DNA Supercoiling Drives the Switch between Long-range Cooperative and Antagonistic RNAP Dynamics

Recent experiments demonstrate that while co-transcribing RNAPs cooperatively increase their efficiency in the active state of the promoter, environmentally induced promoter repression results in long distance antagonistic interactions that drastically reduces RNAP speeds and causes quick synthesis arrest of mRNA. What mechanism underlies this switch between cooperative and antagonistic dynamics? Here we introduce a continuum deterministic model for RNAP translocation where the elongation velocity of an RNAP is coupled to the local supercoiling and RNAP density. Crucial to the model is the hypothesis that transcription factors act as physical barriers to supercoil diffusion, which explains the dependence of gene expression efficiency on the state of the promoter. We show that this simple model exhibits two transcription modes mediated by the supercoiling stress, a fluid mode when the promoter is ON, and a torsionally stressed mode when the promoter is OFF, in good qualitative agreement with experimentally observed dynamics of co-transcribing RNAPS.