ArticleNucleic acids research2022
Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Harnessing Methyltransferase-Guided Targeting for Sequence-Specific Proximity Labeling of DNA.Angewandte Chemie (International ed. in English) · 2026Article
- Dual Stabilization ofJACS Au · 2026Article
- Article
- Genome-wide profiling of unmodified DNA using methyltransferase-directed tagging and enrichment.Cell reports methods · 2025Article
- Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing.bioRxiv : the preprint server for biology · 2025Article
- Long-read structural and epigenetic profiling of a kidney tumor-matched sample with nanopore sequencing and optical genome mapping.NAR genomics and bioinformatics · 2025Article
- Article
- Long-Read Structural and Epigenetic Profiling of a Kidney Tumor-Matched Sample with Nanopore Sequencing and Optical Genome Mapping.bioRxiv : the preprint server for biology · 2024Article
- OM2Seq: learning retrieval embeddings for optical genome mapping.Bioinformatics advances · 2024Article
- The role of imprinting genes' loss of imprints in cancers and their clinical implications.Frontiers in oncology · 2024Review
- Design of optimal labeling patterns for optical genome mapping via information theory.Bioinformatics (Oxford, England) · 2023Article
- Single-molecule approaches for DNA damage detection and repair: A focus on Repair Assisted Damage Detection (RADD).DNA repair · 2023Review
- Review
- Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays.ACS nano · 2023Article
- DeepOM: single-molecule optical genome mapping via deep learning.Bioinformatics (Oxford, England) · 2023Article
- 21 Fluorescent Protein-Based DNA Staining Dyes.Molecules (Basel, Switzerland) · 2022Article
- Long reads capture simultaneous enhancer-promoter methylation status for cell-type deconvolution.Bioinformatics (Oxford, England) · 2021Article
- Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale.Essays in biochemistry · 2021Article
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Authors and funding
13 authors.
Funding
Abstract
DNA methylation, specifically, methylation of cytosine (C) nucleotides at the 5-carbon position (5-mC), is the most studied and significant epigenetic modification. Here we developed a chemoenzymatic procedure to fluorescently label non-methylated cytosines in CpG context, allowing epigenetic profiling of single DNA molecules spanning hundreds of thousands of base pairs. We used a CpG methyltransferase with a synthetic S-adenosyl-l-methionine cofactor analog to transfer an azide to cytosines instead of the natural methyl group. A fluorophore was then clicked onto the DNA, reporting on the amount and position of non-methylated CpGs. We found that labeling efficiency was increased up to 2-fold by the addition of a nucleosidase, presumably by degrading the inactive by-product of the cofactor after labeling, preventing its inhibitory effect. We used the method to determine the decline in global DNA methylation in a chronic lymphocytic leukemia patient and then performed whole-genome methylation mapping of the model plant Arabidopsis thaliana. Our genome maps show high concordance with published bisulfite sequencing methylation maps. Although mapping resolution is limited by optical detection to 500-1000 bp, the labeled DNA molecules produced by this approach are hundreds of thousands of base pairs long, allowing access to long repetitive and structurally variable genomic regions.
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