ArticleNucleic acids research2021
Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 18 citations in OpenAlex.
- Genome mining of insecticidal toxins and comparative genomic analysis of Lysinibacillus pinotti VCRC B653, a promising mosquito biocontrol agent with dual larvicidal and oviposition-attractant activities.World journal of microbiology & biotechnology · 2026Article
- Comparative performance evaluation of bisulfite- and enzyme-based DNA conversion methods.Clinical epigenetics · 2025Article
- Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities.Nucleic acids research · 2025Article
- Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine.Genome research · 2024Article
- Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novelbioRxiv : the preprint server for biology · 2024Article
- Article
- A Survey of Archaeal Restriction-Modification Systems.Microorganisms · 2023Article
- Shaping eukaryotic epigenetic systems by horizontal gene transfer.BioEssays : news and reviews in molecular, cellular and developmental biology · 2023Article
- Loss of p53 Concurrent with RAS and TERT Activation Induces Glioma Formation.Molecular neurobiology · 2023Article
- Complete genome assembly and methylome dissection ofFrontiers in microbiology · 2023Article
- Tuning of Gene Expression inACS synthetic biology · 2022Article
- Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment.Genome researchArticle
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation is widespread amongst eukaryotes and prokaryotes to modulate gene expression and confer viral resistance. 5-Methylcytosine (m5C) methylation has been described in genomes of a large fraction of bacterial species as part of restriction-modification systems, each composed of a methyltransferase and cognate restriction enzyme. Methylases are site-specific and target sequences vary across organisms. High-throughput methods, such as bisulfite-sequencing can identify m5C at base resolution but require specialized library preparations and single molecule, real-time (SMRT) sequencing usually misses m5C. Here, we present a new method called RIMS-seq (rapid identification of methylase specificity) to simultaneously sequence bacterial genomes and determine m5C methylase specificities using a simple experimental protocol that closely resembles the DNA-seq protocol for Illumina. Importantly, the resulting sequencing quality is identical to DNA-seq, enabling RIMS-seq to substitute standard sequencing of bacterial genomes. Applied to bacteria and synthetic mixed communities, RIMS-seq reveals new methylase specificities, supporting routine study of m5C methylation while sequencing new genomes.
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