ArticleNature methods2010
Direct detection of DNA methylation during single-molecule, real-time sequencing.
Article in Nature methods, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 726 papers, 2 of them syntheses that pooled it.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
726 citing papers in PubMed, 2 syntheses or guidelines pooled it, 1,474 citations in OpenAlex.
- Long-Read sequencing in psychiatric omics: a systematic review of current evidence.Molecular psychiatry · 2026Pooled it
- [Advances in the Application of Forensic Microbiome Analysis in Tissue Source Inference].Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · 2025Pooled it
- Small variant calling in the era of long-read sequencing.Nature reviews. Genetics · 2026Review
- Review
- Somatic mosaicism in the brain: linking development, ageing and neurodegeneration.Nature reviews. Neurology · 2026Review
- Integrative Epigenomics: Bioinformatics Strategies for Multi-Omics Data Analysis in Health and Disease.Epigenomes · 2026Review
- DNA Methylation as a Programmable Information Layer: From Molecular Marks to Disease State Engineering.International journal of molecular sciences · 2026Review
- Comprehensive benchmarking of tools for nanopore-based detection of DNA methylation.Nature communications · 2026Article
- Genome-wide DNA methylation analysis in pigs using long-read sequencing unveils high-altitude adaptation and allele-specific regulation.BMC genomics · 2026Article
- Long-read sequencing technologies and bioinformatics: a new perspective for decoding DNA methylation modifications.Journal of translational medicine · 2026Review
- Epigenetic Phase Variation in Bacterial Adaptation to Environmental Stress: A Narrative Review.Current microbiology · 2026Review
- MeDiCNet: Integrating Multi-scale Dynamic Convolution and Enhanced Position-Aware Transformer for DNA Methylation Site Prediction.Interdisciplinary sciences, computational life sciences · 2026Article
- From fragments to full pictures: how long-read sequencing platforms are revolutionizing oncology research.Molecular biology reports · 2026Review
- Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources.Genome research · 2026Article
- MethyNano: supervised contrastive pretraining enables robust and generalizable methylation detection from nanopore sequencing.Bioinformatics (Oxford, England) · 2026Article
- SM-NucSeq, Genetic and Epigenetic Sequencing of Nucleosomes with Single-Molecule Real-Time Sequencing.Nano letters · 2026Article
- Genome-Wide 6mA Map Unveils Epigenetic Adaptation in Deep-Sea Limpet.Ecology and evolution · 2026Article
- How Genomic and Structural Context Could Shape JAK-STAT Variant Pathogenicity.Twin research and human genetics : the official journal of the International Society for Twin Studies · 2026Article
- Z-Calling: a tool for A/Z (2,6-diaminopurine) base calling and dZ-DNA detection using PacBio HiFi reads.Communications biology · 2026Article
- Nanopore direct RNA sequencing for RNA modification analysis: workflow assessment and computational tool benchmarking.Advanced biotechnology · 2026Article
666 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
We describe the direct detection of DNA methylation, without bisulfite conversion, through single-molecule, real-time (SMRT) sequencing. In SMRT sequencing, DNA polymerases catalyze the incorporation of fluorescently labeled nucleotides into complementary nucleic acid strands. The arrival times and durations of the resulting fluorescence pulses yield information about polymerase kinetics and allow direct detection of modified nucleotides in the DNA template, including N6-methyladenine, 5-methylcytosine and 5-hydroxymethylcytosine. Measurement of polymerase kinetics is an intrinsic part of SMRT sequencing and does not adversely affect determination of primary DNA sequence. The various modifications affect polymerase kinetics differently, allowing discrimination between them. We used these kinetic signatures to identify adenine methylation in genomic samples and found that, in combination with circular consensus sequencing, they can enable single-molecule identification of epigenetic modifications with base-pair resolution. This method is amenable to long read lengths and will likely enable mapping of methylation patterns in even highly repetitive genomic regions.
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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.