[Antisense transcription within the hns locus of Escherichia coli].

Scanning the entire genome of E. coli by means of pattern-recognition software PlatProm spotted out more than a thousand of potential start points for antisense transcription. Taking into account possible role of antisense RNAs in the cell regulatory networks, our top-priority interest was focused on the promoter-like sites found within genes of transcription regulators. One of them (hns) encodes a major nucleoid protein affecting expression pattern of many genomic loci. Several potential start points for antisense transcription were found within its coding sequence. Gel-retardation assays, potassium permanganate and DNAse I foot-printings confirmed the ability of the intragenic promoter located approximately 280 bp downstream of ATG to bind RNA polymerase. Primer extension revealed the cDNA of the expected size while Northern blot hybridization assumes the presence of aRNA among cellular RNAs. Relative abundance of antisense RNA and hns-mRNA in vivo exhibited dependence on growth conditions thus assuming existence of regulatory pathways keeping cellular concentration of these two transcripts at the optimal level.

Gains and unexpected lessons from genome-scale promoter mapping.

Potential promoters in the genome of Escherichia coli were searched by pattern recognition software PlatProm and classified on the basis of positions relative to gene borders. Beside the expected promoters located in front of the coding sequences we found a considerable amount of intragenic promoter-like signals with a putative ability to drive either antisense or alternative transcription and revealed unusual genomic regions with extremely high density of predicted transcription start points (promoter 'islands'), some of which are located in coding sequences. PlatProm scores converted into probability of RNA polymerase binding demonstrated certain correlation with the enzyme retention registered by ChIP-on-chip technique; however, in 'dense' regions the value of correlation coefficient is lower than throughout the entire genome. Experimental verification confirmed the ability of RNA polymerase to interact and form multiple open complexes within promoter 'island' associated with appY, yet transcription efficiency was lower than might be expected. Analysis of expression data revealed the same tendency for other promoter 'islands', thus assuming functional relevance of non-productive RNA polymerase binding. Our data indicate that genomic DNA of E. coli is enriched by numerous unusual promoter-like sites with biological role yet to be understood.