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RNA-RNA Interactions
by Frank J. SchmidtIn this volume expert researchers in the field detail many of the methods which are now commonly used to study RNA. These methods are presented as a guidebook to scientists who are experienced with RNA research and want to brush up on a new technique. 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 key tips on troubleshooting and avoiding known pitfalls. Thorough and intuitive, RNA-RNA Interactions: Methods and Protocols guides scientists investigating biological systems and studying RNA.
RNA-seq Data Analysis: A Practical Approach (Chapman & Hall/CRC Computational Biology Series)
by Eija Korpelainen Jarno Tuimala Panu Somervuo Mikael Huss Garry WongThe State of the Art in Transcriptome AnalysisRNA sequencing (RNA-seq) data offers unprecedented information about the transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. RNA-seq Data Analysis: A Practical Approach enables researchers to examine differential expression at gene, exon, and transcript le
RNA-Seq in Drug Discovery and Development (Drugs and the Pharmaceutical Sciences)
by Feng ChengThe research and development process in modern drug discovery and development is a complex and challenging task. Using traditional biological test methods such as PCR to measure the expression levels or function of these genes is costly and time-consuming. RNA-seq can measure the expression patterns of thousands of genes simultaneously and provide insights into functional pathways or regulations in biological processes, which has revolutionized the way biological scientists examine gene functions. This book addresses the various aspects of the RNA-seq technique, especially its application in drug discovery and development. Features • One of the few books that focuses on the applications of the RNA-seq technique in drug discovery and development • Comprehensive and timely publication which relates RNA sequencing to drug targets, mechanisms of action, and resistance • The editor has extensive experience in the field of computational medicinal chemistry, computational biophysics, and bioinformatics • Chapter authors are at the frontline of the academic and industrial science in this particular area of RNA sequencing
RNA, the Epicenter of Genetic Information
by John Mattick Paulo AmaralThe origin story and emergence of molecular biology is muddled. The early triumphs in bacterial genetics and the complexity of animal and plant genomes complicate an intricate history. This book documents the many advances, as well as the prejudices and founder fallacies. It highlights the premature relegation of RNA to simply an intermediate between gene and protein, the underestimation of the amount of information required to program the development of multicellular organisms, and the dawning realization that RNA is the cornerstone of cell biology, development, brain function and probably evolution itself. Key personalities, their hubris as well as prescient predictions are richly illustrated with quotes, archival material, photographs, diagrams and references to bring the people, ideas and discoveries to life, from the conceptual cradles of molecular biology to the current revolution in the understanding of genetic information. Key Features Documents the confused early history of DNA, RNA and proteins - a transformative history of molecular biology like no other. Integrates the influences of biochemistry and genetics on the landscape of molecular biology. Chronicles the important discoveries, preconceptions and misconceptions that retarded or misdirected progress. Highlights major pioneers and contributors to molecular biology, with a focus on RNA and noncoding DNA. Summarizes the mounting evidence for the central roles of non-protein-coding RNA in cell and developmental biology. Provides a thought-provoking retrospective and forward-looking perspective for advanced students and professional researchers.
RNA Abundance Analysis: Methods and Protocols (Methods in Molecular Biology #2170)
by Hailing Jin Isgouhi KaloshianThis updated book covers a wide range of techniques on RNA extraction, detection, quantification, visualization, and genome-wide profiling, from conventional methods to state-of-the-art high throughput approaches. It includes detailed techniques to examine mRNAs, small non-coding RNAs, protein-associated small RNAs, organelle RNAs, endosymbiont RNAs, and alternatively spliced RNA variants from various organisms. RNA editing and the computational data processing for genome-wide datasets is also discussed. Written for the highly successful Methods in Molecular Biology series, 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 practical, RNA Abundance Analysis: Methods and Protocols, Second Edition provides a comprehensive set of techniques and methods on isolating and analyzing mRNAs, small RNAs, and other RNA variants, in order to assist researchers in their gene expression studies.
