Literature DB >> 25768447

Gene regulation and noise reduction by coupling of stochastic processes.

Alexandre F Ramos1, José Eduardo M Hornos2, John Reinitz3.   

Abstract

Here we characterize the low-noise regime of a stochastic model for a negative self-regulating binary gene. The model has two stochastic variables, the protein number and the state of the gene. Each state of the gene behaves as a protein source governed by a Poisson process. The coupling between the two gene states depends on protein number. This fact has a very important implication: There exist protein production regimes characterized by sub-Poissonian noise because of negative covariance between the two stochastic variables of the model. Hence the protein numbers obey a probability distribution that has a peak that is sharper than those of the two coupled Poisson processes that are combined to produce it. Biochemically, the noise reduction in protein number occurs when the switching of the genetic state is more rapid than protein synthesis or degradation. We consider the chemical reaction rates necessary for Poisson and sub-Poisson processes in prokaryotes and eucaryotes. Our results suggest that the coupling of multiple stochastic processes in a negative covariance regime might be a widespread mechanism for noise reduction.

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Year:  2015        PMID: 25768447      PMCID: PMC4476401          DOI: 10.1103/PhysRevE.91.020701

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  22 in total

1.  Prediction and measurement of an autoregulatory genetic module.

Authors:  Farren J Isaacs; Jeff Hasty; Charles R Cantor; J J Collins
Journal:  Proc Natl Acad Sci U S A       Date:  2003-06-13       Impact factor: 11.205

2.  AVIDIN. 1. THE USE OF (14-C)BIOTIN FOR KINETIC STUDIES AND FOR ASSAY.

Authors:  N M GREEN
Journal:  Biochem J       Date:  1963-12       Impact factor: 3.857

3.  A free-energy-based stochastic simulation of the Tar receptor complex.

Authors:  C J Morton-Firth; T S Shimizu; D Bray
Journal:  J Mol Biol       Date:  1999-03-05       Impact factor: 5.469

4.  Self-regulating gene: an exact solution.

Authors:  J E M Hornos; D Schultz; G C P Innocentini; J Wang; A M Walczak; J N Onuchic; P G Wolynes
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-11-04

5.  Phenotypic consequences of promoter-mediated transcriptional noise.

Authors:  William J Blake; Gábor Balázsi; Michael A Kohanski; Farren J Isaacs; Kevin F Murphy; Yina Kuang; Charles R Cantor; David R Walt; James J Collins
Journal:  Mol Cell       Date:  2006-12-28       Impact factor: 17.970

Review 6.  Canalization of development by microRNAs.

Authors:  Eran Hornstein; Noam Shomron
Journal:  Nat Genet       Date:  2006-06       Impact factor: 38.330

7.  Stochastic protein expression in individual cells at the single molecule level.

Authors:  Long Cai; Nir Friedman; X Sunney Xie
Journal:  Nature       Date:  2006-03-16       Impact factor: 49.962

8.  Probing the limits to positional information.

Authors:  Thomas Gregor; David W Tank; Eric F Wieschaus; William Bialek
Journal:  Cell       Date:  2007-07-13       Impact factor: 41.582

9.  Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells.

Authors:  A Arkin; J Ross; H H McAdams
Journal:  Genetics       Date:  1998-08       Impact factor: 4.562

10.  Theoretical and experimental analysis of the phage lambda genetic switch implies missing levels of co-operativity.

Authors:  J Reinitz; J R Vaisnys
Journal:  J Theor Biol       Date:  1990-08-09       Impact factor: 2.691

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  3 in total

1.  Limits of noise for autoregulated gene expression.

Authors:  Peter Czuppon; Peter Pfaffelhuber
Journal:  J Math Biol       Date:  2018-05-24       Impact factor: 2.259

2.  Binary Expression Enhances Reliability of Messaging in Gene Networks.

Authors:  Leonardo R Gama; Guilherme Giovanini; Gábor Balázsi; Alexandre F Ramos
Journal:  Entropy (Basel)       Date:  2020-04-22       Impact factor: 2.524

Review 3.  Lessons and perspectives for applications of stochastic models in biological and cancer research.

Authors:  Alan U Sabino; Miguel Fs Vasconcelos; Misaki Yamada Sittoni; Willian W Lautenschlager; Alexandre S Queiroga; Mauro Cc Morais; Alexandre F Ramos
Journal:  Clinics (Sao Paulo)       Date:  2018-09-21       Impact factor: 2.365

  3 in total

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