Figure 1.

Schematic representation of the proposed thermodynamic model. The accumulated amount of each transcript is in pseudo-equilibrium between influx and efflux. The velocity of synthesis for a transcript (v_s) is determined according to the Gibbs free energy $\Delta G_{\text{p}}^0$ (for equilibrium between binding and dissociation of RNA polymerase II to the promoter) and activation energy E_p (energy barrier for the start of polymerase elongation). The velocity of degradation (v_d) is determined by E_d (required to start hydrolysis). All energies are determined for interactions between special nucleotide sequences and the protein factors.