ArticlePLoS genetics2014
Methylome diversification through changes in DNA methyltransferase sequence specificity.
Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.Cell host & microbe · 2026Article
- Expanding the landscape of BREX diversity: uncovering multi-layered functional frameworks and identification of novel BREX-related defense systems.Nucleic acids research · 2026Article
- Towards molecular evolutionary epigenomics with an expanded nucleotide code involving methylated bases.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Long-read metagenomics for strain tracking after faecal microbiota transplant.Nature microbiology · 2025Article
- Long read metagenomics-based precise tracking of bacterial strains and genomic changes after fecal microbiota transplantation.bioRxiv : the preprint server for biology · 2025Article
- ThemBio · 2025Article
- Horizontal acquisition of the Type I restriction-modification system enhances bacterial pathogenicity by mediating methylation of transcription factor-encoding genes.Nucleic acids research · 2025Article
- Host-encoded DNA methyltransferases modify the epigenome and host tropism of invading phages.iScience · 2025Article
- Decoding Adenine DNA Methylation Effects in Streptococcus Mutans: Insights Into Self-DNA Protection and Autoaggregation.Molecular oral microbiology · 2025Article
- Understanding prokaryotic adaptation through advanced DNA methylation detection techniques.The ISME journal · 2025Review
- Intercellular mosaic methylation in fast-growingNAR molecular medicine · 2024Article
- Emerging methylation-based approaches in microbiome engineering.Biotechnology for biofuels and bioproducts · 2024Review
- Review
- TheJournal of bacteriology · 2024Article
- Acquisition of Type I methyltransferase via horizontal gene transfer increases the drug resistance ofMicrobial genomics · 2023Article
- Methylome evolution suggests lineage-dependent selection in the gastric pathogen Helicobacter pylori.Communications biology · 2023Article
- Base-excision restriction enzymes: expanding the world of epigenetic immune systems.DNA research : an international journal for rapid publication of reports on genes and genomes · 2023Article
- Extension of bacterial rDNA sequencing for simultaneous methylation detection and its application in microflora analysis.Scientific reports · 2023Article
- Characterization of theFrontiers in microbiology · 2023Article
- Diverse DNA modification in marine prokaryotic and viral communities.Nucleic acids research · 2022Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Epigenetic modifications such as DNA methylation have large effects on gene expression and genome maintenance. Helicobacter pylori, a human gastric pathogen, has a large number of DNA methyltransferase genes, with different strains having unique repertoires. Previous genome comparisons suggested that these methyltransferases often change DNA sequence specificity through domain movement--the movement between and within genes of coding sequences of target recognition domains. Using single-molecule real-time sequencing technology, which detects N6-methyladenines and N4-methylcytosines with single-base resolution, we studied methylated DNA sites throughout the H. pylori genome for several closely related strains. Overall, the methylome was highly variable among closely related strains. Hypermethylated regions were found, for example, in rpoB gene for RNA polymerase. We identified DNA sequence motifs for methylation and then assigned each of them to a specific homology group of the target recognition domains in the specificity-determining genes for Type I and other restriction-modification systems. These results supported proposed mechanisms for sequence-specificity changes in DNA methyltransferases. Knocking out one of the Type I specificity genes led to transcriptome changes, which suggested its role in gene expression. These results are consistent with the concept of evolution driven by DNA methylation, in which changes in the methylome lead to changes in the transcriptome and potentially to changes in phenotype, providing targets for natural or artificial selection.
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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.