ArticleGenome research2014
High resolution mapping of modified DNA nucleobases using excision repair enzymes.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 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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Who cites it
49 citing papers in PubMed, 85 citations in OpenAlex.
- Methods and applications of genome-wide profiling of DNA damage and rare mutations.Nature reviews. Genetics · 2024Review
- Genome-wide impact of cytosine methylation and DNA sequence context on UV-induced CPD formation.Environmental and molecular mutagenesis · 2024Article
- DNA Damage Atlas: an atlas of DNA damage and repair.Nucleic acids research · 2024Article
- Genomic mutation landscape of skin cancers from DNA repair-deficient xeroderma pigmentosum patients.Nature communications · 2023Article
- UV irradiation remodels the specificity landscape of transcription factors.Proceedings of the National Academy of Sciences of the United States of America · 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
- Sequence dependent UV damage of complete pools of oligonucleotides.Scientific reports · 2023Article
- Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing.Nature communications · 2023Review
- A new technique for genome-wide mapping of nucleotide excision repair without immunopurification of damaged DNA.The Journal of biological chemistry · 2022Article
- Mapping atypical UV photoproductsSTAR protocols · 2022Article
- Damage mapping techniques and the light they have shed on canonical and atypical UV photoproducts.Frontiers in genetics · 2022Review
- Fragile sites, chromosomal lesions, tandem repeats, and disease.Frontiers in genetics · 2022Review
- Genome-wide mapping of genomic DNA damage: methods and implications.Cellular and molecular life sciences : CMLS · 2021Review
- Base-Resolution Analysis of Deoxyuridine at the Genome Scale Based on the Artificial Incorporation Modified Nucleobase.ACS central science · 2021Article
- aniFOUND: analysing the associated proteome and genomic landscape of the repaired nascent non-replicative chromatin.Nucleic acids research · 2021Article
- Detection of Genomic Uracil Patterns.International journal of molecular sciences · 2021Review
- Exons and introns exhibit transcriptional strand asymmetry of dinucleotide distribution, damage formation and DNA repair.NAR genomics and bioinformatics · 2021Article
- Visualization of uracils created by APOBEC3A using UdgX shows colocalization with RPA at stalled replication forks.Nucleic acids research · 2020Article
- Atypical UV Photoproducts Induce Non-canonical Mutation Classes Associated with Driver Mutations in Melanoma.Cell reports · 2020Article
- Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments.eLife · 2020Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
The incorporation and creation of modified nucleobases in DNA have profound effects on genome function. We describe methods for mapping positions and local content of modified DNA nucleobases in genomic DNA. We combined in vitro nucleobase excision with massively parallel DNA sequencing (Excision-seq) to determine the locations of modified nucleobases in genomic DNA. We applied the Excision-seq method to map uracil in E. coli and budding yeast and discovered significant variation in uracil content, wherein uracil is excluded from the earliest and latest replicating regions of the genome, possibly driven by changes in nucleotide pool composition. We also used Excision-seq to identify sites of pyrimidine dimer formation induced by UV light exposure, where the method could distinguish between sites of cyclobutane and 6-4 photoproduct formation. These UV mapping data enabled analysis of local sequence bias around pyrimidine dimers and suggested a preference for an adenosine downstream from 6-4 photoproducts. The Excision-seq method is broadly applicable for high precision, genome-wide mapping of modified nucleobases with cognate repair enzymes.
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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.