earticle

영어

Compaction of the bacterial nucleoid should not only allow for efficient replication and segregation during cell division, but it must also simultaneously participate in transcription and other processes involving the genome. The compact nucleoid body in a bacterial cell is extensively bound by several nucleoid- associated proteins (NAPs), which include HNS, HU, IHF, Fis, and Dps. A recent genome-wide analysis of NAPs association in E. coli genome identified several hundred binding regions but was limited in the ability to define binding motif. Here we improve on the resolution of chromatin immunoprecipitation coupled with massive sequencing (ChIP-seq) to determine the binding motif at single nucleotide resolution along with the distribution of the HNS-binding sites on a genome-scale. To this end, we optimized the ChIP-exo approach for bacterial applications, where an exonuclease trims ChIP DNA to a precise distance from the crosslinking site. Due to the ability to bridge adjacent tracts of DNA, HNS can locally induce some type of higher-order compaction, resulting in specific regulatory role in transcription. However, the molecular basis for the recognition of the local binding events has not been revealed. Our data enable the refinement of the HNS-binding motif in the DNA region bridged by HNS at single nucleotide resolution, providing a direct explanation for the mechanism underlying the transcription repression by HNS.