Transcriptional kinetic synergy: a complex landscape revealed by integrating modelling and synthetic biology

Abstract

1Gene regulation involves synergistic interactions between transcription factors (TFs). Classical thermodynamic models offer a biophysical understanding of synergy based on binding cooperativity and regulated recruitment of RNA polymerase. However, transcription requires polymerase to transition through multiple states. Accordingly, recent work has suggested that "kinetic synergy" can arise through TFs differentially regulating distinct steps of the transcription cycle. Disentangling both sources of synergy has been challenging. Here, we combine theory and experiment to analyze TFs binding to a single shared site, thereby removing simultaneous specific DNA binding. Using the graph-based linear framework, we integrate TF binding with regulation of the transcription cycle, and reveal a complex kinetic synergy landscape dependent on TF concentration, DNA binding and transcriptional activity. We exploit synthetic zinc-finger TF fusions to experimentally interrogate these predictions. Our results confirm that transcription cycle regulation must be integrated with recruitment for a quantitative understanding of transcriptional control.