Fig. 1.

Modeling gene regulatory interactions. Representation of a regulatory network consisting of promoters from which mRNA is transcribed, followed by translation of protein in accordance with the central dogma. Each gene expression pathway involves reactions that modify gene expression products posttranscriptionally and posttranslationally, as well as regulatory interactions that change the promoter state such as chromatin remodeling or DNA looping. In addition, we consider upstream regulation via transcription factors (transcriptional feedback) or via RNA-binding proteins (translational feedback). We define a slow promoter network as one in which reactions that alter its state are less frequent (light arrows, slow) compared with ones that leave it unchanged (heavy arrows, fast). The separation of physiological abundances, with only one or two copies of each promoter per cell, but few to tens of mRNA and tens to thousands of protein molecules, is taken into account explicitly by the conditional LNA.