ArticleACS nano2018
Epigenetic Optical Mapping of 5-Hydroxymethylcytosine in Nanochannel Arrays.
Article in ACS nano, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Harnessing Methyltransferase-Guided Targeting for Sequence-Specific Proximity Labeling of DNA.Angewandte Chemie (International ed. in English) · 2026Article
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- 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
- DOGMA: de novo assembly of densely labelled optical DNA maps using a matrix profile approach.PloS one · 2025Article
- Exploring Chromoanagenesis with DAFCA (Dam Assisted Fluorescent Tagging of Chromatin Accessibility): Integrating Chromatin Accessibility and Optical Genome Mapping for Enhanced Structural Variant Detection.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Methods for Detection and Mapping of Methylated and Hydroxymethylated Cytosine in DNA.Biomolecules · 2024Review
- Review
- 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
- Predicting gene expression state and prioritizing putative enhancers using 5hmC signal.Genome biology · 2024Article
- OM2Seq: learning retrieval embeddings for optical genome mapping.Bioinformatics advances · 2024Article
- 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
- 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
- Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping.Nucleic acids research · 2022Article
- Computational challenges in detection of cancer using cell-free DNA methylation.Computational and structural biotechnology journal · 2022Review
- Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies.Biophysical reports · 2021Review
- A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids.Micromachines · 2021Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The epigenetic mark 5-hydroxymethylcytosine (5-hmC) is a distinct product of active DNA demethylation that is linked to gene regulation, development, and disease. In particular, 5-hmC levels dramatically decline in many cancers, potentially serving as an epigenetic biomarker. The noise associated with next-generation 5-hmC sequencing hinders reliable analysis of low 5-hmC containing tissues such as blood and malignant tumors. Additionally, genome-wide 5-hmC profiles generated by short-read sequencing are limited in providing long-range epigenetic information relevant to highly variable genomic regions, such as the 3.7 Mbp disease-related Human Leukocyte Antigen (HLA) region. We present a long-read, highly sensitive single-molecule mapping technology that generates hybrid genetic/epigenetic profiles of native chromosomal DNA. The genome-wide distribution of 5-hmC in human peripheral blood cells correlates well with 5-hmC DNA immunoprecipitation (hMeDIP) sequencing. However, the long single-molecule read-length of 100 kbp to 1 Mbp produces 5-hmC profiles across variable genomic regions that failed to show up in the sequencing data. In addition, optical 5-hmC mapping shows a strong correlation between the 5-hmC density in gene bodies and the corresponding level of gene expression. The single-molecule concept provides information on the distribution and coexistence of 5-hmC signals at multiple genomic loci on the same genomic DNA molecule, revealing long-range correlations and cell-to-cell epigenetic variation.
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