Gene silencing and large-scale domain structure of the E. coli genome

Mol Biosyst. 2013 Apr 5;9(4):758-67. doi: 10.1039/c3mb25364c.


The H-NS chromosome-organizing protein in E. coli can stabilize genomic DNA loops, and form oligomeric structures connected to repression of gene expression. Motivated by the link between chromosome organization, protein binding and gene expression, we analyzed publicly available genomic data sets of various origins, from genome-wide protein binding profiles to evolutionary information, exploring the connections between chromosomal organization, gene-silencing, pseudo-gene localization and horizontal gene transfer. We report the existence of transcriptionally silent contiguous areas corresponding to large regions of H-NS protein binding along the genome, their position indicates a possible relationship with the known large-scale features of chromosome organization.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / metabolism
  • Binding Sites
  • Chromosome Mapping
  • DNA-Binding Proteins / metabolism
  • Escherichia coli / genetics*
  • Escherichia coli / metabolism
  • Gene Expression Regulation, Bacterial
  • Gene Silencing*
  • Genome, Bacterial*
  • Protein Binding


  • Bacterial Proteins
  • DNA-Binding Proteins
  • H-NS protein, bacteria