title: Effect of Dynamic Interaction between microRNA and Transcription Factor on Gene Expression.
abstract: MicroRNAs (miRNAs) are endogenous noncoding RNAs which participate in diverse biological processes in animals and plants. They are known to join together with transcription factors and downstream gene, forming a complex and highly interconnected regulatory network. To recognize a few overrepresented motifs which are expected to perform important elementary regulatory functions, we constructed a computational model of miRNA-mediated feedforward loops (FFLs) in which a transcription factor (TF) regulates miRNA and targets gene. Based on the different dynamic interactions between miRNA and TF on gene expression, four possible structural topologies of FFLs with two gate functions (AND gate and OR gate) are introduced. We studied the dynamic behaviors of these different motifs. Furthermore, the relationship between the response time and maximal activation velocity of miRNA was investigated. We found that the curve of response time shows nonmonotonic behavior in Co1 loop with OR gate. This may help us to infer the mechanism of miRNA binding to the promoter region. At last we investigated the influence of important parameters on the dynamic response of system. We identified that the stationary levels of target gene in all loops were insensitive to the initial value of miRNA.
authors.affiliation: Department of Physics, College of Physics Science and Technology, Xiamen University, Xiamen 361005, China; School of Mathematics, Liaoning University, Shenyang 110036, China; Research Center for Computer Simulating and Information Processing of Bio-Macromolecules of Liaoning Province, Shenyang 110036, China.
authors.forename: Qi
authors.identifier: 0000-0001-9713-1864
authors.initials: Q
authors.lastname: Zhao
authors.affiliation: Research Center for Computer Simulating and Information Processing of Bio-Macromolecules of Liaoning Province, Shenyang 110036, China; School of life science, Liaoning University, Shenyang 110036, China.
authors.forename: Hongsheng
authors.initials: H
authors.lastname: Liu
authors.affiliation: Department of Mathematics, Shaoxing University, Shaoxing 312000, China.
authors.forename: Chenggui
authors.initials: C
authors.lastname: Yao
authors.affiliation: Department of Physics, College of Physics Science and Technology, Xiamen University, Xiamen 361005, China.
authors.forename: Jianwei
authors.identifier: 0000-0002-8712-0544
authors.initials: J
authors.lastname: Shuai
authors.affiliation: Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510000, China; School of Mathematical and Computational Science, Sun Yat-Sen University, Guangzhou 510275, China.
authors.forename: Xiaoqiang
authors.identifier: 0000-0002-3399-7260
authors.initials: X
authors.lastname: Sun
mesh_terms: D005786:Gene Expression Regulation / Q000235:genetics / Q000502:physiology; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D059372:Nucleotide Motifs; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors