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Summing up the noise in gene networks

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  • Johan Paulsson

    (Princeton University
    Centre for Mathematical Sciences, University of Cambridge)

Abstract

Random fluctuations in genetic networks are inevitable as chemical reactions are probabilistic and many genes, RNAs and proteins are present in low numbers per cell. Such ‘noise’ affects all life processes and has recently been measured using green fluorescent protein (GFP). Two studies show that negative feedback suppresses noise, and three others identify the sources of noise in gene expression. Here I critically analyse these studies and present a simple equation that unifies and extends both the mathematical and biological perspectives.

Suggested Citation

  • Johan Paulsson, 2004. "Summing up the noise in gene networks," Nature, Nature, vol. 427(6973), pages 415-418, January.
    • Handle: RePEc:nat:nature:v:427:y:2004:i:6973:d:10.1038_nature02257
    DOI: 10.1038/nature02257
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    Cited by:

    1. Lee, Julian, 2023. "Poisson distributions in stochastic dynamics of gene expression: What events do they count?," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 630(C).
    2. Jason P Glotzbach & Michael Januszyk & Ivan N Vial & Victor W Wong & Alexander Gelbard & Tomer Kalisky & Hariharan Thangarajah & Michael T Longaker & Stephen R Quake & Gilbert Chu & Geoffrey C Gurtner, 2011. "An Information Theoretic, Microfluidic-Based Single Cell Analysis Permits Identification of Subpopulations among Putatively Homogeneous Stem Cells," PLOS ONE, Public Library of Science, vol. 6(6), pages 1-10, June.
    3. Hui Zhang & Yueling Chen & Yong Chen, 2012. "Noise Propagation in Gene Regulation Networks Involving Interlinked Positive and Negative Feedback Loops," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-8, December.
    4. Jin Wang & Bo Huang & Xuefeng Xia & Zhirong Sun, 2006. "Funneled Landscape Leads to Robustness of Cell Networks: Yeast Cell Cycle," PLOS Computational Biology, Public Library of Science, vol. 2(11), pages 1-10, November.
    5. Ruoyu Luo & Lin Ye & Chenyang Tao & Kankan Wang, 2013. "Simulation of E. coli Gene Regulation including Overlapping Cell Cycles, Growth, Division, Time Delays and Noise," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-10, April.
    6. Keun-Young Kim & Jin Wang, 2007. "Potential Energy Landscape and Robustness of a Gene Regulatory Network: Toggle Switch," PLOS Computational Biology, Public Library of Science, vol. 3(3), pages 1-13, March.
    7. dos Santos, Renato Vieira & da Silva, Linaena Méricy, 2015. "Discreteness induced extinction," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 438(C), pages 17-25.
    8. Kyung H Kim & Herbert M Sauro, 2012. "Adjusting Phenotypes by Noise Control," PLOS Computational Biology, Public Library of Science, vol. 8(1), pages 1-14, January.
    9. Jérémie Bourdon & Damien Eveillard & Anne Siegel, 2011. "Integrating Quantitative Knowledge into a Qualitative Gene Regulatory Network," PLOS Computational Biology, Public Library of Science, vol. 7(9), pages 1-11, September.
    10. Cappelletti, Daniele & Pal Majumder, Abhishek & Wiuf, Carsten, 2021. "The dynamics of stochastic mono-molecular reaction systems in stochastic environments," Stochastic Processes and their Applications, Elsevier, vol. 137(C), pages 106-148.
    11. Luca Cardelli & Rosa D Hernansaiz-Ballesteros & Neil Dalchau & Attila Csikász-Nagy, 2017. "Efficient Switches in Biology and Computer Science," PLOS Computational Biology, Public Library of Science, vol. 13(1), pages 1-16, January.
    12. Abhyudai Singh & Mohammad Soltani, 2013. "Quantifying Intrinsic and Extrinsic Variability in Stochastic Gene Expression Models," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-12, December.
    13. Chen, Aimin & Tian, Tianhai & Chen, Yiren & Zhou, Tianshou, 2022. "Stochastic analysis of a complex gene-expression model," Chaos, Solitons & Fractals, Elsevier, vol. 160(C).
    14. Arjun Raj & Charles S Peskin & Daniel Tranchina & Diana Y Vargas & Sanjay Tyagi, 2006. "Stochastic mRNA Synthesis in Mammalian Cells," PLOS Biology, Public Library of Science, vol. 4(10), pages 1-13, September.
    15. Mayu Sugiyama & Takashi Saitou & Hiroshi Kurokawa & Asako Sakaue-Sawano & Takeshi Imamura & Atsushi Miyawaki & Tadahiro Iimura, 2014. "Live Imaging-Based Model Selection Reveals Periodic Regulation of the Stochastic G1/S Phase Transition in Vertebrate Axial Development," PLOS Computational Biology, Public Library of Science, vol. 10(12), pages 1-16, December.
    16. Namiko Mitarai & Ian B Dodd & Michael T Crooks & Kim Sneppen, 2008. "The Generation of Promoter-Mediated Transcriptional Noise in Bacteria," PLOS Computational Biology, Public Library of Science, vol. 4(7), pages 1-9, July.
    17. Elijah Roberts & Andrew Magis & Julio O Ortiz & Wolfgang Baumeister & Zaida Luthey-Schulten, 2011. "Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study," PLOS Computational Biology, Public Library of Science, vol. 7(3), pages 1-21, March.
    18. Wang, Jia-Zeng & Ma, Shu & Ji, Yu & Sun, Qi, 2023. "Response to multiplicative noise: The cross-spectrum of membrane voltage fluctuation and voltage-independent conductance noise," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 622(C).
    19. Tim Lijster & Christoffer Åberg, 2020. "Asymmetry of nanoparticle inheritance upon cell division: Effect on the coefficient of variation," PLOS ONE, Public Library of Science, vol. 15(11), pages 1-18, November.
    20. Yuval Elhanati & Naama Brenner, 2012. "Metabolic Variability in Micro-Populations," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-9, December.
    21. Benjamin B Kaufmann & Qiong Yang & Jerome T Mettetal & Alexander van Oudenaarden, 2007. "Heritable Stochastic Switching Revealed by Single-Cell Genealogy," PLOS Biology, Public Library of Science, vol. 5(9), pages 1-8, September.
    22. Deena R Schmidt & Roberto F Galán & Peter J Thomas, 2018. "Stochastic shielding and edge importance for Markov chains with timescale separation," PLOS Computational Biology, Public Library of Science, vol. 14(6), pages 1-35, June.
    23. Tina Toni & Bruce Tidor, 2013. "Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology," PLOS Computational Biology, Public Library of Science, vol. 9(3), pages 1-17, March.

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