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The activation/repression of a given gene is typically regulated by multipletranscription factors (TFs) that bind at the gene regulatory region and recruitRNA polymerase (RNAP). The interactions between the promoter region and TFs andbetween different TFs specify the dynamic responses of the gene under differentphysiological conditions. By choosing specific regulatory interactions with upto three transcription factors, we designed several functional motifs, each ofwhich is shown to perform a certain function and can be integrated into largernetworks. We analyzed three kinds of networks: (i) Motifs derived fromincoherent feedforward motifs, which behave as `amplitude filters', or`concentration detectors'. These motifs respond maximally to inputtranscription factors with concentrations within a certain range. From thesemotifs homeostatic and pulse generating networks are derived. (ii) Tunablenetwork motifs, which can behave as oscillators or switches for low and highconcentrations of an input transcription factor, respectively. (iii)Transcription factor controlled adjustable gates, which switch between AND/ORgate characteristics, depending on the concentration of the input transcriptionfactor. This study has demonstrated the utility of feedforward networks and theflexibility of specific transcriptional binding kinetics in generating newnovel behaviors. The flexibility of feedforward networks as dynamic units mayexplain the apparent frequency that such motifs are found in real biologicalnetworks.

Fundamental Dynamic Units: Feedforward Networks and Adjustable Gates