ArticleGenome biology2017
Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite Leishmania.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 59 citations in OpenAlex.
- SMUG1 DNA glycosylase modulates reward behaviour through regulation of olfactory receptor gene expression.Nucleic acids research · 2025Article
- DNA methylation in esophageal cancer: technological advances and early detection clinical applications.Frontiers in oncology · 2025Review
- Characterization of the enzyme for 5-hydroxymethyluridine production and its role in silencing transposable elements in dinoflagellates.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Bacteriophage-related epigenetic natural and non-natural pyrimidine nucleotides and their influence on transcription with T7 RNA polymerase.Communications chemistry · 2024Article
- Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome.Genome biology · 2024Article
- A data-adaptive methods in detecting exogenous methyltransferase accessible chromatin in human genome using nanopore sequencing.Bioinformatics (Oxford, England) · 2024Article
- Epigenetic marks or not? The discovery of novel DNA modifications in eukaryotes.The Journal of biological chemistry · 2024Review
- Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in thebioRxiv : the preprint server for biology · 2023Article
- Review
- The paradigm of intracellular parasite survival and drug resistance in leishmanial parasite through genome plasticity and epigenetics: Perception and future perspective.Frontiers in cellular and infection microbiology · 2023Review
- Epigenetic Pyrimidine Nucleotides in Competition with Natural dNTPs as Substrates for Diverse DNA Polymerases.ACS chemical biology · 2022Article
- Oxime formation coordination-directed detection of genome-wide thymine oxides with nanogram-scale sample input.Chemical science · 2022Article
- Homologues of epigenetic pyrimidines: 5-alkyl-, 5-hydroxyalkyl and 5-acyluracil and -cytosine nucleotides: synthesis, enzymatic incorporation into DNA and effect on transcription with bacterial RNA polymerase.RSC chemical biology · 2022Article
- An enzyme-mediated bioorthogonal labeling method for genome-wide mapping of 5-hydroxymethyluracil.Chemical science · 2021Article
- Quantification and mapping of DNA modifications.RSC chemical biology · 2021Review
- Detection of Genomic Uracil Patterns.International journal of molecular sciences · 2021Review
- Epigenetic Regulation of Genomic Stability by Vitamin C.Frontiers in genetics · 2021Review
- Strain-specific genome evolution in Trypanosoma cruzi, the agent of Chagas disease.PLoS pathogens · 2021Article
- Long-range single-molecule mapping of chromatin accessibility in eukaryotes.Nature methods · 2020Article
- Sequencing abasic sites in DNA at single-nucleotide resolution.Nature chemistry · 2019Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
background5-Hydroxymethyluracil (5hmU) is a thymine base modification found in the genomes of a diverse range of organisms. To explore the functional importance of 5hmU, we develop a method for the genome-wide mapping of 5hmU-modified loci based on a chemical tagging strategy for the hydroxymethyl group.
resultsWe apply the method to generate genome-wide maps of 5hmU in the parasitic protozoan Leishmania sp. In this genus, another thymine modification, 5-(β-glucopyranosyl) hydroxymethyluracil (base J), plays a key role during transcription. To elucidate the relationship between 5hmU and base J, we also map base J loci by introducing a chemical tagging strategy for the glucopyranoside residue. Observed 5hmU peaks are highly consistent among technical replicates, confirming the robustness of the method. 5hmU is enriched in strand switch regions, telomeric regions, and intergenic regions. Over 90% of 5hmU-enriched loci overlapped with base J-enriched loci, which occurs mostly within strand switch regions. We also identify loci comprising 5hmU but not base J, which are enriched with motifs consisting of a stretch of thymine bases.
conclusionsBy chemically detecting 5hmU we present a method to provide a genome-wide map of this modification, which will help address the emerging interest in the role of 5hmU. This method will also be applicable to other organisms bearing 5hmU.
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