TFs induce changes to transcriptional rate constants. (A) The compartment model of transcription contains rate constants for RNA polymerase II (Pol II) initiation/recruitment, premature termination, pause release, and elongation. Polymerase occupancy in the pause or gene body compartment is measured directly from PRO-seq. Differential equations relate rate constants to the rate of change of polymerase density in the compartments. (B) We use the compartment model to estimate how rate constants change between 0 and 20 min for the 174 genes regulated solely by GR (left), 60 and 120 min for the 1127 genes regulated by SP (middle), and 40 and 60 min for the 1224 genes regulated by AP-1 (right). For each estimation, we hold kpre and kelong constant and calculate values of kinit and krel that fit the observed occupancy in the pause and body regions. (C,D) We simulated composite profiles for a set of parameters from B, left and middle.
