Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

Nat Biotechnol. 2012 Dec;30(12):1232-9. doi: 10.1038/nbt.2432. Epub 2012 Nov 8.


Single-molecule real-time (SMRT) DNA sequencing allows the systematic detection of chemical modifications such as methylation but has not previously been applied on a genome-wide scale. We used this approach to detect 49,311 putative 6-methyladenine (m6A) residues and 1,407 putative 5-methylcytosine (m5C) residues in the genome of a pathogenic Escherichia coli strain. We obtained strand-specific information for methylation sites and a quantitative assessment of the frequency of methylation at each modified position. We deduced the sequence motifs recognized by the methyltransferase enzymes present in this strain without prior knowledge of their specificity. Furthermore, we found that deletion of a phage-encoded methyltransferase-endonuclease (restriction-modification; RM) system induced global transcriptional changes and led to gene amplification, suggesting that the role of RM systems extends beyond protecting host genomes from foreign DNA.

Publication types

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

MeSH terms

  • 5-Methylcytosine / metabolism
  • Adenine / analogs & derivatives
  • Adenine / metabolism
  • Biotechnology
  • Chromosome Mapping
  • DNA Methylation / genetics
  • DNA Restriction-Modification Enzymes / deficiency
  • DNA Restriction-Modification Enzymes / genetics
  • DNA Restriction-Modification Enzymes / metabolism
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • DNA, Bacterial / metabolism
  • Escherichia coli / genetics*
  • Escherichia coli / metabolism
  • Escherichia coli / pathogenicity
  • Gene Amplification
  • Gene Deletion
  • Genome, Bacterial
  • Sequence Analysis, DNA / methods
  • Spiro Compounds
  • Substrate Specificity


  • BAS 100
  • DNA Restriction-Modification Enzymes
  • DNA, Bacterial
  • Spiro Compounds
  • 5-Methylcytosine
  • Adenine
  • 6-methyladenine