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

doi:10.1088/1674-1056/27/2/028706

中国物理B ›› 2018, Vol. 27 ›› Issue (2): 28706-028706.doi: 10.1088/1674-1056/27/2/028706

所属专题： SPECIAL TOPIC — Soft matter and biological physics

• SPECIAL TOPIC—Soft matter and biological physics • 上一篇下一篇

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

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)

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

收稿日期:2017-09-27 修回日期:2017-11-14 出版日期:2018-02-05 发布日期:2018-02-05
通讯作者: Ming Yi E-mail:yiming@mail.hzau.edu.cn
基金资助:
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).

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

Received:2017-09-27 Revised:2017-11-14 Online:2018-02-05 Published:2018-02-05
Contact: Ming Yi E-mail:yiming@mail.hzau.edu.cn
About author:87.18.Tt; 87.16.dj; 02.50.-r
Supported by:
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).

摘要/Abstract

摘要： 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.

关键词: feed-forward loop, noise propagation, noise decomposition, linear noise approximation

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.

Key words: feed-forward loop, noise propagation, noise decomposition, linear noise approximation

中图分类号: (Noise in biological systems)

87.18.Tt

87.16.dj (Dynamics and fluctuations) 02.50.-r (Probability theory, stochastic processes, and statistics)

桂容, 李治泓, 胡丽君, 程光晖, 刘泉, 熊娟, 贾亚, 易鸣. Noise decomposition algorithm and propagation mechanism in feed-forward gene transcriptional regulatory loop[J]. 中国物理B, 2018, 27(2): 28706-028706.

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[J]. Chin. Phys. B, 2018, 27(2): 28706-028706.

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

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

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