Abstract
There is a special node, which the large noise of the upstream element may not always lead to a broad distribution of downstream elements. This node is DNA, with upstream element TF and downstream elements mRNA and proteins. By applying the stochastic simulation algorithm (SSA) on gene circuits inspired by the fim operon in Escherichia coli, we found that cells exchanged the distribution of the upstream transcription factor (TF) for the transitional frequency of DNA. Then cells do an inverse transform, which exchanges the transitional frequency of DNA for the distribution of downstream products. Due to this special feature, DNA in the system of frequency modulation is able to reset the noise. By probability generating function, we know the ranges of parameter values that grant such an interesting phenomenon.
Highlights
There is a special node, which the large noise of the upstream element may not always lead to a broad distribution of downstream elements
We will briefly go through the noise propagation in the system of amplitude modulation (AM) in this study, but we are interested in the system of frequency modulation (FM) where the transcription factor (TF) shortens the lifetime of DNA state and modulate frequency[29]
In the FM system (Fig. 1B), inspired by FimE and FimB in E coli[19], we accounted for T FB which switches DNA configuration in both directions at equal rates and TFE increases koff, the rate constant switching DNA from ON to OFF
Summary
There is a special node, which the large noise of the upstream element may not always lead to a broad distribution of downstream elements. In FM, many research articles discussed the systems without concerning the noise of the TF30 They include the studies examining how the switching of DNA affects the downstream elements[19,31,32]. If we count the active state as one and the inactive zero, the mean value over the population automatically reveals the variance as well as all other higher moments Due to this unique feature, it is impossible to store the information of the TF noise by the distribution of the DNA states. We aim to unveil the mystery of DNA, as a special node in gene regulation, being super powerful in blocking the noise of upstream elements
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