Figure 1.

Schematic illustration of transcription modelling. (a) Simplified sketch of polymerase II (Pol II)-mediated transcription (see [21] for details). First, the activator binds to the DNA at a specific promoter, then some general transcription factors (GTFs) bind before the recruitment of Pol II, which is followed by the association of the mediator. When mRNA production initiates, Pol II is released from the transcription complex, forming a scaffold which is capable of reinitiation until the whole complex falls off the DNA and finishes a transcription cycle. (b–d) General stochastic models for gene activation and transcription. Panel (b) is the two-state model: an active state (V, VI), which is capable of mRNA production, and an inactive state (I, II, III, IV). Panel (c) is a three-state model: an active state (V), an inactive state (I, II, III, IV) and the reinitiation scaffold (VI), where the mRNA production and the reinitiation scaffold formation are independent events. Panel (d) is another three-state model that takes the transcription coupling into account, which incorporates a new elementary reaction of simultaneous mRNA production and reinitiation scaffold formation. The rate constant for each step is indicated in the model. (Online version in colour.)