ArticleNucleic acids research2012
Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 215 papers.
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Who cites it
215 citing papers in PubMed.
- LEMONmethyl-seq: Targeted long-read DNA methylation profiling reveals dynamics of CRISPR epigenome editing and endogenous DNA methylation patterns.bioRxiv : the preprint server for biology · 2026Article
- Epigenetic regulation in prokaryotes: transcriptional and phenotypic outcomes of DNA methyltransferase activity.FEMS microbiology reviews · 2026Review
- Carboxymethylcytosine is a natural base modification and a handle for bacteriophage DNA hypermodification.Nature communications · 2025Article
- Lactococcal mobile genetic elements harbour a diverse phage defensome rich in restriction-modification systems.Nucleic acids research · 2025Article
- From sequence to activity: the HgaI-homologous restriction modification system RM.MhoVI of Mycoplasma hominis.BMC microbiology · 2025Article
- Comparative and functional genomic analysis of foreign DNA defense mechanisms inMicrobiology spectrum · 2025Article
- Genome-Wide Identification of DNA Methyltransferase and Demethylase inPlants (Basel, Switzerland) · 2025Article
- Complete genome sequence data ofData in brief · 2025Article
- methylMapR-an R package to generate the functional prokaryotic methylome.Microbiology resource announcements · 2025Article
- Genome sequence and methylome profile ofMicrobiology resource announcements · 2025Article
- Exploring the Significance of Somaclonal Variations in Horticultural Crops.Molecular biotechnology · 2025Review
- Revealing long-range heterogeneous organization of nucleoproteins with 6mA footprinting by ipdTrimming.Genome biology · 2025Article
- Comprehensive comparison of the third-generation sequencing tools for bacterial 6mA profiling.Nature communications · 2025Article
- Quorum sensing and DNA methylation play active roles in clinicalJournal of bacteriology · 2025Article
- PneumoBrowse 2: an integrated visual platform for curated genome annotation and multiomics data analysis of Streptococcus pneumoniae.Nucleic acids research · 2025Article
- 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
- Matching excellence: Oxford Nanopore Technologies' rise to parity with Pacific Biosciences in genome reconstruction of non-model bacterium with high G+C content.Microbial genomics · 2024Article
- Phage defence loci of Streptococcus thermophilus-tip of the anti-phage iceberg?Nucleic acids research · 2024Article
155 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
Abstract
DNA methylation is the most common form of DNA modification in prokaryotic and eukaryotic genomes. We have applied the method of single-molecule, real-time (SMRT®) DNA sequencing that is capable of direct detection of modified bases at single-nucleotide resolution to characterize the specificity of several bacterial DNA methyltransferases (MTases). In addition to previously described SMRT sequencing of N6-methyladenine and 5-methylcytosine, we show that N4-methylcytosine also has a specific kinetic signature and is therefore identifiable using this approach. We demonstrate for all three prokaryotic methylation types that SMRT sequencing confirms the identity and position of the methylated base in cases where the MTase specificity was previously established by other methods. We then applied the method to determine the sequence context and methylated base identity for three MTases with unknown specificities. In addition, we also find evidence of unanticipated MTase promiscuity with some enzymes apparently also modifying sequences that are related, but not identical, to the cognate site.
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