Fig. 3
Transcription regulation of EcoRV R-M system. The promoter configuration in the figure is based on the experimentally mapped promoter elements from [5]. Note that the promoters for CR (PCR) and M (PM) genes are divergent, as schematically shown in Fig. 1b. C and R genes are co-transcribed from the rightward promoter (PCR, see Fig. 1b), with RNAP bound to the promoter as indicated in the first and the third configuration (from top to bottom). M gene is transcribed from the divergent PM promoter (see Fig. 1b), with RNAP bound to the promoter as indicated in the last three configurations. PM and PCR core promoters partially overlap each other, so that RNAP cannot simultaneously bind to PM and PCR. The explanations for the first four configurations are equivalent as in Fig. 2a. Note that ω′ denotes the binding cooperativity between the dimer bound at the distal position and RNAP. For the last three configurations, note that binding of C does not directly influence binding of RNAP to PM [5]