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The dynamics of a feed-forward loop depends on the regulator type in its indirect pathway

  • Molecular Biophysics
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Abstract

Gene networks frequently contain a motif with a feed-forward loop, in which a transcription factor regulates target-gene expression both directly and indirectly via another regulator that also controls the target gene. The results of mathematical modeling of the feed-forward loops with either transcription factor or miRNA as a repressor in the indirect pathway are described. The behavior of such loops in time has been studied. As has been shown, replacement of the second transcription factor with miRNA changes the dynamics of feed-forward loops, conferring new properties to a biological system that are critical for fine tuning of its functions.

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Abbreviations

TF:

transcription factor

References

  1. H. Heranz and S. Cohen, Genes Dev. 24, 1339 (2010).

    Article  Google Scholar 

  2. S. Magnan and U. Alon, Proc. Natl. Acad. Sci. U. S. A. 100 (21), 11980 (2003).

    Article  ADS  Google Scholar 

  3. U. Alon, Nat. Rev. Genet. 8, 450 (2007).

    Article  Google Scholar 

  4. N. Bushati and S. Cohen, Annu. Rev. Cell Dev. Biol. 23, 175 (2007).

    Article  Google Scholar 

  5. M. Osella, C. Bosia, D. Cora, and M. Caselle, PLoS Comput. Biol. 7 (3), e1001101 (2010).

    Article  Google Scholar 

  6. M. A. Duk, M. G. Samsonova, and A. M. Samsonov, BMC Genomics 15 (Suppl. 12), S9 (2014). doi 10.1186/1471-2164-15-S12-S9.

    Article  Google Scholar 

  7. S. Kaplan, A. Bren, E. Dekel, and U. Alon, Mol. Syst. Biol. 4, 203 (2008).

    Article  Google Scholar 

  8. L. Goentoro, O. Shoval, M. W. Kirschner, and U. Alon, Mol. Cell 36, 894 (2009).

    Article  Google Scholar 

  9. O. Shoval, L. Goentoro, Y. Hart, et al., Proc. Natl. Acad. Sci. U. S. A. 107 (36), 15995 (2010).

    Article  ADS  Google Scholar 

  10. M. A. Duk, A. M. Samsonov, and M. G. Samsonova, in Proc. Int. Conf. “Days on Diffraction-2013” (IEEE Publ., 2013), p. 42.

    Book  Google Scholar 

  11. J. H. Park and C. Shin, BMB Rep. 47 (8), 417 (2014).

    Article  Google Scholar 

  12. A. Baccarini, H. Chauhan, T. J. Gardner, et al., Curr. Biol. 21, 369 (2011).

    Article  Google Scholar 

  13. E. Levine, P. McHale, and H. Levine, PLoS Comput. Biol. 3 (11), e233 (2007).

    Article  MathSciNet  ADS  Google Scholar 

Download references

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Authors and Affiliations

  1. Ioffe Physical-Technical Institute, Russian Academy of Sciences, St. Petersburg, 194021, Russia

    M. A. Duk & A. M. Samsonov

  2. St. Petersburg State Polytechnic University, St. Petersburg, 195251, Russia

    M. A. Duk, A. M. Samsonov & M. G. Samsonova

Authors
  1. M. A. Duk
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  2. A. M. Samsonov
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  3. M. G. Samsonova
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Correspondence to M. A. Duk.

Additional information

Original Russian Text © M.A. Duk, A.M. Samsonov, M.G. Samsonova, 2015, published in Biofizika, 2015, Vol. 60, No. 2, pp. 213–224.

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Duk, M.A., Samsonov, A.M. & Samsonova, M.G. The dynamics of a feed-forward loop depends on the regulator type in its indirect pathway. BIOPHYSICS 60, 163–172 (2015). https://doi.org/10.1134/S0006350915020062

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  • DOI: https://doi.org/10.1134/S0006350915020062

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