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Energy Cost and Mean Dwell Times for the Activity of Promoter with Complex Structure

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Abstract

Regulatory molecules present on the core promoter of a gene interact often in a dynamic, highly combinatorial and possibly energy-dependent manner, leading to complex promoter structure and even complex global dynamics. The authors analyze dynamics of an arbitrarily complex promoter from the view of thermodynamics combined with statistic physics. First, the authors formulize transcription factors-mediated promoter kinetics in terms of energy. Then, the authors analyze energetic cost in several representative cases of promoter structure, deriving useful analytical results. Third, the authors derive analytical expressions for mean dwell times of the promoter activity states, experimentally measurable quantities related to the energy cost of promoter dynamics. The overall framework lays a theoretical foundation for analysis of complex promoter kinetics and gene expression dynamics.

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Authors and Affiliations

  1. Guangdong Province Key Laboratory of Computational Science, School of Mathematics, Sun Yat-Sen University, Guangzhou, 510275, China

    Qingqing Li, Anwarud Din & Tianshou Zhou

Authors
  1. Qingqing Li
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  2. Anwarud Din
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  3. Tianshou Zhou
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Corresponding author

Correspondence to Tianshou Zhou.

Additional information

This research was supported by Science and Technology Department under Grant No. 2014CB964703 and the Natural Science Foundation under Grant Nos. 91530320 and 11761025.

This paper was recommended for publication by Editor HU Xiaoming.

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Li, Q., Din, A. & Zhou, T. Energy Cost and Mean Dwell Times for the Activity of Promoter with Complex Structure. J Syst Sci Complex 32, 510–525 (2019). https://doi.org/10.1007/s11424-018-7180-2

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  • DOI: https://doi.org/10.1007/s11424-018-7180-2

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