ArticleNature biotechnology2012
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing.
Article in Nature biotechnology, 2012. 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 211 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.
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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
211 citing papers in PubMed, 378 citations in OpenAlex.
- Yeast nuclei-mediated precise delivery of synthetic megabase-scale human DNA into mammalian embryos.Nature protocols · 2026Review
- Genome-Wide 6mA Map Unveils Epigenetic Adaptation in Deep-Sea Limpet.Ecology and evolution · 2026Article
- Host-Filtered Blood Nucleic Acids for Pathogen Detection: Shared Background, Sparse Signal, and Methodological Limits.Pathogens (Basel, Switzerland) · 2026Article
- Epigenetic regulation and antimicrobial resistance: functional roles of DNA methylation.FEMS microbiology reviews · 2026Review
- Long-read metagenomics for strain tracking after faecal microbiota transplant.Nature microbiology · 2025Article
- Dam-dependent epigenetic memory regulates prophage reintegration in Salmonella.Nucleic acids research · 2025Article
- Prophage-encoded methyltransferase drives adaptation of community-acquired methicillin-resistant Staphylococcus aureus.The Journal of clinical investigation · 2025Article
- The emerging role of DNA methylation in the pathogenicity of bacterial pathogens.Journal of bacteriology · 2025Review
- DNA methylation affects gene expression but not global chromatin structure inJournal of bacteriology · 2025Article
- 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
- De novo assembly and delivery of synthetic megabase-scale human DNA into mouse early embryos.Nature methods · 2025Article
- Revealing long-range heterogeneous organization of nucleoproteins with 6mA footprinting by ipdTrimming.Genome biology · 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
- Decoding the genome and epigenome of avianFrontiers in veterinary science · 2025Article
- The multifaceted role of m5C RNA methylation in digestive system tumorigenesis.Frontiers in cell and developmental biology · 2025Review
- Critical assessment of nanopore sequencing for the detection of multiple forms of DNA modifications.bioRxiv : the preprint server for biology · 2024Article
- SUPREM: an engineered non-site-specific m6A RNA methyltransferase with highly improved efficiency.Nucleic acids research · 2024Article
- Adenosine Deaminase-Like Gene-Carried Lentivirus Toolkit for Identification of DNA NAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
151 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
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- Erratum issued
Authors and funding
23 authors at 9 institutions in 2 countries.
Funding
Abstract
Single-molecule real-time (SMRT) DNA sequencing allows the systematic detection of chemical modifications such as methylation but has not previously been applied on a genome-wide scale. We used this approach to detect 49,311 putative 6-methyladenine (m6A) residues and 1,407 putative 5-methylcytosine (m5C) residues in the genome of a pathogenic Escherichia coli strain. We obtained strand-specific information for methylation sites and a quantitative assessment of the frequency of methylation at each modified position. We deduced the sequence motifs recognized by the methyltransferase enzymes present in this strain without prior knowledge of their specificity. Furthermore, we found that deletion of a phage-encoded methyltransferase-endonuclease (restriction-modification; RM) system induced global transcriptional changes and led to gene amplification, suggesting that the role of RM systems extends beyond protecting host genomes from foreign DNA.
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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.