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Regulation by competition: a hidden layer of gene regulatory network

  • Lei Wei
  • Ye Yuan
  • Tao Hu
  • Shuailin Li
  • Tianrun Cheng
  • Jinzhi Lei
  • Zhen Xie
  • Michael Q. Zhang
  • Xiaowo WangEmail author
Research Article
  • 40 Downloads

Abstract

Background

Molecular competition brings about trade-offs of shared limited resources among the cellular components, and thus introduces a hidden layer of regulatory mechanism by connecting components even without direct physical interactions. Several molecular competition scenarios have been observed recently, but there is still a lack of systematic quantitative understanding to reveal the essence of molecular competition.

Methods

Here, by abstracting the analogous competition mechanism behind diverse molecular systems, we built a unified coarse-grained competition motif model to systematically integrate experimental evidences in these processes and analyzed general properties shared behind them from steady-state behavior to dynamic responses.

Results

We could predict in what molecular environments competition would reveal threshold behavior or display a negative linear dependence. We quantified how competition can shape regulator-target dose-response curve, modulate dynamic response speed, control target expression noise, and introduce correlated fluctuations between targets.

Conclusions

This work uncovered the complexity and generality of molecular competition effect as a hidden layer of gene regulatory network, and therefore provided a unified insight and a theoretical framework to understand and employ competition in both natural and synthetic systems.

Keywords

systems biology computational modeling molecular competition regulation synthetic biology network motif 

Notes

Acknowledgements

This work has been supported by the National Natural Science Foundation of China (Nos. 61773230, 31371341, 61721003, 91730301, 31671384 and 91729301), National Basic Research Program of China (2017YFA0505503), Initiative Scientific Research Program (No. 20141081175) and Cross-discipline Foundation of Tsinghua University, and the Open Research Fund of State Key Laboratory of Bioelectronics Southeast University.

Supplementary material

40484_2018_162_MOESM1_ESM.pdf (1.4 mb)
Supplemental Materials for “Regulation by competition: a hidden layer of gene regulatory network”

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Copyright information

© Higher Education Press and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Lei Wei
    • 1
    • 2
  • Ye Yuan
    • 1
    • 2
  • Tao Hu
    • 1
    • 2
  • Shuailin Li
    • 3
  • Tianrun Cheng
    • 1
    • 2
  • Jinzhi Lei
    • 4
  • Zhen Xie
    • 1
    • 2
  • Michael Q. Zhang
    • 1
    • 2
    • 5
    • 6
  • Xiaowo Wang
    • 1
    • 2
    Email author
  1. 1.Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Department of AutomationTsinghua UniversityBeijingChina
  2. 2.Beijing National Research Center for Information Science and TechnologyBeijingChina
  3. 3.School of Life SciencesTsinghua UniversityBeijingChina
  4. 4.Zhou Pei-Yuan Center for Applied MathematicsTsinghua UniversityBeijingChina
  5. 5.Department of Basic Medical Sciences, School of MedicineTsinghua UniversityBeijingChina
  6. 6.Department of Biological Sciences, Center for Systems BiologyThe University of TexasRichardsonUSA

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