ArticlePLoS biology2020
Precise genomic mapping of 5-hydroxymethylcytosine via covalent tether-directed sequencing.
Article in PLoS biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 25 citations in OpenAlex.
- Biochemical engineering of 5hmdC-DNA using a Tet3 double-mutant.Computational and structural biotechnology journal · 2026Article
- 5-Hydroxymethylcytosine modifications in circulating cell-free DNA: frontiers of cancer detection, monitoring, and prognostic evaluation.Biomarker research · 2025Review
- Review
- One-pot trimodal mapping of unmethylated, hydroxymethylated, and open chromatin sites unveils distinctive 5hmC roles at dynamic chromatin loci.Cell chemical biology · 2024Article
- An Overview of Global, Local, and Base-Resolution Methods for the Detection of 5-Hydroxymethylcytosine in Genomic DNA.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Selective chemical tracking of Dnmt1 catalytic activity in live cells.Molecular cell · 2022Article
- Distribution and regulatory roles of oxidized 5-methylcytosines in DNA and RNA of the basidiomycete fungiOpen biology · 2022Article
- DNA Labeling Using DNA Methyltransferases.Advances in experimental medicine and biology · 2022Article
- Calculation of Fetal Fraction for Non-Invasive Prenatal Testing.Biotech (Basel (Switzerland)) · 2021Review
- Methyltransferase-directed orthogonal tagging and sequencing of miRNAs and bacterial small RNAs.BMC biology · 2021Article
- Modern epigenetics methods in biological research.Methods (San Diego, Calif.) · 2021Review
- Selective Chemical Labeling and Sequencing of 5-Hydroxymethylcytosine in DNA at Single-Base Resolution.Frontiers in genetics · 2021Article
- Multiomics Analysis of Neuroblastoma Cells Reveals a Diversity of Malignant Transformations.Frontiers in cell and developmental biology · 2021Article
- Identification of fetal unmodified and 5-hydroxymethylated CG sites in maternal cell-free DNA for non-invasive prenatal testing.Clinical epigenetics · 2020Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
5-hydroxymethylcytosine (5hmC) is the most prevalent intermediate on the oxidative DNA demethylation pathway and is implicated in regulation of embryogenesis, neurological processes, and cancerogenesis. Profiling of this relatively scarce genomic modification in clinical samples requires cost-effective high-resolution techniques that avoid harsh chemical treatment. Here, we present a bisulfite-free approach for 5hmC profiling at single-nucleotide resolution, named hmTOP-seq (5hmC-specific tethered oligonucleotide-primed sequencing), which is based on direct sequence readout primed at covalently labeled 5hmC sites from an in situ tethered DNA oligonucleotide. Examination of distinct conjugation chemistries suggested a structural model for the tether-directed nonhomologous polymerase priming enabling theoretical evaluation of suitable tethers at the design stage. The hmTOP-seq procedure was optimized and validated on a small model genome and mouse embryonic stem cells, which allowed construction of single-nucleotide 5hmC maps reflecting subtle differences in strand-specific CG hydroxymethylation. Collectively, hmTOP-seq provides a new valuable tool for cost-effective and precise identification of 5hmC in characterizing its biological role and epigenetic changes associated with human disease.
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