title: Dynamics of simple gene-network motifs subject to extrinsic fluctuations.
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 EN on the dynamics of biochemical networks and can also be used to improve the interpretation of data from single-cell gene-expression experiments.
authors.affiliation: Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA.
authors.forename: Elijah
authors.initials: E
authors.lastname: Roberts
authors.affiliation: Racah Institute of Physics, Hebrew University of Jerusalem, Jerusalem 91904, Israel.
authors.forename: Shay
authors.initials: S
authors.lastname: Be'er
authors.affiliation: Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Bohrer
authors.affiliation: Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA.
authors.forename: Rati
authors.initials: R
authors.lastname: Sharma
authors.affiliation: Racah Institute of Physics, Hebrew University of Jerusalem, Jerusalem 91904, Israel.
authors.forename: Michael
authors.initials: M
authors.lastname: Assaf
mesh_terms: D005786:Gene Expression Regulation / Q000235:genetics; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D009010:Monte Carlo Method; D011506:Proteins / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism
chemical_list: D011506:Proteins; D012333:RNA, Messenger