Dynamics of simple gene-network motifs subject to extrinsic fluctuations

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Elijah RobertsMichael Assaf

Abstract

Cellular processes do not follow deterministic rules; even in identical environments genetically identical cells can make random choices leading to different phenotypes. This randomness originates from fluctuations present in the biomolecular interaction networks. Most previous work has been focused on the intrinsic noise (IN) of these networks. Yet, especially for high-copy-number biomolecules, extrinsic or environmental noise (EN) has been experimentally shown to dominate the variation. Here, we develop an analytical formalism that allows for calculation of the effect of EN on gene-expression motifs. We introduce a method for modeling bounded EN as an auxiliary species in the master equation. The method is fully generic and is not limited to systems with small EN magnitudes. We focus our study on motifs that can be viewed as the building blocks of genetic switches: a nonregulated gene, a self-inhibiting gene, and a self-promoting gene. The role of the EN properties (magnitude, correlation time, and distribution) on the statistics of interest are systematically investigated, and the effect of fluctuations in different reaction rates is compared. Due to its analytical nature, our formalism can be used to quantify the effect of ...Continue Reading

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Citations

Aug 1, 2016·The Journal of Chemical Physics·K G Petrosyan, Chin-Kun Hu
Sep 3, 2016·Chaos·Martha BauverLora Billings
Mar 18, 2017·Reports on Progress in Physics·Markus F Weber, Erwin Frey
Sep 17, 2019·PLoS Computational Biology·Sanggeun SongJaeyoung Sung
Jan 24, 2020·The Journal of Chemical Physics·Max C Klein, Elijah Roberts
Jul 30, 2016·Physical Review Letters·Antun Skanata, Edo Kussell
Aug 17, 2020·Physical Review Letters·Ami TaitelbaumMauro Mobilia
Apr 27, 2018·Bulletin of Mathematical Biology·Pavol BokesAbhyudai Singh
Mar 15, 2020·Physical Review. E·Tom Israeli, Michael Assaf
May 11, 2018·Scientific Reports·Ling Wei, Elijah Roberts
Jun 4, 2019·Chaos·Dhanushka KularatneM Ani Hsieh
Jan 21, 2021·Physical Review. E·Jayant Pande, Nadav M Shnerb
Jul 18, 2021·Physical Review. E·Michael AssafElijah Roberts
Jul 29, 2021·PLoS Computational Biology·Saurabh ModiAbhyudai Singh
Aug 21, 2021·Physical Review. E·Ernesto Berríos-Caro, Tobias Galla

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