Transcriptional interference between convergent promoters caused by elongation over the promoter

Abstract

Transcriptional interference with convergent transcription from face-to-face promoters is a potentially important form of gene regulation in all organisms. Using LacZ reporter studies, the mechanism of interference was determined for a pair of face-to-face prokaryotic promoters in which a strong promoter interferes 5.6-fold with a weak promoter, 62 bp away. The promoters were variously rearranged to test different models of interference. Terminating transcription from the strong promoter before it reached the weak promoter dramatically reduced interference, indicating a requirement for the passage of the converging RNAP over the weak promoter. Based on in vitro experiments showing a slow rate of escape for open complexes at the weak promoter and their sensitivity to head-on collisions with elongating RNAP, a "sitting duck" model of interference is proposed and supported with in vivo permanganate footprinting. The model is further supported by the analysis of a second set of prokaryotic face-to-face promoters.