The expression of genes is based on stochastic processes, which lead to temporal fluctuations in the number of proteins of each gene. If such fluctuations become too large they can be detrimental to the fitness of an organisms, because most cellular processes are based on the precise interaction of proteins. This PhD thesis explores the role of post-transcriptional regulatory mechanisms in the control of stochasticity in gene expression, with a focus on microRNAs, common regulators in multicellular organisms. Bioinformatic data analysis, mathematical modeling and single cell expression experiments are used to analyze the conditions under which microRNAs can lead to the reduction of fluctuations in gene expression. The central insight of this thesis is that microRNAs can indeed reduce fluctuations for most genes and that they are likely used by organisms for this purpose, thus ensuring precision to gene expression during development and the maintenance of the adult body. Der Expression von Genen liegen stochastische Prozesse zu Grunde, die zu Fluktuationen in der Menge von Proteinen eines jeden Gens führen. Zu starke Fluktuationen in Proteinmengen können für Organismen schädlich sein, da die meisten zellulären Prozesse auf der präzisen Wechselwirkung von Proteinen beruhen. Diese Dissertationsschrift befasst sich mit dem Einfluss von post-transkriptionellen Regulationsmechanismen auf die stochastischen Prozesse der Genexpression. Mittels bioinformatischer Datenanalyse, mathematischer Modellierung und gezielten Einzelzellexperimenten wird mit Fokus auf die in Mehrzellern weitverbreiteten microRNAs erforscht unter welchen Voraussetzungen Organismen post-transkriptionelle Regulation zu Verringerung von Fluktuationen benutzen können. Die zentrale Erkenntnis der vorliegenden Arbeit ist, dass microRNAs für die meisten Gene Fluktuationen verringern können und auch zu diesem Zweck genutzt werden.

This book discusses topics related to the topological structure and biological function of gene networks regulated by microRNAs. It focuses on analyzing the relation between topological structure and biological function, applying these theoretical results to gene networks involving microRNA, illustrating their biological mechanisms, and identifying the roles of microRNA in controlling various phenomena emerging from the networks. In addition, the book explains how to control the complex biological phenomena using mathematical tools and offers a new perspective on studying microRNA. It is a useful resource for graduate students and researchers who are working on or interested in microRNAs and gene network.

MicroRNA (miRNA) biology is a cutting-edge topic in basic as well as biomedical research. This is a specialized book focusing on the current understanding of the role of miRNAs in the development, progression, invasion, and metastasis of diverse types of cancer. It also reviews their potential for applications in cancer diagnosis, prognosis, and th

MicroRNAs (miRNAs) are a class of small non-coding RNAs which play important roles in post transcriptional gene regulation. miRNAs regulate more than half of mammalian protein-coding genes. They have been found to participate in almost every cellular process and their dysregulation is associated with many diseases. miRNAs recognize their targets by base paring to miRNA response elements (MREs), which are predominantly located at 3' untranslated region (3'UTR) of mRNAs. This thesis focuses on a microRNA activity reporter system to investigate various aspects of miRNA regulation on its endogenous 3'UTR targets. Mutation of selected MREs on 3'UTRs (MutUTRs) was designed and validated as miRNA unregulated control. It does not require genetic modifications of cellular background and effectively abolishes the majority of miRNA regulation with minimum perturbation to the UTR sequences. MicroRNAs can induce target silencing via mRNA transcript degradation and translational inhibition. But the relative contributions from the two sources have been under debate. It is also unclear how miRNA regulation varies for different target expression. MicroRNA regulation at the transcriptional and translational levels was quantified at single cell resolution over a target expression range of more than 100 fold using our reporter system. The transcriptional regulation was found to be uniform throughout the range of measurement, whereas translational regulation decreases at high target expression. Our data also suggests that translational regulation increase initially at low target expression for certain targets. For all UTRs under study, miRNA regulation from the two sources were found to be on the same order. In addition to target repression, miRNAs also control target expression noise. MicroRNAs decrease protein expression noise for lowly expressed genes, but increase noise for highly expressed genes, and the noise regulation seems to happen at translational level. By linking reporter assays to transcriptome expression, our findings suggest that microRNAs confer precision to protein expression in vivo, and transcriptional regulation might dominate for endogenous targets. Finally we applied the reporter system as miRNA decoys to study miRNA-mediated- crosstalk. We also propose that the reporter systems could be used to study alternative polyadenylation, which is usually accompanied by consequential loss of MREs.

This book includes updated information about microRNA regulation, for example, in the fields of circular RNAs, multiomics analysis, biomarkers and oncogenes. The variety of topics included in this book reaffirms the extent to which microRNA regulation affects biological processes. Although microRNAs are not translated to proteins, their importance for biological processes is not less than proteins. An understanding of their roles in various biological processes is critical to understanding gene function in these biological processes. Although non-coding RNAs other than microRNAs have recently come under investigation, microRNA still remains the front runner as the subject of genetic and biological studies. In reading the collection of papers, readers can grasp the most updated information regarding microRNA regulation, which will continue to be an important topic in genetics and biology.

In the face of random perturbations in environment as well as genetic mutations, complex organisms manage to maintain remarkably robust developmental stability. Despite originating from a single cell and sharing a common genome, tissue-based organisms contain many different cellular phenotypes. The robustness of the developmental programs of these organisms depends on their underlying gene regulatory network (GRN), which is composed of a diverse set of mechanisms that help the cell achieve a desired state and stay there. One curiosity of tissue-based organisms is their near-universal dependence on non-coding RNAs, of which the largest class is the 18-22nt long microRNAs (miRNAs). These short RNAs typically, but not always, repress the translation of messenger RNAs (mRNAs) into functional proteins in a sequence-specific manner. Nonetheless, identifying the relationship between tissue-based organism development and miRNAs has been challenging. Within a single model organism, a large number of synthesis and functional pathways contribute to this overall effect. Furthermore, despite their overall dependence on miRNAs, it has been demonstrated that only a small subset of the total set of DNA-encoded miRNAs (the miRNAome) is required for proper development, and the loss of individual miRNAs often causes no change in phenotype. This dissertation aims to postulate a "fundamental law of miRNAs" in the development of these organisms. The complexities of miRNA-mediated gene regulation can often obscure their commonalities; by using a common abstraction of GRNs and gene expression, my aim is to show that miRNA-mediated regulation is innately tied to the notion of stem cells and cell differentiation. Using a multiple different models of gene expression and cell differentiation, I show how the specific type of regulation imparted by miRNAs can help create a stable, undifferentiated state and control the duration of that state. This role for miRNAs is supported independently by each model and agrees with experimentally-observed data.