Widespread divergent transcription from bacterial and archaeal promoters is a consequence of DNA sequence symmetry

Transcription initiates at promoters, DNA regions recognised by a DNA-dependent RNA polymerase. We previously identified horizontally acquired Escherichia coli promoters where the direction of transcription was unclear. Here, we show that more than half of these promoters are bidirectional. Using genome-scale approaches, we demonstrate that 19% of all transcription start sites detected in E. coli are associated with a bidirectional promoter. Bidirectional promoters are similarly common in diverse bacteria and archaea and have inherent symmetry: specific bases required for transcription initiation are reciprocally co-located on opposite DNA strands. Bidirectional promoters enable co-regulation of divergent genes and are enriched in both intergenic and horizontally acquired regions. Divergent transcription is conserved among bacteria, archaea and eukaryotes, but the underlying mechanisms for bidirectionality are different.