ArticleNature communications2015
Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes.
Article in Nature communications, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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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.
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Who cites it
67 citing papers in PubMed.
- Growth Phase-Related DNA Methylation and Localized DNA Fragment Density Variation inEpigenomes · 2026Article
- Heterogeneity in microbial antibiotic responses: genetic basis and within-host evolution.Trends in genetics : TIG · 2026Review
- Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.Cell host & microbe · 2026Article
- Long-read sequencing technologies and bioinformatics: a new perspective for decoding DNA methylation modifications.Journal of translational medicine · 2026Review
- Epigenetic regulation in prokaryotes: transcriptional and phenotypic outcomes of DNA methyltransferase activity.FEMS microbiology reviews · 2026Review
- Epigenetic regulation and antimicrobial resistance: functional roles of DNA methylation.FEMS microbiology reviews · 2026Review
- Replication-coupled hemimethylation inFrontiers in microbiology · 2026Review
- From Methylomes to CRISPR Epigenetic Editing: New Paths in Antibiotic Resistance.Pathogens (Basel, Switzerland) · 2025Review
- Long-read metagenomics for strain tracking after faecal microbiota transplant.Nature microbiology · 2025Article
- Computational analysis of DNA methylation from long-read sequencing.Nature reviews. Genetics · 2025Review
- Long read metagenomics-based precise tracking of bacterial strains and genomic changes after fecal microbiota transplantation.bioRxiv : the preprint server for biology · 2025Article
- Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis?Microorganisms · 2025Review
- Deep-learning of Nanopore sequences reveals the 6mA distribution and dynamics in human gut microbiome.National science review · 2025Article
- SMAC: identifying DNA N6-methyladenine (6mA) at the single-molecule level using SMRT CCS data.Briefings in bioinformatics · 2025Article
- Understanding prokaryotic adaptation through advanced DNA methylation detection techniques.The ISME journal · 2025Review
- KinMethyl: robust methylation detection in prokaryotic SMRT sequencing via kinetic signal modeling and deep feature integration.Bioinformatics advances · 2025Article
- Methods for Detection and Mapping of Methylated and Hydroxymethylated Cytosine in DNA.Biomolecules · 2024Review
- Intercellular mosaic methylation in fast-growingNAR molecular medicine · 2024Article
- Emerging methylation-based approaches in microbiome engineering.Biotechnology for biofuels and bioproducts · 2024Review
- Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
Beyond its role in host defense, bacterial DNA methylation also plays important roles in the regulation of gene expression, virulence and antibiotic resistance. Bacterial cells in a clonal population can generate epigenetic heterogeneity to increase population-level phenotypic plasticity. Single molecule, real-time (SMRT) sequencing enables the detection of N6-methyladenine and N4-methylcytosine, two major types of DNA modifications comprising the bacterial methylome. However, existing SMRT sequencing-based methods for studying bacterial methylomes rely on a population-level consensus that lacks the single-cell resolution required to observe epigenetic heterogeneity. Here, we present SMALR (single-molecule modification analysis of long reads), a novel framework for single molecule-level detection and phasing of DNA methylation. Using seven bacterial strains, we show that SMALR yields significantly improved resolution and reveals distinct types of epigenetic heterogeneity. SMALR is a powerful new tool that enables de novo detection of epigenetic heterogeneity and empowers investigation of its functions in bacterial populations.
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