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[Assays on comparing the local concentration of HU protein in the different regions of Escherichia coli genomic DNA].

HU, a nonspecific histone-like DNA binding protein is a major component of the bacterial nucleoid. HU is referred to as an accessory factor for complex protein-DNA assembly and as a protein involved in DNA compaction. In this study we investigated in vivo HU binding along the different regions of E. coli genome. For this purpose we used ChIP--in vivo formaldehyde crosslinking and immunoprecipitation of protein-DNA complexes with antiHU-antibodies. This technique allows to compare the local concentration of HU protein in the different regions of E. coli genomic DNA. In this study we analysed the HU-DNA crosslinking both in exponentially growing and stationary phase of bacteria in the following regions of E. coli genome: oriC region, promoter and structural regions of hupA and hupB genes coding two different subunits of HU, and structural parts of dps and glgS genes which are active only in stationary phase. Our results indicate that in exponentially growing E. coli cells the local concentration of HU protein is uniform for all analysed regions of genome and does not depend on their transcriptional status. The twofold increase of local concentration of HU protein was also shown for all analysed genome regions in the stationary phase cells.