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.
Post-transcriptional regulation of gene expression is essential for cell function. MicroRNAs (miRNAs), small (~22nt) non-coding RNAs, are negative regulators of post-transcriptional expression. MiRNAs recruit the RNA induced silencing complex (RISC), which includes an Argonaute (AGO) protein, to partially complementary target sites located in 3' untranslated regions (UTRs), and induce accelerated mRNA decay and translational inhibition of target mRNAs. Each miRNA has potential to regulate many hundreds of mRNAs via this pathway. Although, miRNAs typically elicit a modest effect per mRNA, hundreds of such small changes result in a substantial cumulative impact on the transcriptome. Additionally, miRNA regulatory networks incorporate master regulators such as transcription factors downstream of miRNAs, enabling miRNAs to trigger substantial changes in gene regulatory networks. Understanding the biological impact of miRNAs requires knowledge of their targets, and robust distinction of miRNA direct targets from cascading downstream regulatory changes remains challenging. In this work, I developed a simple experimental approach to robustly uncouple post-transcriptional and transcriptional changes using RNA-seq and Precision Run-On sequencing (PRO-seq), a method for profiling actively transcribing RNA polymerases. The net change in mRNA abundance results from changes in synthesis and decay. I demonstrated that by subtracting the changes in mRNA synthesis (PRO-seq) from the changes in mRNA abundance (RNA-seq), a robust estimate of post-transcriptional regulation by miRNAs could be derived. I refer to this approach as CARP: Combined Analysis of RNA-seq and PRO-seq. Using CARP, I successfully separated true direct targets of specific miRNAs from the downstream indirect changes, which I validated using orthogonal assays such as Argonaute eCLIP-seq and ribosome profiling. Additionally, CARP analysis revealed that the majority of miRNAs used in the study elicited sizable indirect targeting at both transcriptional and post-transcriptional levels, which are often disregarded. Using motif enrichment analysis, I found candidate transcription factors underlying the miRNA-mediated indirect regulation at transcriptional level. I also demonstrated that CARP facilitates effective dissection of complex regulatory changes triggered by miRNAs. Furthermore, my analysis revealed that many miRNAs elicit discernible repression of target sites located in open reading frames (ORFs); the significance of ORF target sites is a potentially important aspect of miRNA biology, but the extent to which it occurs has been controversial. My data demonstrated that while ORF sites to certain miRNAs often mediate subtle repression, their likely role is in assisting the miRNA-mediated regulation of weaker 3'UTR sites to collectively elicit significant post-transcriptional repression of the target mRNA. Overall, the tools I developed in my graduate work facilitate robust distinction of direct target from indirect regulatory changes aiding in the study of miRNA regulatory networks at the systems-level. Finally, I apply CARP and other genomic approaches to better understand biological roles of miRNAs in the immune response of CD8+ T-cells in mouse models.
This work is a showcase for the integration of systems biology and bioinformatics tools, algorithms and models for deciphering biological phenomena. More specifically, it integrates (i) prediction algorithms for identifying and characterizing molecular interactions, (ii) structural modelling of molecule complexes, (iii) network analysis approaches, and (iv) mathematical modelling and simulation. Two comprehensive workflows are implemented for the analysis of collective target gene regulation by microRNAs and for the prediction of cooperating microRNA pairs and their mutual target genes. In two case studies mechanisms of fine-tuned target gene regulation are revealed for different cellular processes and the phenomenon of cooperative target regulation is identified as frequent mechanism of gene regulation in humans.
This edited reflects the current state of knowledge about the role of microRNAs in the formation and progression of solid tumours. The main focus lies on computational methods and applications, together with cutting edge experimental techniques that are used to approach all aspects of microRNA regulation in cancer. We are sure that the emergence of high-throughput quantitative techniques will make this integrative approach absolutely necessary in the near future. This book will be a resource for researchers starting out with cancer microRNA research, but is also intended for the experienced researcher who wants to incorporate concepts and tools from systems biology and bioinformatics into his work. Bioinformaticians and modellers are provided with a general perspective on microRNA biology in cancer, and the state-of-the-art in computational microRNA biology.
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
This detailed volume provides a collection of protocols for the study of miRNA functions in plants. Beginning with coverage of miRNA function, biogenesis, activity, and evolution in plants, the book continues by guiding readers through methods on the identification and detection of plant miRNAs, bioinformatic analyses, and strategies for functional analyses of miRNAs. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Plant MicroRNAs: Method and Protocols aims to ensure successful results in the further study of this vital area of plant science.
RNAs form complexes with proteins and other RNAs. The RNA‐infrastructure represents the spatiotemporal interaction of these proteins and RNAs in a cell‐wide network. RNA Infrastructure and Networks brings together these ideas to illustrate the scope of RNA‐based biology, and how connecting RNA mechanisms is a powerful tool to investigate regulatory pathways. This book is but a taste of the wide range of RNA‐based mechanisms that connect in the RNA infrastructure.
This book presents recent methods for Systems Genetics (SG) data analysis, applying them to a suite of simulated SG benchmark datasets. Each of the chapter authors received the same datasets to evaluate the performance of their method to better understand which algorithms are most useful for obtaining reliable models from SG datasets. The knowledge gained from this benchmarking study will ultimately allow these algorithms to be used with confidence for SG studies e.g. of complex human diseases or food crop improvement. The book is primarily intended for researchers with a background in the life sciences, not for computer scientists or statisticians.
