Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine

Nucleic Acids Res. 2011 Nov;39(21):9294-305. doi: 10.1093/nar/gkr607. Epub 2011 Aug 3.


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.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5-Methylcytosine / analogs & derivatives
  • Amino Acid Sequence
  • Animals
  • Chromosome Mapping
  • Conserved Sequence
  • Cytosine / analogs & derivatives*
  • Cytosine / analysis
  • Cytosine / metabolism
  • DNA Cleavage
  • DNA Restriction Enzymes / chemistry
  • DNA Restriction Enzymes / classification
  • DNA Restriction Enzymes / metabolism*
  • Genomics
  • Molecular Sequence Data
  • Rats
  • Substrate Specificity


  • 5-hydroxymethylcytosine
  • 5-Methylcytosine
  • Cytosine
  • DNA Restriction Enzymes
  • endodeoxyribonuclease Rts1