title: Constructing the energy landscape for genetic switching system driven by intrinsic noise.
abstract: Genetic switching driven by noise is a fundamental cellular process in genetic regulatory networks. Quantitatively characterizing this switching and its fluctuation properties is a key problem in computational biology. With an autoregulatory dimer model as a specific example, we design a general methodology to quantitatively understand the metastability of gene regulatory system perturbed by intrinsic noise. Based on the large deviation theory, we develop new analytical techniques to describe and calculate the optimal transition paths between the on and off states. We also construct the global quasi-potential energy landscape for the dimer model. From the obtained quasi-potential, we can extract quantitative results such as the stationary distributions of mRNA, protein and dimer, the noise strength of the expression state, and the mean switching time starting from either stable state. In the final stage, we apply this procedure to a transcriptional cascades model. Our results suggest that the quasi-potential energy landscape and the proposed methodology are general to understand the metastability in other biological systems with intrinsic noise.
authors.affiliation: School of Physics, Peking University, Beijing, China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Lv
authors.affiliation: LMAM and School of Mathematical Sciences, Peking University, Beijing, China.
authors.forename: Xiaoguang
authors.initials: X
authors.lastname: Li
authors.affiliation: School of Physics, Peking University, Beijing, China ; Center of Quantitative Biology, Peking University, Beijing, China.
authors.forename: Fangting
authors.initials: F
authors.lastname: Li
authors.affiliation: LMAM and School of Mathematical Sciences, Peking University, Beijing, China ; Beijing International Center for Mathematical Research, Beijing, China.
authors.forename: Tiejun
authors.initials: T
authors.lastname: Li
mesh_terms: D019295:Computational Biology; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D007700:Kinetics; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D013269:Stochastic Processes; D013816:Thermodynamics; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D012333:RNA, Messenger; D014157:Transcription Factors