Network motifs: theory and experimental approaches

Uri Alon, Network motifs: theory and experimental approaches, Nature Reviews Genetics 8, 2007

The transcription networks of well-studied microorganisms appear to be made up of a small set of recurring regulation patterns, called network motifs. The same network motifs have recently been found in diverse organisms from bacteria to humans, suggesting that they serve as basic building blocks of transcription networks.

The review discusses two types of transcription network: sensory networks that respond to signals such as stresses and nutrients, and developmental networks that guide differentiation events.

When transcription begins, the concentration of the gene product X rises and converges to a steady-state level. This level is equal to the ratio of the production and degradation rates, where degradation includes both active degradation and the effect of dilution by cell growth. When production stops, the concentration of the gene product decays exponentially.

Single-input modules motif can generate a temporal expression program me, with a defined order of activation of each of the target promoters. X often has different activation thresholds for each gene, owing to variations in the sequence and context of its binding site in each promoter.

Developmental transcription networks have different constraints: they usually function on the timescale of one or several cell generations, and often need to make irreversible decisions that last even after the input signal has vanished.

It therefore seems that, in many cases, evolution has converged independently on the same regulation circuit.

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