The Effect Of Protein Degration Kinetics On The Stochastic Steady-State Structure Of Gene Regulatory Network

Gene regulatory network refers to a network formed by a group of interacting genes in a cell.Due to the fluctuation of the environment inside and outside the cell,the regulation of gene expression has complex stochastic dynamics.The rate of protein degradation is one of the important factors that affect the random behavior of the network.This article aims to study the effect of protein degradation kinetics on the stochastic steady-state structure of gene regulatory networks.Consider the single-gene no feedback model,the self-excitation system with double operon binding sites in the promoter,and the self-repression system with double operon binding sites in the promoter,and establish the chemical master equation.Use Monte Carlo simulation to explore the steady-state structure and transformation of gene expression.This article is divided into four chapters:Chapter 1 introduces the research background and preliminary knowledge of this article.Introduces the basic concepts,common methods and research progress of systems biology,and also introduces the structure and characteristics of the λ phage repressor gene regulatory network.Chapter 2 introduces the mathematical and numerical methods of gene regulatory networks.For complex gene regulatory networks,the analysis and calculation of the master equation are difficult,and it is necessary to apply appropriate approximation methods to simplify the model.We take a single-gene network without feedback as an example to introduce how to apply the simplified model of diffusion approximation.Chapter 3 mainly studies the effect of protein degradation rate on the steady-state structure of the self-excitation system of genes with double binding sites in the promoter.According to the two situations of protein linear degradation and nonlinear degradation,the corresponding chemical master equations were established respectively,and the changes of the steady-state structure of the system under different protein degradation rates were observed through Monte Carlo simulation.Quasi-equilibrium approximation and diffusion approximation are used to simplify the model.The results of the Monte Carlo simulation showed the effectiveness of these approximations.Chapter 4 takes the λ repressor gene model as an example to study the effect of protein degradation rate on the steady-state structure of a gene self-suppression system with double binding sites in the promoter.According to λ phage repressor gene c I expression regulates chemical reactions,and establishes chemical master equations for the linear degradation and non-linear degradation of CI protein.Through Monte Carlo simulation,we observed the different steady-state structure of gene regulation under different degradation rate constants,and explored the mechanism of switching between different growth states of E.coli infected by λ phage.