Mathematical aspects of the regulation of gene transcription by promoters

Journal article, 2017

Although the transcriptional regulation of gene expression has been a subject of intense experimental and theoretical studies over the past several decades, the understanding of this process is still incomplete. In particular, the models focused on the function of transcription factors usually take into account only the lateral interactions between them in the ground bound state. The rates of attachment and detachment of transcription factors on the promoter sites depend, however, also on the lateral interactions in the activated state. I present general equations describing the effect of both these interactions on the rates of attachment and detachment and illustrate their role in the kinetics of gene expression by using a generic model focused on the function of a gene regulated via two promoter sites. The corresponding analytical treatment and Monte Carlo simulations show that the lateral interaction in the activated state is significant if the genes are expressed in the regime of stochastic bursts of high and low transcriptional activity and RNA and protein populations. In particular, the duration and shape of bursts depend on this interaction.