(A) A model utilizing two promoter states (active and inactive) contains two mechanisms that can account for the increase in the transcription rates observed by qPCR. Model 1: loci are slowly recruited into a transcriptionally active state upon first induction and more rapidly upon second induction. Once active, loci produce new mRNAs at a constant rate equivalent to the rate at which new RNA Pol II molecules enter productive elongation. Model 2: all cells are rapidly recruited into an active state, and the rate of transcription increases over time, slowly upon first induction and quickly upon second induction. (B). Model describing the rate of recruitment into the active state kA, into the inactive state k-A, and the rate of recruiting RNA Pol II molecules into productive elongation kPol. The presence of 20E permits kA to be larger than k-A. The production rate as a function of time is given by the RNA Pol II recruitment rate multiplied by the fraction of active loci. In Model 1, kA increases and kPol is constant during 20E exposure, whereas in Model 2, kPol increases and kA is constant. (C–N). Histograms (cyan) show distribution of measured total instantaneous transcriptional activity in normalized units (C.U.), obtained from smFISH of E74 as shown in Figure 1. Lines represent predicted values generated by simulation using best-fitting parameters for Model 1 (green) and Model 2 (magenta) under conditions of control (C–H) or Nup98 knockdown conditions (I–N) during the first (C,F,I,L), second (D,G,J,M), or fourth (E,H,K,N) hour of the first (C–E, I–K) or second (F–H, L–N) inductions.