Effects of transcriptional pausing on gene expression dynamics

Abstract

Stochasticity in gene expression affects many cellular processes and is a source of phenotypic diversity between genetically identical individuals. Events in elongation, particularly RNA polymerase pausing, are a source of this noise. Since the rate and duration of pausing are sequence-dependent, this regulatory mechanism of transcriptional dynamics is evolvable. The dependency of pause propensity on regulatory molecules makes pausing a response mechanism to external stress. Using a delayed stochastic model of bacterial transcription at the single nucleotide level that includes the promoter open complex formation, pausing, arrest, misincorporation and editing, pyrophosphorolysis, and premature termination, we investigate how RNA polymerase pausing affects a gene's transcriptional dynamics and gene networks. We show that pauses' duration and rate of occurrence affect the bursting in RNA production, transcriptional and translational noise, and the transient to reach mean RNA and protein levels. In a genetic repressilator, increasing the pausing rate and the duration of pausing events increases the period length but does not affect the robustness of the periodicity. We conclude that RNA polymerase pausing might be an important evolvable feature of genetic networks.

Figure 1. Pausing effect on the intervals between the production of consecutive RNAs.

Intervals of successive RNA completions for (A) various rates of pausing and, (B) various average pause durations. The fraction of RNAs completed within intervals smaller than 5 seconds grows especially when increasing pauses mean duration (the black peak in 1B).

Figure 2. Pausing and the fraction of microbursts.

Fraction of two or more consecutive RNAs produced within an interval smaller than 5 seconds for various values of (A) pausing rate (k_pause) and, (B) pause duration (d_pause). Note the different scales in the y-axis in 2A and 2B.

Figure 3. Maximum microburst size as a function of the kinetics of pausing.

Average size of the largest RNA microburst, over 10 cells, for various values of k_pause (s⁻¹) and d_pause (s).

Figure 4. Pausing and the initial transient.

Average initial transient with one standard deviation error bars (red bars) before reaching the homeostasis level of protein production as (A) pausing rate, and (B) pause duration vary (x-axis in log scale).

Figure 5. Noise of protein and RNA levels.

CV (standard deviation over the mean) of RNA and protein levels at homeostasis measured for 50000 s, 1 s sampling frequency: (A) CV of RNA when varying pausing rate, (B) CV of RNA when varying pause duration, (C) CV of proteins when varying pausing rate, and (D) CV of proteins when varying pause duration. Note the different scales in the y-axis.

Figure 6. Pausing effects on the period of a genetic oscillator.

Average period length of the repressilator as (A) pausing rate, and (B) pause duration vary.

Figure 7. Dynamical effects of pauses on the repressilator dynamics.

Sample of the time series of the 3 proteins (P_{i = 1,2,3}) of the repressilator from t = 20000 to 50000 s (sampling frequency of 1 s) for (A) k_pause = 0.55 s⁻¹ and d_pause = 3 s, (B) k_pause = 10 s⁻¹ and d_pause = 3 s, and (C) k_pause = 0.55 s⁻¹ and d_pause = 100 s. Black line is P₁, red line is P₂, and blue line is P₃.

Figure 8. Pausing and the noise in protein time series in the repressilator.

CV (standard deviation over the mean) of proteins of the repressilator (P₁+P₂+P₃) when varying (A) pausing rate, and (B) pause duration.

Figure 9. Effects of a sequence-specific long-duration pause.

Time interval between the completion of consecutive RNA molecules in a gene with 400 nucleotides in case (A) without long-duration pause sites, case (B) with one long-pause site at nucleotide 200 where k_pause is half the value of the rate of stepwise elongation and d_pause is 1 min, and case (C), identical to case (B) but with a 20% chance that a long-paused RNAP will lead to premature termination.