Mathematical analysis and quantification of fluorescent proteins as transcriptional reporters

Fluorescent proteins are often used as reporters of transcriptional activity. Here we present a mathematical characterization of a novel fluorescent reporter that was recently engineered to have a short half-life (similar to 12 min). The advantage of this destabilized protein is that it can track the transient transcriptional response often exhibited by signaling pathways. Our mathematical model takes into account the maturation time and half-life of the fluorescent protein. We demonstrate that our characterization allows transient transcript profiles to be inferred from fluorescence data. We also investigate a stochastic version of the model. Our analysis reveals that fluorescence measurements can both underestimate and overestimate fluctuations in protein levels that arise from the stochastic nature of biochemical reactions.