To explore scenarios that permit transcription regulation by activator recruitment of RNA polymerase and competition in vivo, we used an equilibrium model of RNA polymerase binding to DNA constrained by the values of total RNA polymerase (E) and 70 per cell measured in this work. Our numbers of E and 70 per cell, which are consistent with most of the primary data in the literature, suggest that in vivo (i) only a minor fraction of RNA polymerase (<20%) is involved in elongation and (ii) 70 is in excess of total E. Modeling the partitioning of RNA polymerase between promoters, nonspecific DNA binding sites, and the cytoplasm suggested that even weak promoters will be saturated with E 70 in vivo unless nonspecific DNA binding by E 70 is rather significant. In addition, the model predicted that s compete for binding to E only when their total number exceeds the total amount of RNA polymerase (excluding that involved in elongation) and that weak promoters will be preferentially subjected to competition.nonspecific DNA binding ͉ gene regulation promoter ͉ systems biology ͉ Escherichia coli I n bacteria transcription is initiated by RNA polymerase (RNAP) holoenzyme (E ), which is formed when core RNAP (E) binds the transcription initiation factor (1). E initially binds to promoter sites in a closed complex, which then transits to an open complex, competent for transcription. The number of intermediates between the closed and open complex is variable and promoter-dependent; each step may be subject to regulation in vivo (2, 3). At least for some promoters, E binding to promoters is thought to be reversible on the time scale of transcription initiation in vivo (3); reversibility has also been demonstrated in vitro for several promoters (3-6). Even binding to the strong lac UV5 promoter is reversible in vitro when tested under conditions that approximate the in vivo situation (6).Recruitment of E to promoters in vivo is thought to depend on the intrinsic binding affinity of the promoter and is modulated by repressors that prevent and activators that stabilize interactions between E and the promoter (3). Based on in vitro studies of the mechanism of activator function, it is believed that promoters that bind E weakly require activators to recruit E . In addition, cells contain multiple s, which direct E to various sets of promoters specific to the factors (1). These s are believed to compete with each other for binding to E (7-10). By changing the relative levels of the s, Escherichia coli is thought to coordinate its transcriptional program with growth conditions (11-13). This view is based on observations indicating that (i) overexpressing one decreases expression of genes controlled by another (7), (ii) mutationally altering binding constants of one for E alters expression by another (14), and (iii) physiological effectors such as ppGpp may act by altering relative binding of s to E (8-10). In the present work, we use an equilibrium model of RNAP binding to DNA to explore in vivo scenarios that permit transcription reg...