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Based on the measurements of noise in gene expression performed during thelast decade, it has become customary to think of gene regulation in terms of atwo-state model, where the promoter of a gene can stochastically switch betweenan ON and an OFF state. As experiments are becoming increasingly precise andthe deviations from the two-state model start to be observable, we ask aboutthe experimental signatures of complex multi-state promoters, as well as thefunctional consequences of this additional complexity. In detail, we (i) extendthe calculations for noise in gene expression to promoters described by statetransition diagrams with multiple states, (ii) systematically compute theexperimentally accessible noise characteristics for these complex promoters,and (iii) use information theory to evaluate the channel capacities of complexpromoter architectures and compare them to the baseline provided by thetwo-state model. We find that adding internal states to the promotergenerically decreases channel capacity, except in certain cases, three of which(cooperativity, dual-role regulation, promoter cycling) we analyze in detail.

Noise and information transmission in promoters with multiple internal states