damage mapping techniques and the light they have shed on canonical and atypical UV photoproducts.Frontiers in genetics · 2022Review
- Genome-wide mapping of genomic DNA damage: methods and implications.Cellular and molecular life sciences : CMLS · 2021Review
- RESCOT: Restriction Enzyme Set and Combination Optimization Tools for rNMP Capture Techniques.Theoretical computer science · 2021Article
- CTCF binding modulates UV damage formation to promote mutation hot spots in melanoma.The EMBO journal · 2021Article
- Novel Escherichia coli active site dnaE alleles with altered base and sugar selectivity.Molecular microbiology · 2021Article
- Evaluation of repair activity by quantification of ribonucleotides in the genome.Genes to cells : devoted to molecular & cellular mechanisms · 2021Article
- Atypical UV Photoproducts Induce Non-canonical Mutation Classes Associated with Driver Mutations in Melanoma.Cell reports · 2020Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Ribonucleotides are the most common noncanonical nucleotides incorporated into the genome of replicating cells. They are efficiently removed by ribonucleotide excision repair initiated by RNase H2 cleavage. In the absence of RNase H2, such embedded ribonucleotides can be used to track DNA polymerase activity in vivo. To determine their precise location in Saccharomyces cerevisiae, we developed embedded ribonucleotide sequencing (emRiboSeq), which uses recombinant RNase H2 to selectively create ligatable 3'-hydroxyl groups, in contrast to alternative methods that use alkaline hydrolysis. EmRiboSeq allows reproducible, strand-specific and potentially quantitative detection of embedded ribonucleotides at single-nucleotide resolution. For the genome-wide mapping of other noncanonical bases, RNase H2 can be replaced with specific nicking endonucleases in this protocol; we term this method endonuclease sequencing (EndoSeq). With the protocol taking <5 d to complete, these methods allow the in vivo study of DNA replication and repair, including the identification of replication origins and termination regions.
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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.