REP-elements of the Escherichia coli genome and transcription signals: positional and functional analysis

In the intergenic regions of the Escherichia coli genome there are 356 REP-elements, containing 1–12 repeated sequences with degenerated consensus. Their biological role is poorly understood, but multiplicity in the genome, preferential localization between convergent genes and ability to form hairpin structures have led to the assumption that REP-elements participate in the transcription termination and processes affecting stability of the corresponding RNAs. Though the direct experiments did not confirm the ability of the studied REP-sequence to stop RNA synthesis and some ambiguity regarding their primary function still exists. In this study, positional and functional analysis was undertaken for the entire set of annotated REP-sequences and the reduced efficiency of RNA synthesis behind the many REP-modules was observed. For all that some REP-modules did not affect the processivity of RNA synthesis, assuming their read-through transcription and further possibility to be involved in the regulatory events. We also observed REP-associated transcription activation and found overlapping promoters. The most unexpected was specific distribution of REP-sequences nearby the promoter islands, which assumes an insulator-like action of these sequences, maintaining transcriptional autonomy of the islands, and indicates functional significance of the island-born RNAs.