The dynamic mechanism of noisy signal decoding in gene regulation

Peijiang Liu,Haohua Wang,Tianshou Zhou,Lifang Huang

doi:10.1038/srep42128

Peijiang Liu, Haohua Wang + Show 2 more

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https://doi.org/10.1038/srep42128

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Abstract

Experimental evidence supports that signaling pathways can induce different dynamics of transcription factor (TF) activation, but how an input signal is encoded by such a dynamic, noisy TF and further decoded by downstream genes remains largely unclear. Here, using a system of stochastic transcription with signal regulation, we show that (1) keeping the intensity of the signal noise invariant but prolonging the signal duration can both enhance the mutual information (MI) and reduce the energetic cost (EC); (2) if the signal duration is fixed, the larger MI needs the larger EC, but if the signal period is fixed, there is an optimal time that the signal spends at one lower branch, such that MI reaches the maximum; (3) if both the period and the duration are simultaneously fixed, increasing the input noise can always enhance MI in the case of transcription regulation rather than in the case of degradation regulation. In addition, we find that the input noise can induce stochastic focusing in a regulation-dependent manner. These results reveal not only the dynamic mechanism of noisy signal decoding in gene regulation but also the essential role of external noise in controlling gene expression levels.

Highlights

Experimental evidence supports that signaling pathways can induce different dynamics of transcription factor (TF) activation, but how an input signal is encoded by such a dynamic, noisy TF and further decoded by downstream genes remains largely unclear
These results reveal the dynamic mechanism of noisy signal decoding in gene regulation and the essential role of external noise in controlling gene expression levels
The time-dependent modulation of the transcription or degradation rate may arise from propagation of changes in upstream signals as in fluctuations in regulatory networks[8,10] or it may be a result of intrinsic switching of the gene between ON and OFF states in the absence of any genetic regulation or external signal[39]

Summary

OPEN The dynamic mechanism of noisy signal decoding in gene regulation

Peijiang Liu1,*, Haohua Wang1,2,*, Lifang Huang3 & Tianshou Zhou[1] received: 26 September 2016 accepted: 06 January 2017. Hansen and O’Shea[1] applied information theory to quantify how much gene expression information the yeast TF Msn[2] can transduce to target genes in the amplitude or frequency of its activation dynamics, and found that the amount of information transmitted by Msn[2] to single target genes is limited, information transduction can be increased by modulating promoter cis-elements or by integrating information from multiple genes Motivated mainly by these two works, we introduce a biologically reasonable model of stochastic transcription, where the transcription rate or the mRNA degradation rate is supposed to be regulated directly by a TF signal.

Result

Conclusion and Discussion

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