ArticleNucleic acids research2014
The complex methylome of the human gastric pathogen Helicobacter pylori.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT02788214 (Helicobacter Pylori Genome Project), which is not on this map. Cited by 80 papers.
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.
Helicobacter Pylori Genome Project (HpGP)
Who cites it
80 citing papers in PubMed, 124 citations in OpenAlex.
- Comprehensive benchmarking of tools for nanopore-based detection of DNA methylation.Nature communications · 2026Article
- Methylation Dynamics inMicroorganisms · 2026Article
- Within-host diversity and phased variant analysis reveal structures and recombination of Helicobacter pylori subpopulations in stomach.GigaScience · 2026Article
- MPore: database-driven identification of active methyltransferases in prokaryotic genomes from nanopore sequencing.Bioinformatics advances · 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
- ThemBio · 2025Article
- Advances in Diversity, Evolutionary Dynamics and Biotechnological Potential of Restriction-Modification Systems.Microorganisms · 2025Review
- Host-encoded DNA methyltransferases modify the epigenome and host tropism of invading phages.iScience · 2025Article
- Article
- Snappy: fast identification of DNA methylation motifs based on oxford nanopore reads.Bioinformatics advances · 2025Article
- Epigenetics and environmental health.Frontiers of medicine · 2024Review
- Article
- Review
- TheJournal of bacteriology · 2024Article
- Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads.Bioinformatics (Oxford, England) · 2023Article
- Methylome evolution suggests lineage-dependent selection in the gastric pathogen Helicobacter pylori.Communications biology · 2023Article
- Helicobacter pylori infection.Nature reviews. Disease primers · 2023Review
- PADLOC: a web server for the identification of antiviral defence systems in microbial genomes.Nucleic acids research · 2022Article
- Biomarker Characterization and Prediction of Virulence and Antibiotic Resistance fromBiomolecules · 2022Review
- Metagenomic Sequencing for Microbial DNA in Human Samples: Emerging Technological Advances.International journal of molecular sciences · 2022Review
20 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
13 authors at 4 institutions in 2 countries.
Funding
Abstract
The genome of Helicobacter pylori is remarkable for its large number of restriction-modification (R-M) systems, and strain-specific diversity in R-M systems has been suggested to limit natural transformation, the major driving force of genetic diversification in H. pylori. We have determined the comprehensive methylomes of two H. pylori strains at single base resolution, using Single Molecule Real-Time (SMRT®) sequencing. For strains 26695 and J99-R3, 17 and 22 methylated sequence motifs were identified, respectively. For most motifs, almost all sites occurring in the genome were detected as methylated. Twelve novel methylation patterns corresponding to nine recognition sequences were detected (26695, 3; J99-R3, 6). Functional inactivation, correction of frameshifts as well as cloning and expression of candidate methyltransferases (MTases) permitted not only the functional characterization of multiple, yet undescribed, MTases, but also revealed novel features of both Type I and Type II R-M systems, including frameshift-mediated changes of sequence specificity and the interaction of one MTase with two alternative specificity subunits resulting in different methylation patterns. The methylomes of these well-characterized H. pylori strains will provide a valuable resource for future studies investigating the role of H. pylori R-M systems in limiting transformation as well as in gene regulation and host interaction.
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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.