Fig. 7: Understanding the link between responsiveness, transport, and mRNA half-life.
From: Kinetics of mRNA nuclear export regulate innate immune response gene expression
A Simulations of gene induction with different parameter values for mRNA decay (with indicated half-lives, HL) and effective nuclear transport rates ranging from 0.03 to 0.3 cytoFPKM/caFPKM min−1 as observed for the fitted genes. Responsiveness is measured as time to half induction. B Heatmap of responsiveness for various k2’ and kcyto_deg parameter values. There are three main regimes, in the top left corner, the responsiveness is determined solely by half-life, in the bottom right corner the responsiveness is solely defined by k2, and the diagonal may depend on both. The parameter valued for the immune response genes are overlaid on top. Most genes fall in the region where responsiveness is solely determined by the cytoplasmic decay rate. C Scatterplots to show the correlation of gene responsiveness to a step function with half-life (left panel) and transport (right panel). A strong relationship between half-life and responsiveness is observed. There is a weaker, nonlinear relationship with the transport rate. D Scatterplot to show the correlation between the chromatin-to-cytoplasm transport rate and the cytoplasmic decay rates. E Heatmap of relative cytoplasmic mRNA abundance as a function the effective transport and cytoplasmic degradation rate. F Scatterplots between the peak cytoplasmic expression level of each gene with either the effective transport rate or the half-life of its mRNA. This confirms that neither quantity is correlated with the expression level, supporting the model that the two balance each other to render the level of expression controlled by other mechanisms, such as transcriptional initiation.
