Research On The Effects Of MicroRNA On Gene Regulatory Networks

Molecular biology is the20th century science. Biologists had revealed a large of de-tails about bio-molecules in biological systems. Scientists recognized that the essence of biological phenomena is the results of interaction among large amounts of bio-molecules including genes, proteins and RNAs. Therefore, to comprehensively summarize the ex-isting experimental results and to investigate their interaction from system level has become the inexorable trend. Then system biology gradually developed as one of the important field of modern life science. The mechanism of gene regulatory network is one of the hot topics in recent system biology research. In fact, almost all of the life activity is regulated by gene regulatory network. To research gene regulatory network from system level will helpful to clarify the essence of life and mechanism of disease.It has been believed that almost all of the specific physiological functions are executed by coded protein. However, as a number of important non-coding small RNA discovered, more and more biological experiments demonstrated that non-coding small RNA has the function of regulating gene express and it gradually become one of the hot topics of life science research. Specially, microRNA (miRNA) is a class of small non-coding RNA molecules, occurring widely in eukaryotes. It can inhibit gene expression at post-transcription level and plays a large role in many life process including cell growth, cell proliferation, cell differentiation, apoptosis and disease occurring. Thus, much attention has been attracted from related researchers.In this thesis, we studied the miRNA’s effect on the dynamical behaviors of gene regulatory network by nonlinear dynamical modeling. Here, we described the main contents and the innovative results as follows:(1) MiRNA’s effects on the dynamical behaviors of Rb-E2F pathway.In the past few years, extensive research was dedicated to the mechanism of cell proliferation and cancer occurring, which demonstrated that Rb-E2F pathway plays an important regulatory role during cell cycle, especially for initiating DNA replication. However, the control of Rb-E2F pathway is disrupted in virtually all human cancers, which indicate that this pathway has particular biological function in cancer occurring and tumor suppression. E2F is a positive regulator during cell cycle. It can promote cell cycle transition from G1phase to S phase as well as cell apoptosis. In recent years, experiment research showed that E2F heavily upregulates miR449expression. In turn, E2F is inhibited by miR449through regulating several transcripts, including Myc, Cdk2and Cdk4/6, thus forming several negative feedback loops in the interaction network.On the basis of existing relevant experimental evidence and data, a mathematical model of nonlinear ordinary differential equations is constructed and nonlinear dynami-cal behaviors are discussed in the second chapter of this thesis. A comparison is given to reveal the fundamental differences of dynamical behavior of Rb-E2F pathway between regulation and deregulation of miR449. Coherent with the experiments it predicts that miR449plays a critical role in regulating the cell cycle progression and provides a twofold safety mechanism to avoid excessive E2Finduced proliferation by cell cycle arrest and apoptosis. Moreover, bifurcation analysis and numerical simulation shows that the mechanisms of the negative regulation of miR449to E2F through three dif-ferent transcripts are quite distinctive which needs to be verified experimentally. The study of this part may help us to analyze the mechanism of other miRNA in regulating signal pathway and the whole cell cycle process mediated by other miRNA more easily.(2) The dynamical mechanism of combinatorial regulations between transcription factors and miRNAs.Transcription factors and miRNAs are the most important families of gene regula-tory molecules in multicellular organisms. They can independently mediate a series of gene expression at transcription level. But experimental study verified that interaction between them can regulate gene express more sophisticated and more accurate. Combi-nation of the two might well provide all kinds of advantages to cell evolution. Thus, to clarify the mechanism of combinatorial regulations between transcription factors and miRNAs will helpful to understand all kinds of life process. Upon DNA damage, cells must decide between different fates including growth arrest, DNA repair, and apopto-sis. P53and E2F1are critical transcription factors involved in the decision between different cell fates. Recent experiments have shown that p53and E2F heavily induces miR34and miR449respectively and then these two miRNAs regulate the activity of p53and E2F in turn, which might have an important role in cell fate decision. Therefore, to understand the mechanism of combinatorial regulations between two transcription factors p53and E2F and two miRNAs miR34and miR449is a great challenge.For the cell fate decision process after DNA damage, we constructed nonlinear differential equations in the third chapter to investigate the mechanism of combinatorial regulations between two transcription factors p53and E2F and two miRNAs miR34and miR449. By analyzing nonlinear dynamical behaviors of the model, we found that p53exhibits pulsatile behavior, which is coherent with existing experimental and theoretical results. Moreover, a comparison is given to reveal the subtle differences of the cell fate decision process between regulation and deregulation of miR34on E2F1. It predicts that miR34plays a critical role in promoting the cell cycle arrest. In addition, a computer simulation result also predicts that the miR449is necessary for apoptosis in response to sustained DNA damage. All of these results are in agreement with experimental observations. Our results demonstrated the intricate regulatory relationship between these two transcription factors and two miRNAs in the cell fate decision process after DNA damaged. They indicate that miR34and miR449are effective tumor suppressor and play important role in the cell fate decision process.(3) Dynamical mechanism of oscillation in a gene regulatory network mediated by miRNA with time delays.It is well known that time delays are widely exist in cell life processes due to regula-tion of gene express is conducted by signal transfer, especially during the transcription, translation and protein synthesis in gene regulation process. It plays important role in many cell life processes and has significant effects on the dynamical behaviors of biological systems.In the fourth chapter, the dynamical mechanism of oscillation in a gene regulatory network mediated by miRNA with time delays is investigated. By using Hopf bifur-cation theory, we designed a biological oscillator with time delays. First, nonlinear mathematical model is given. Through theoretical analysis, we obtained the dynamical process of this model and given the sufficient conditions of oscillation occurring. Second, by linearizing the system at the positive equilibrium and analyzing the associated char-acteristic equation, the asymptotic stability of the positive equilibrium is investigated and Hopf bifurcations are demonstrated. Third, the direction of Hopf bifurcation and the stability of the bifurcating periodic solutions are determined by the normal form theory and the center manifold theorem for functional differential equations. Finally, some numerical simulations are carried out for illustrating the theoretical results. The results of this part indicate that the oscillation can not only be induced by the interplay between two RNAs and one protein but also be induced by the time delays. It will be helpful to further understand the mechanism of biological oscillator and the dynamical function of miRNA.In the end, we summarized this thesis and provide the further study direction in the fifth chapter.