Gene silencing by H‐NS from distal DNA site

Summary In the modern concept of gene regulation, ‘ DNA looping’ is the most common underlying mechanism in the interaction between RNA polymerase ( RNAP ) and transcription factors acting at a distance. This study demonstrates an additional mechanism by which DNA ‐bound proteins communicate with each other, by analysing the bacterial histone‐like nucleoid‐structuring protein ( H‐NS ), a general transcriptional silencer. The LEE5 promoter ( LEE5 p ) of enteropathogenic Escherichia coli was used as a model system to investigate the mechanism of H‐NS ‐mediated transcription repression. We found that H‐NS represses LEE5 p by binding to a cluster of A tracks upstream of −114, followed by spreading to a site at the promoter through the oligomerization of H‐NS molecules. At the promoter, the H‐NS makes a specific contact with the carboxy terminal domain of the α subunit of RNAP , which prevents the processing of RNAP –promoter complexes into initiation‐competent open promoter complexes, thereby regulating LEE5 p from distance.