Interplay of master regulatory proteins and mRNA in gene expression: 3D Monte Carlo simulations

We present 3D spatio-temporal Monte Carlo simulations of gene expression for a generic model with negative feedback between the mRNA and regulatory-protein production. The attention is focused on the role of mRNA diffusion between the nucleus and cytoplasm. For rapid diffusion, the model predicts that the fluctuations of the mRNA and protein numbers are comparable to those corresponding to the Poissonian distribution. With decreasing diffusion rate, the fluctuations become much larger. Specifically, the time dependence of the mRNA and protein numbers exhibits huge bursts.

Cross-sections of the spherical cell including the nucleus (central white area), ribosomes (plus signs), cytoplasm (peripheral white area), and mRNA (filled circles).