Literature DB >> 25314467

Facilitated diffusion buffers noise in gene expression.

Armin P Schoech1, Nicolae Radu Zabet1.   

Abstract

Transcription factors perform facilitated diffusion [three-dimensional (3D) diffusion in the cytosol and 1D diffusion on the DNA] when binding to their target sites to regulate gene expression. Here, we investigated the influence of this binding mechanism on the noise in gene expression. Our results showed that, for biologically relevant parameters, the binding process can be represented by a two-state Markov model and that the accelerated target finding due to facilitated diffusion leads to a reduction in both the mRNA and the protein noise.

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Year:  2014        PMID: 25314467      PMCID: PMC4241468          DOI: 10.1103/PhysRevE.90.032701

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


  46 in total

1.  The lac repressor displays facilitated diffusion in living cells.

Authors:  Petter Hammar; Prune Leroy; Anel Mahmutovic; Erik G Marklund; Otto G Berg; Johan Elf
Journal:  Science       Date:  2012-06-22       Impact factor: 47.728

2.  A systems approach to measuring the binding energy landscapes of transcription factors.

Authors:  Sebastian J Maerkl; Stephen R Quake
Journal:  Science       Date:  2007-01-12       Impact factor: 47.728

3.  Distance matters: the impact of gene proximity in bacterial gene regulation.

Authors:  Otto Pulkkinen; Ralf Metzler
Journal:  Phys Rev Lett       Date:  2013-05-10       Impact factor: 9.161

4.  Intracellular facilitated diffusion: searchers, crowders, and blockers.

Authors:  C A Brackley; M E Cates; D Marenduzzo
Journal:  Phys Rev Lett       Date:  2013-09-03       Impact factor: 9.161

5.  The lac repressor-operator interaction. 3. Kinetic studies.

Authors:  A D Riggs; S Bourgeois; M Cohn
Journal:  J Mol Biol       Date:  1970-11-14       Impact factor: 5.469

6.  Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise.

Authors:  John R S Newman; Sina Ghaemmaghami; Jan Ihmels; David K Breslow; Matthew Noble; Joseph L DeRisi; Jonathan S Weissman
Journal:  Nature       Date:  2006-05-14       Impact factor: 49.962

Review 7.  Transcription dynamics.

Authors:  Gordon L Hager; James G McNally; Tom Misteli
Journal:  Mol Cell       Date:  2009-09-24       Impact factor: 17.970

8.  A single-molecule characterization of p53 search on DNA.

Authors:  Anahita Tafvizi; Fang Huang; Alan R Fersht; Leonid A Mirny; Antoine M van Oijen
Journal:  Proc Natl Acad Sci U S A       Date:  2010-12-22       Impact factor: 11.205

9.  Single-molecule dynamics of enhanceosome assembly in embryonic stem cells.

Authors:  Jiji Chen; Zhengjian Zhang; Li Li; Bi-Chang Chen; Andrey Revyakin; Bassam Hajj; Wesley Legant; Maxime Dahan; Timothée Lionnet; Eric Betzig; Robert Tjian; Zhe Liu
Journal:  Cell       Date:  2014-03-13       Impact factor: 41.582

10.  Physical constraints determine the logic of bacterial promoter architectures.

Authors:  Daphne Ezer; Nicolae Radu Zabet; Boris Adryan
Journal:  Nucleic Acids Res       Date:  2014-01-29       Impact factor: 16.971

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  2 in total

1.  What matters for lac repressor search in vivo--sliding, hopping, intersegment transfer, crowding on DNA or recognition?

Authors:  Anel Mahmutovic; Otto G Berg; Johan Elf
Journal:  Nucleic Acids Res       Date:  2015-03-16       Impact factor: 16.971

2.  Transcription factor target site search and gene regulation in a background of unspecific binding sites.

Authors:  J Hettich; J C M Gebhardt
Journal:  J Theor Biol       Date:  2018-06-02       Impact factor: 2.691

  2 in total

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