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

Summary 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. Nucleoid‐associated protein H‐NS represses transcription by nucleoprotein complex formation on AT‐rich DNA. We show that transcription directed into H‐NS repressed promoters relieves their repression suggesting that the transcribing RNA polymerases can remodel the repressing H‐NS–DNA complex. This implies that efficient transcription may hinder formation of repressing H‐NS–DNA complexes, while poorly transcribed loci are prone to H‐NS repression.