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Chin. Phys. B, 2018, Vol. 27(2): 028706    DOI: 10.1088/1674-1056/27/2/028706
Special Issue: SPECIAL TOPIC — Soft matter and biological physics
SPECIAL TOPIC—Soft matter and biological physics Prev   Next  

Noise decomposition algorithm and propagation mechanism in feed-forward gene transcriptional regulatory loop

Rong Gui(桂容)1, Zhi-Hong Li(李治泓)1, Li-Jun Hu(胡丽君)1, Guang-Hui Cheng(程光晖)2, Quan Liu(刘泉)1, Juan Xiong(熊娟)1, Ya Jia(贾亚)3, Ming Yi(易鸣)1,4
1. Department of Physics, College of Science, Huazhong Agricultural University, Wuhan 430070, China;
2. Department of Electrical and Electronic Engineering, Wuhan Polytechnic University, Wuhan 430048, China;
3. Department of Physics and Institute of Biophysics, Central China Normal University, Wuhan 430079, China;
4. Institute of Applied Physics, Huazhong Agricultural University, Wuhan 430070, China
Abstract  Feed-forward gene transcriptional regulatory networks, as a set of common signal motifs, are widely distributed in the biological systems. In this paper, the noise characteristics and propagation mechanism of various feed-forward gene transcriptional regulatory loops are investigated, including (i) coherent feed-forward loops with AND-gate, (ii) coherent feed-forward loops with OR-gate logic, and (iii) incoherent feed-forward loops with AND-gate logic. By introducing logarithmic gain coefficient and using linear noise approximation, the theoretical formulas of noise decomposition are derived and the theoretical results are verified by Gillespie simulation. From the theoretical and numerical results of noise decomposition algorithm, three general characteristics about noise transmission in these different kinds of feed-forward loops are observed. i) The two-step noise propagation of upstream factor is negative in the incoherent feed-forward loops with AND-gate logic, that is, upstream factor can indirectly suppress the noise of downstream factors. ii) The one-step propagation noise of upstream factor is non-monotonic in the coherent feed-forward loops with OR-gate logic. iii) When the branch of the feed-forward loop is negatively controlled, the total noise of the downstream factor monotonically increases for each of all feed-forward loops. These findings are robust to variations of model parameters. These observations reveal the universal rules of noise propagation in the feed-forward loops, and may contribute to our understanding of design principle of gene circuits.
Keywords:  feed-forward loop      noise propagation      noise decomposition      linear noise approximation  
Received:  27 September 2017      Revised:  14 November 2017      Accepted manuscript online: 
PACS:  87.18.Tt (Noise in biological systems)  
  87.16.dj (Dynamics and fluctuations)  
  02.50.-r (Probability theory, stochastic processes, and statistics)  
Fund: Project supported by the Fundamental Research Funds for the Central Universities, China (Grant Nos. 2662015QC041 and 2662014BQ069), the Huazhong Agricultural University Scientific & Technological Self-innovation Foundation, China (Grant No. 2015RC021), and the National Natural Science Foundation of China (Grant Nos. 11675060, 91730301, 11547244, and 11474117).
Corresponding Authors:  Ming Yi     E-mail:  yiming@mail.hzau.edu.cn
About author:  87.18.Tt; 87.16.dj; 02.50.-r

Cite this article: 

Rong Gui(桂容), Zhi-Hong Li(李治泓), Li-Jun Hu(胡丽君), Guang-Hui Cheng(程光晖), Quan Liu(刘泉), Juan Xiong(熊娟), Ya Jia(贾亚), Ming Yi(易鸣) Noise decomposition algorithm and propagation mechanism in feed-forward gene transcriptional regulatory loop 2018 Chin. Phys. B 27 028706

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