ArticleNucleic acids research2022
Diverse DNA modification in marine prokaryotic and viral communities.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 22 citations in OpenAlex.
- Growth Phase-Related DNA Methylation and Localized DNA Fragment Density Variation inEpigenomes · 2026Article
- Community structure and methylation of microbes in an artificially forced sediment core.Microbiology spectrum · 2026Article
- Epigenetic regulation in prokaryotes: transcriptional and phenotypic outcomes of DNA methyltransferase activity.FEMS microbiology reviews · 2026Review
- Viromics approaches for the study of viral diversity and ecology in microbiomes.Nature reviews. Genetics · 2026Review
- Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota.Nature microbiology · 2025Article
- Host-encoded DNA methyltransferases modify the epigenome and host tropism of invading phages.iScience · 2025Article
- Understanding prokaryotic adaptation through advanced DNA methylation detection techniques.The ISME journal · 2025Review
- Multiple roles of DNA methylation in sea-ice bacterial communities and associated viruses.The ISME journal · 2025Article
- Insights Into Phylogeny, Diversity and Functional Potential of Poseidoniales Viruses.Environmental microbiology · 2025Article
- Genetic and functional diversity of β-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis.Nature communications · 2024Article
- Curcumin can improve spinal cord injury by inhibiting DNA methylation.Molecular and cellular biochemistry · 2024Article
- A sequential one-pot approach for rapid and convenient characterization of putative restriction-modification systems.mSystems · 2023Article
- Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species.The ISME journal · 2023Article
- Long-Read Sequencing Reveals Extensive DNA Methylations in Human Gut Phagenome Contributed by Prevalently Phage-Encoded Methyltransferases.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Trait biases in microbial reference genomes.Scientific data · 2023Article
- Bacterial Epigenomics: Coming of Age.mSystems · 2021Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA chemical modifications, including methylation, are widespread and play important roles in prokaryotes and viruses. However, current knowledge of these modification systems is severely biased towards a limited number of culturable prokaryotes, despite the fact that a vast majority of microorganisms have not yet been cultured. Here, using single-molecule real-time sequencing, we conducted culture-independent 'metaepigenomic' analyses (an integrated analysis of metagenomics and epigenomics) of marine microbial communities. A total of 233 and 163 metagenomic-assembled genomes (MAGs) were constructed from diverse prokaryotes and viruses, respectively, and 220 modified motifs and 276 DNA methyltransferases (MTases) were identified. Most of the MTase genes were not genetically linked with the endonuclease genes predicted to be involved in defense mechanisms against extracellular DNA. The MTase-motif correspondence found in the MAGs revealed 10 novel pairs, 5 of which showed novel specificities and experimentally confirmed the catalytic specificities of the MTases. We revealed novel alternative specificities in MTases that are highly conserved in Alphaproteobacteria, which may enhance our understanding of the co-evolutionary history of the methylation systems and the genomes. Our findings highlight diverse unexplored DNA modifications that potentially affect the ecology and evolution of prokaryotes and viruses in nature.
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