Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli

Nat Biotechnol. 1998 Jun;16(6):566-71. doi: 10.1038/nbt0698-566.


A global methylation-based technique was used to identify, display, and quantitate the in vivo occupancy of numerous protein-binding sites within the Escherichia coli genome. The protein occupancy profiles of these sites showed variation across different growth conditions and genetic backgrounds. Of the 25 sites identified in this study, 24 occurred within 5' noncoding regions. Protein occupancy at 13 of these sites was supported by independent biochemical and genetic evidence. Most of the remaining 12 sites fell upstream of genes with no previously known function. A multivariate statistical analysis was utilized to group such uncharacterized genes with well-characterized ones, providing insights into their function based on a common pattern of transcriptional regulation.

Publication types

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

MeSH terms

  • DNA Modification Methylases / metabolism*
  • DNA, Bacterial / genetics*
  • DNA-Binding Proteins / genetics*
  • DNA-Cytosine Methylases / metabolism
  • Escherichia coli / genetics*
  • Escherichia coli / growth & development
  • Escherichia coli Proteins
  • Genome, Bacterial*
  • Models, Biological
  • Site-Specific DNA-Methyltransferase (Adenine-Specific) / metabolism


  • DNA, Bacterial
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • DNA Modification Methylases
  • DNA modification methylase SssI
  • DNA-Cytosine Methylases
  • Dam methyltransferase
  • Site-Specific DNA-Methyltransferase (Adenine-Specific)
  • dam protein, E coli