ArticleNucleic acids research2012
The methylomes of six bacteria.
Article in Nucleic acids research, 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 165 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
165 citing papers in PubMed, 269 citations in OpenAlex.
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- Comparative genomics and methylome profiling ofMicrobial genomics · 2026Article
- Replication-coupled hemimethylation inFrontiers in microbiology · 2026Review
- Genome sequence and methylome of the extremely halophilic bacteriumMicrobiology resource announcements · 2025Article
- Lactococcal mobile genetic elements harbour a diverse phage defensome rich in restriction-modification systems.Nucleic acids research · 2025Article
- Improving the Transformation Efficiency ofACS synthetic biology · 2025Article
- Advances in Diversity, Evolutionary Dynamics and Biotechnological Potential of Restriction-Modification Systems.Microorganisms · 2025Review
- Comprehensive comparison of the third-generation sequencing tools for bacterial 6mA profiling.Nature communications · 2025Article
- Host-encoded DNA methyltransferases modify the epigenome and host tropism of invading phages.iScience · 2025Article
- Quorum sensing and DNA methylation play active roles in clinicalJournal of bacteriology · 2025Article
- Development of a Pre-Modification Strategy to Overcome Restriction-Modification Barriers and Enhance Genetic Engineering inInternational journal of molecular sciences · 2025Article
- Article
- Understanding prokaryotic adaptation through advanced DNA methylation detection techniques.The ISME journal · 2025Review
- Resolving the chromatin impact of mosaic variants with targeted Fiber-seq.Genome research · 2024Article
- DNA-m6A calling and integrated long-read epigenetic and genetic analysis withGenome research · 2024Article
- Crosstalk between 6-methyladenine and 4-methylcytosine iniScience · 2024Article
- Changes in DNA methylation contribute to rapid adaptation in bacterial plant pathogen evolution.PLoS biology · 2024Article
- Resolving the chromatin impact of mosaic variants with targeted Fiber-seq.bioRxiv : the preprint server for biology · 2024Article
- The elimination of two restriction enzyme genes allows for electroporation-based transformation and CRISPR-Cas9-based base editing in the non-competent Gram-negative bacteriumApplied and environmental microbiology · 2024Article
- Article
105 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
Six bacterial genomes, Geobacter metallireducens GS-15, Chromohalobacter salexigens, Vibrio breoganii 1C-10, Bacillus cereus ATCC 10987, Campylobacter jejuni subsp. jejuni 81-176 and C. jejuni NCTC 11168, all of which had previously been sequenced using other platforms were re-sequenced using single-molecule, real-time (SMRT) sequencing specifically to analyze their methylomes. In every case a number of new N(6)-methyladenine ((m6)A) and N(4)-methylcytosine ((m4)C) methylation patterns were discovered and the DNA methyltransferases (MTases) responsible for those methylation patterns were assigned. In 15 cases, it was possible to match MTase genes with MTase recognition sequences without further sub-cloning. Two Type I restriction systems required sub-cloning to differentiate their recognition sequences, while four MTase genes that were not expressed in the native organism were sub-cloned to test for viability and recognition sequences. Two of these proved active. No attempt was made to detect 5-methylcytosine ((m5)C) recognition motifs from the SMRT® sequencing data because this modification produces weaker signals using current methods. However, all predicted (m6)A and (m4)C MTases were detected unambiguously. This study shows that the addition of SMRT sequencing to traditional sequencing approaches gives a wealth of useful functional information about a genome showing not only which MTase genes are active but also revealing their recognition sequences.
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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.