ArticleNucleic acids research2014
qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Type I restriction-modification systems regulate gene expression through DNA topology.Nucleic acids research · 2026Article
- Long-read sequencing technologies and bioinformatics: a new perspective for decoding DNA methylation modifications.Journal of translational medicine · 2026Review
- Exploring the Significance of Somaclonal Variations in Horticultural Crops.Molecular biotechnology · 2025Review
- The SpxA1-TenA toxin-antitoxin system regulates epigenetic variations of Streptococcus pneumoniae by targeting protein synthesis.PLoS pathogens · 2024Article
- Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing.Clinical epigenetics · 2022Review
- The acquisition of clinically relevant amoxicillin resistance in Streptococcus pneumoniae requires ordered horizontal gene transfer of four loci.PLoS pathogens · 2022Article
- DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites.Briefings in bioinformatics · 2021Article
- DCNN-4mC: Densely connected neural network based N4-methylcytosine site prediction in multiple species.Computational and structural biotechnology journal · 2021Article
- Prevalence of phase variable epigenetic invertons among host-associated bacteria.Nucleic acids research · 2020Article
- Regulation of pneumococcal epigenetic and colony phases by multiple two-component regulatory systems.PLoS pathogens · 2020Article
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- Genome-wide systematic identification of methyltransferase recognition and modification patterns.Nature communications · 2019Article
- Molecular Mechanisms ofJournal of bacteriology · 2019Article
- Phase Variation ofMicrobiology spectrum · 2019Article
- Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39.Nucleic acids research · 2018Article
- Observation of Pneumococcal Phase Variation in Colony Morphology.Bio-protocol · 2017Article
- Epigenetic Switch Driven by DNA Inversions Dictates Phase Variation in Streptococcus pneumoniae.PLoS pathogens · 2016Article
- Addiction of Hypertransformable Pneumococcal Isolates to Natural Transformation for In Vivo Fitness and Virulence.Infection and immunity · 2016Article
- Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio single-molecule real-time (SMRT) technology.Nucleic acids research · 2016Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In an isogenic cell population, phenotypic heterogeneity among individual cells is common and critical for survival of the population under different environment conditions. DNA modification is an important epigenetic factor that can regulate phenotypic heterogeneity. The single molecule real-time (SMRT) sequencing technology provides a unique platform for detecting a wide range of DNA modifications, including N6-methyladenine (6-mA), N4-methylcytosine (4-mC) and 5-methylcytosine (5-mC). Here we present qDNAmod, a novel bioinformatic tool for genome-wide quantitative profiling of intercellular heterogeneity of DNA modification from SMRT sequencing data. It is capable of estimating proportion of isogenic haploid cells, in which the same loci of the genome are differentially modified. We tested the reliability of qDNAmod with the SMRT sequencing data of Streptococcus pneumoniae strain ST556. qDNAmod detected extensive intercellular heterogeneity of DNA methylation (6-mA) in a clonal population of ST556. Subsequent biochemical analyses revealed that the recognition sequences of two type I restriction-modification (R-M) systems are responsible for the intercellular heterogeneity of DNA methylation initially identified by qDNAmod. qDNAmod thus represents a valuable tool for studying intercellular phenotypic heterogeneity from genome-wide DNA modification.
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