Fig. 7: Transcription system in Yeast cells.
From: Advanced methods for gene network identification and noise decomposition from single-cell data
A Synthetic circuit in yeast cells. In the presence of light, EL222 can dimerize, bind to EL222-binding sites (EL-BS), and activate the expression of the downstream gene. The transcribed RNAs contain stem-loops to which fluorescent reporters can attach, allowing visualization of RNA dynamics. B Reaction network model for the gene circuit. In this model, the gene has three states: one inactive state G0 and two active states G1 and G2. In the first active state G1, the mRNA is transcribed at a rate \({k}_{{p}_{1}}\). In the second active state G2, the mRNA is transcribed at a higher rate \({k}_{{p}_{1}}+{k}_{{p}_{2}}\), where \({k}_{{p}_{2}}\) represents an additional rate of transcription beyond \({k}_{{p}_{1}}\). The parameters k1, …, k4, \({k}_{{p}_{1}}\), and \({k}_{{p}_{2}}\) are unknown but fixed over time, and the mRNA degrades at a linear rate with the rate constant 1. Under the setting in this paper, our algorithm consistently classifies G1 and G2 as leader species, with the remaining elements categorized as follower components. The follower part has four subsystems: the first subsystem consists of G0, k1, and k2, the second subsystem consists of k3, the third subsystem consists of k4, and the last subsystem consists of \({k}_{{p}_{1}}\), \({k}_{{p}_{2}}\) and mRNA.
