Interference of transcription across H-NS binding sites and repression by H-NS

Mol Microbiol. 2018 May;108(3):226-239. doi: 10.1111/mmi.13926. Epub 2018 Feb 23.


Nucleoid-associated protein H-NS represses transcription by forming extended DNA-H-NS complexes. Repression by H-NS operates mostly at the level of transcription initiation. Less is known about how DNA-H-NS complexes interfere with transcription elongation. In vitro H-NS has been shown to enhance RNA polymerase pausing and to promote Rho-dependent termination, while in vivo inhibition of Rho resulted in a decrease of the genome occupancy by H-NS. Here we show that transcription directed across H-NS binding regions relieves H-NS (and H-NS/StpA) mediated repression of promoters in these regions. Further, we observed a correlation of transcription across the H-NS-bound region and de-repression. The data suggest that the transcribing RNA polymerase is able to remodel the H-NS complex and/or dislodge H-NS from the DNA and thus relieve repression. Such an interference of transcription and H-NS mediated repression may imply that poorly transcribed AT-rich loci are prone to be repressed by H-NS, while efficiently transcribed loci escape repression.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / biosynthesis
  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism*
  • Binding Sites / genetics
  • DNA, Bacterial / metabolism
  • DNA-Binding Proteins / biosynthesis
  • DNA-Binding Proteins / genetics*
  • DNA-Binding Proteins / metabolism*
  • DNA-Directed RNA Polymerases / metabolism
  • Enzyme Repression
  • Escherichia coli / genetics
  • Escherichia coli Proteins / genetics
  • Gene Expression Regulation, Bacterial / genetics
  • Promoter Regions, Genetic / genetics
  • Transcription, Genetic / genetics
  • Transcription, Genetic / physiology


  • Bacterial Proteins
  • DNA, Bacterial
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • H-NS protein, bacteria
  • DNA-Directed RNA Polymerases