Dynamical Analysis on Gene Activity in the Presence of Repressors and an   Interfering Promoter
  Transcription is regulated through interplay between transcription factors, an RNA polymerase(RNAP), and a promoter. Even for a simple repressive transcription factor that disturbs promoter activity at the initial binding of RNAP, its repression level is not determined solely by the dissociation constant of transcription factor but is sensitive to the time scales of processes in RNAP. We first analyse the promoter activity under strong repression by a slow binding repressor, in which case transcriptions occur in a burst, followed by a long quiescent period while a repressor binds to the operator; the number of transcriptions, the bursting and the quiescent times are estimated by reaction rates. We then examine interference effect from an opposing promoter, using the correlation function of transcription initiations for a single promoter. The interference is shown to de-repress the promoter because RNAP's from the opposing promoter most likely encounter the repressor and remove it in case of strong repression. This de-repression mechanism should be especially prominent for the promoters that facilitate fast formation of open complex with the repressor whose binding rate is slower than about 1/sec. Finally, we discuss possibility of this mechanism for high activity of promoter PR in the hyp-mutant of lambda phage. 
Hiizu Nakanishi, Namiko Mitarai, and Kim Sneppen