ArticleNucleic acids research2011
Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 74 citations in OpenAlex.
- A bacterial defense system targeting modified cytosine of phage genomic DNA.Nature communications · 2026Article
- Biology of host-dependent restriction-modification in prokaryotes.EcoSal Plus · 2025Review
- Structural analysis of the BisI family of modification dependent restriction endonucleases.Nucleic acids research · 2024Article
- Loci cg06256735 and cg15815843 in the MFAP5 gene regulatory regions are hypomethylated in varicose veins apparently due to active demethylation.Bioscience reports · 2024Article
- Recent Advances on DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications.Advances in experimental medicine and biology · 2022Article
- Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns.Advances in experimental medicine and biology · 2022Article
- Integrated single-cell sequencing of 5-hydroxymethylcytosine and genomic DNA using scH&G-seq.STAR protocols · 2021Article
- DNA methylation methods: Global DNA methylation and methylomic analyses.Methods (San Diego, Calif.) · 2021Review
- Structure-Based Deep Mining Reveals First-Time Annotations for 46 Percent of the Dark Annotation Space of the 9,671-Member Superproteome of the Nucleocytoplasmic Large DNA Viruses.Journal of virology · 2020Article
- The structure of theThe Journal of biological chemistry · 2020Article
- Article
- A protein architecture guided screen for modification dependent restriction endonucleases.Nucleic acids research · 2019Article
- Crystal structure of the modification-dependent SRA-HNH endonuclease TagI.Nucleic acids research · 2018Article
- Article
- Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion identifies evolutionarily unconserved CpGs as TET targets.Genome biology · 2016Article
- DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications.Advances in experimental medicine and biology · 2016Review
- Structure-guided sequence specificity engineering of the modification-dependent restriction endonuclease LpnPI.Nucleic acids research · 2015Article
- Expression and purification of a single-chain Type IV restriction enzyme Eco94GmrSD and determination of its substrate preference.Scientific reports · 2015Article
- Chemical methods for decoding cytosine modifications in DNA.Chemical reviews · 2015Review
- A novel method to analyze 5-hydroxymethylcytosine in CpG sequences using maintenance DNA methyltransferase, DNMT1.FEBS open bio · 2015Article
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9 authors at 1 institution in 1 country.
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Abstract
PvuRts1I is a modification-dependent restriction endonuclease that recognizes 5-hydroxymethylcytosine (5hmC) as well as 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA. Using PvuRts1I as the founding member, we define a family of homologous proteins with similar DNA modification-dependent recognition properties. At the sequence level, these proteins share a few uniquely conserved features. We show that these enzymes introduce a double-stranded cleavage at the 3'-side away from the recognized modified cytosine. The distances between the cleavage sites and the modified cytosine are fixed within a narrow range, with the majority being 11-13 nt away in the top strand and 9-10 nt away in the bottom strand. The recognition sites of these enzymes generally require two cytosines on opposite strand around the cleavage sites, i.e. 5'-CN(11-13)↓N(9-10)G-3'/3'-GN(9-10)↓N(11-13)C-5', with at least one cytosine being modified for efficient cleavage. As one potential application for these enzymes is to provide useful tools for selectively mapping 5hmC sites, we have compared the relative selectivity of a few PvuRts1I family members towards different forms of modified cytosines. Our results show that the inherently different relative selectivity towards modified cytosines can have practical implications for their application. By using AbaSDFI, a PvuRts1I homolog with the highest relative selectivity towards 5ghmC, to analyze rat brain DNA, we show it is feasible to map genomic 5hmC sites close to base resolution. Our study offers unique tools for determining more accurate hydroxymethylomes in mammalian cells.
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