Computational screen of promoter configurations that robustly sense transcription factor dynamics

Transcription factors (TFs) respond to external stimuli with time-varying changes in activity or localization (TF dynamics), driving differential transcriptional programs. Previous studies indicated that TF dynamics can be decoded at the promoter level in eukaryotes, yet a systematic understanding of robust solutions is lacking. By computationally screening over 10,000 mathematical models of multi-state promoters with various forms of TF-mediated regulation, we identify robust configurations that selectively respond to sustained (“pulse filtering”) or pulsatile (“pulse boosting”) TF dynamics. Promoters that activate via intermediate states and have negatively regulated deactivation robustly perform pulse filtering. In contrast, robust pulse boosting is achieved by promoters with a TF-mediated refractory state that permits short activation and recovers between pulses. Bifunctional TFs that exert activator- and repressor-like regulation extend the design space for pulse boosting. These results reveal general principles by which promoters interpret TF dynamics and suggest strategies to engineer synthetic systems to exploit them.