Literature DB >> 15772163

Stochastic simulations of the origins and implications of long-tailed distributions in gene expression.

Sandeep Krishna1, Bidisha Banerjee, T V Ramakrishnan, G V Shivashankar.   

Abstract

Gene expression noise results in protein number distributions ranging from long-tailed to Gaussian. We show how long-tailed distributions arise from a stochastic model of the constituent chemical reactions and suggest that, in conjunction with cooperative switches, they lead to more sensitive selection of a subpopulation of cells with high protein number than is possible with Gaussian distributions. Single-cell-tracking experiments are presented to validate some of the assumptions of the stochastic simulations. We also examine the effect of DNA looping on the shape of protein distributions. We further show that when switches are incorporated in the regulation of a gene via a feedback loop, the distributions can become bimodal. This might explain the bimodal distribution of certain morphogens during early embryogenesis.

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Year:  2005        PMID: 15772163      PMCID: PMC555697          DOI: 10.1073/pnas.0406415102

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  32 in total

1.  Transcriptional control: rheostat converted to on/off switch.

Authors:  F M Rossi; A M Kringstein; A Spicher; O M Guicherit; H M Blau
Journal:  Mol Cell       Date:  2000-09       Impact factor: 17.970

2.  Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations.

Authors:  T B Kepler; T C Elston
Journal:  Biophys J       Date:  2001-12       Impact factor: 4.033

3.  Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion.

Authors:  A Becskei; B Séraphin; L Serrano
Journal:  EMBO J       Date:  2001-05-15       Impact factor: 11.598

4.  Regulation of noise in the expression of a single gene.

Authors:  Ertugrul M Ozbudak; Mukund Thattai; Iren Kurtser; Alan D Grossman; Alexander van Oudenaarden
Journal:  Nat Genet       Date:  2002-04-22       Impact factor: 38.330

5.  DNA looping and physical constraints on transcription regulation.

Authors:  José M G Vilar; Stanislas Leibler
Journal:  J Mol Biol       Date:  2003-08-29       Impact factor: 5.469

6.  Intrinsic and extrinsic contributions to stochasticity in gene expression.

Authors:  Peter S Swain; Michael B Elowitz; Eric D Siggia
Journal:  Proc Natl Acad Sci U S A       Date:  2002-09-17       Impact factor: 11.205

7.  Control of stochasticity in eukaryotic gene expression.

Authors:  Jonathan M Raser; Erin K O'Shea
Journal:  Science       Date:  2004-05-27       Impact factor: 47.728

8.  Resilient circadian oscillator revealed in individual cyanobacteria.

Authors:  Irina Mihalcescu; Weihong Hsing; Stanislas Leibler
Journal:  Nature       Date:  2004-07-01       Impact factor: 49.962

9.  On the relation between fluctuation and response in biological systems.

Authors:  Katsuhiko Sato; Yoichiro Ito; Tetsuya Yomo; Kunihiko Kaneko
Journal:  Proc Natl Acad Sci U S A       Date:  2003-11-13       Impact factor: 11.205

10.  Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays.

Authors:  Felix Naef; Coleen R Hacker; Nila Patil; Marcelo Magnasco
Journal:  Genome Biol       Date:  2002-03-22       Impact factor: 13.583

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  18 in total

1.  Stochastic variation: from single cells to superorganisms.

Authors:  Maria L Kilfoil; Paul Lasko; Ehab Abouheif
Journal:  HFSP J       Date:  2009-10-09

2.  Classical versus stochastic kinetics modeling of biochemical reaction systems.

Authors:  John Goutsias
Journal:  Biophys J       Date:  2007-01-11       Impact factor: 4.033

3.  Stochastic receptor expression allows sensitive bacteria to evade phage attack. Part II: theoretical analyses.

Authors:  E Chapman-McQuiston; X L Wu
Journal:  Biophys J       Date:  2008-02-29       Impact factor: 4.033

4.  Exact results for the evolution of stochastic switching in variable asymmetric environments.

Authors:  Bernadett Gaál; Jonathan W Pitchford; A Jamie Wood
Journal:  Genetics       Date:  2010-01-25       Impact factor: 4.562

Review 5.  Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images.

Authors:  Svetlana Surkova; Ekaterina Myasnikova; Hilde Janssens; Konstantin N Kozlov; Anastasia A Samsonova; John Reinitz; Maria Samsonova
Journal:  Fly (Austin)       Date:  2008-03-08       Impact factor: 2.160

6.  Relationship among phenotypic plasticity, phenotypic fluctuations, robustness, and evolvability; Waddington's legacy revisited under the spirit of Einstein.

Authors:  Kunihiko Kaneko
Journal:  J Biosci       Date:  2009-10       Impact factor: 1.826

Review 7.  Measuring and modeling apoptosis in single cells.

Authors:  Sabrina L Spencer; Peter K Sorger
Journal:  Cell       Date:  2011-03-18       Impact factor: 41.582

8.  Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses.

Authors:  Maciej Dobrzyński; Lan K Nguyen; Marc R Birtwistle; Alexander von Kriegsheim; Alfonso Blanco Fernández; Alex Cheong; Walter Kolch; Boris N Kholodenko
Journal:  J R Soc Interface       Date:  2014-09-06       Impact factor: 4.118

9.  Eye movement dynamics and cognitive self-organization in typical and atypical development.

Authors:  Daniel Mirman; Julia R Irwin; Damian G Stephen
Journal:  Cogn Neurodyn       Date:  2011-11-12       Impact factor: 5.082

10.  Hybrid stochastic simplifications for multiscale gene networks.

Authors:  Alina Crudu; Arnaud Debussche; Ovidiu Radulescu
Journal:  BMC Syst Biol       Date:  2009-09-07
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