Fig. 6.

Investigating the molecular character of transcriptional quiescence. (A) Two hypotheses explaining promoter quiescence onset: (A, i) a transition into an alternative, long-lived transcriptionally silent state and (A, ii) the modulation of one or more bursting parameters over time. (B–F) Division of the stripe into 5 regions (B) for our analysis of the fraction of quiescent nuclei (C), the transition rate from OFF to ON (D), the rate of RNAP loading when the promoter is in the ON state (E), and the transition rate from ON to OFF as a function of time and position along the stripe (F). Gray shaded region indicates the onset of transcriptional quiescence. (In C, error bars indicate bootstrap estimate of the SEM; in D–F, error bars indicate the magnitude of the difference between the first and third quartiles of cpHMM inference results for bootstrapped samples of experimental data; see Materials and Methods for details.)