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. Author manuscript; available in PMC: 2010 Jun 12.
Published in final edited form as: Mol Cell. 2009 Jun 12;34(5):545–555. doi: 10.1016/j.molcel.2009.04.018

Figure 7. Substantial occlusion can only be obtained with RNAP pausing.

Figure 7

(A) Analytical model of occlusion by RNAP pausing. RNAP with an occlusion length of l bp, travelling at velocity v bp/sec, arrive at an operator of length m bp, with flux f (RNAP/second). The RNAP move to the end of the operator with rate v.(l + m) −1, whereupon they reach a pause site and remain paused for an average duration P sec. Thus with rate P−1 the paused state can change to a vacant state, or with rate f another RNAP may arrive at the start of the operator. The fraction of time the operator is occluded is given by the equation shown. This result is independent of whether the pause site is positioned at the start or end of the operator.

(B) Occlusion as a function of pause duration and RNAP flux, calculated for a m = 10bp operator being occluded by l = 30bp long RNAPs which elongate at a rate of v = 60 bp/sec.

(C) Genetic arrangements where occlusion by pausing may regulate gene expression. Transcription may be tandem (upper) or convergent (lower) to the interfered promoter and may be either coding or noncoding. Pausing of RNAP over the promoter itself, or over associated elements such as transcription factor binding sites (TF) or enhancer sequences, may lead to reduction in promoter activity.