Periodic Transcriptional Organization of the E. coli Genome

The organization of transcription within the prokaryotic nucleoid may be expected to both depend on and determine the structure of the chromosome. Indeed, immunofluorescence localization of transcriptional regulators has revealed foci in actively transcribing Escherichia coli cells. Furthermore, structural and biochemical approaches suggest that there are ∼50 independent loop domains per genome. Here I show that in four E. coli strains, genes that are controlled by a sequence-specific transcriptional regulator tend to locate next to the gene encoding this regulator, or at regular distances that are multiples of 1/50th of the chromosome length. This periodicity is consistent with a solenoidal epi-organization of the chromosome, which would gather into foci the interacting partners; the regulator molecules and their DNA binding sites. Binding at genuine regulatory sites on DNA would thus be optimized by co-transcriptionally translating regulators in their vicinity.