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Intrinsic and extrinsic contributions to stochasticity in gene expression

Swain, Peter S. and Elowitz, Michael B. and Siggia, Eric D. (2002) Intrinsic and extrinsic contributions to stochasticity in gene expression. Proceedings of the National Academy of Sciences of the United States of America, 99 (20). pp. 12795-12800. ISSN 0027-8424. PMCID PMC130539. https://resolver.caltech.edu/CaltechAUTHORS:SWApnas02

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Abstract

Gene expression is a stochastic, or "noisy," process. This noise comes about in two ways. The inherent stochasticity of biochemical processes such as transcription and translation generates "intrinsic" noise. In addition, fluctuations in the amounts or states of other cellular components lead indirectly to variation in the expression of a particular gene and thus represent "extrinsic" noise. Here, we show how the total variation in the level of expression of a given gene can be decomposed into its intrinsic and extrinsic components. We demonstrate theoretically that simultaneous measurement of two identical genes per cell enables discrimination of these two types of noise. Analytic expressions for intrinsic noise are given for a model that involves all the major steps in transcription and translation. These expressions give the sensitivity to various parameters, quantify the deviation from Poisson statistics, and provide a way of fitting experiment. Transcription dominates the intrinsic noise when the average number of proteins made per mRNA transcript is greater than similar or equal to 2. Below this number, translational effects also become important. Gene replication and cell division, included in the model, cause protein numbers to tend to a limit cycle. We calculate a general form for the extrinsic noise and illustrate it with the particular case of a single fluctuating extrinsic variable-a repressor protein, which acts on the gene of interest. All results are confirmed by stochastic simulation using plausible parameters for Escherichia coli.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC130539/PubMed CentralArticle
https://doi.org/10.1073/pnas.162041399DOIUNSPECIFIED
https://doi.org/10.1073/pnas.162041399DOIUNSPECIFIED
ORCID:
AuthorORCID
Elowitz, Michael B.0000-0002-1221-0967
Additional Information:© 2002 by the National Academy of Sciences. Edited by Robert H. Austin, Princeton University, Princeton, NJ, and approved June 17, 2002 (received for review January 23, 2002). Published online before print September 17, 2002, 10.1073/pnas.162041399. We are grateful for conversations with S. Bekiranov, A. J. Levine, J. Paulsson, N. Rajewsky, B. Shraiman, N. Socci, and M. Zapotocky. P.S.S., M.B.E., and E.D.S. acknowledge support from the National Institutes of Health (GM59018), the Seaver Institute and Burroughs-Wellcome Fund, and the National Science Foundation (DMR0129848), respectively. This paper was submitted directly (Track II) to the PNAS office.
Subject Keywords:Escherichia-coli; noise; transcription; fluctuations; simulation; networks; model; cell
Issue or Number:20
PubMed Central ID:PMC130539
Record Number:CaltechAUTHORS:SWApnas02
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:SWApnas02
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:1494
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:24 Jan 2006
Last Modified:02 Oct 2019 22:44

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