  The activation/repression of a given gene is typically regulated by multiple
transcription factors (TFs) that bind at the gene regulatory region and recruit
RNA polymerase (RNAP). The interactions between the promoter region and TFs and
between different TFs specify the dynamic responses of the gene under different
physiological conditions. By choosing specific regulatory interactions with up
to three transcription factors, we designed several functional motifs, each of
which is shown to perform a certain function and can be integrated into larger
networks. We analyzed three kinds of networks: (i) Motifs derived from
incoherent feedforward motifs, which behave as `amplitude filters', or
`concentration detectors'. These motifs respond maximally to input
transcription factors with concentrations within a certain range. From these
motifs homeostatic and pulse generating networks are derived. (ii) Tunable
network motifs, which can behave as oscillators or switches for low and high
concentrations of an input transcription factor, respectively. (iii)
Transcription factor controlled adjustable gates, which switch between AND/OR
gate characteristics, depending on the concentration of the input transcription
factor. This study has demonstrated the utility of feedforward networks and the
flexibility of specific transcriptional binding kinetics in generating new
novel behaviors. The flexibility of feedforward networks as dynamic units may
explain the apparent frequency that such motifs are found in real biological
networks.