RNA Activation
by Long-Cheng LiThis book offers an essential guide to RNA activation (RNAa), an emerging and fascinating new field. RNAa is a small RNA-guided and Argonaute-dependent gene regulation phenomenon in which promoter-targeted short double-stranded RNAs (dsRNAs) induce target gene expression at the transcriptional level. It occurs primarily in the nucleus and can be mediated by artificially designed short duplex RNAs that target regulatory sequences (e.g., promoters, genes’ 3’ termini and enhancers) and naturally occurring small RNAs (e.g., miRNAs and C. elegans 22G-RNAs). With contributions from internationally respected RNA experts, this book provides comprehensive coverage of different RNAa mechanisms and a timely update on recent advances in RNAa research, with a focus on developing RNAa-based therapeutics. Special chapters are also devoted to the topics of gene activation induced by antisense oligonucleotides and the CRISPR system. As the first book to cover RNAa, it will be of interest to a wide audience, from scientists in academia and the pharmaceutical industry to clinicians who wish to further explore the biology of RNAa and related phenomena, so as to harness their full potential for use in biotechnology and drug development.
RNAi: Design and Application
by Sailen BarikRNA interference (RNAi) is the most recent discovery to revolutionize the study of biology. In this book, leaders in the field contribute state-of-the-art, easy to follow methods and bench protocols designed for practical, everyday use of RNAi in biological research. Cutting edge and clearly written, this book enables a researcher with standard molecular biological training to perform major RNAi-related experiments and contribute to this revolutionary, growing field.
RNAi (Advanced Methods)
by Martin LatterichOne of the major recent discoveries in molecular and cellular biology is that small double-stranded RNA molecules selectively turn off gene expression in all types of cell, a phenomenon known as RNA silencing. This discovery led to the development of RNA interference (known as RNAi) as a powerful research tool in the functional study of individual genes and their products, and in functional genomics. In RNAi, specific small double-stranded RNA molecules (small interfering RNAs or siRNAs) are introduced into cells to selectively silence certain genes. RNAi covers the basic concepts and mechanisms of RNAi, transfection of cells with siRNAs, the design and validation of RNAi reagents, RNAi techniques in different organisms, large-scale RNAi screening, applications of RNAi in drug discovery, and potential uses of RNAi as a therapeutic agent. A key feature of RNAi is the highlighting of the pitfalls that can occur and how to minimize them. The book also contains a complete list of abbreviations.
RNAi and microRNA-Mediated Gene Regulation in Stem Cells
by Baohong Zhang Edmund J. StellwagRecent stem cell research has revealed that miRNA and RNAi-mediated gene regulation is one of the vital determinates controlling the state of cell differentiation, with the small RNAs serving as key elements involved in regulatory network control of pluripotent cell fate determination. In RNAi and microRNA-Mediated Gene Regulation in Stem Cells: Methods, Protocols, and Applications, expert authors from laboratories across the globe contribute an accessible compendium of up-to-date, proven methods focused on the study of the titular topic. Divided into three sections, the book first gives a brief introduction to RNAi and miRNAs in stem cells, with a focus on the current status of research and future perspectives, then it continues with detailed methods and protocols for RNAi screening, transfection, and the knockdown of specific genes and pathways in several animal species, including humans and mice, concluding with a section on recently developed methods for identification of miRNAs, including a general protocol for preparation and analysis of miRNA libraries for deep sequencing, knock down of a specific gene using miRNA-based shRNA, and miRNA expression analysis using qRT-PCR. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes highlighting tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNAi and microRNA-Mediated Gene Regulation in Stem Cells: Methods, Protocols, and Applications serves as a valuable resource for scientists and aspiring graduate students interested in the intersection of RNAi, miRNA, and stem cell molecular biology and the exciting areas of medicine, including regenerative medicine, aging, cancer, and neurological disorders, that can be advanced through this expanding area of research.
RNAi and Plant Gene Function Analysis
by Atsushi Komamine Hiroaki KodamaThe use of RNAi technology is essential for most plant science researchers. As DNA sequence information increases, so the need for functional annotation of target genes also increases. Authoritative and accessible, RNAi and Plant Gene Function Analysis: Methods and Protocols seeks to serve as an ideal guide to scientists of all backgrounds looking to further their knowledge of this fundamental science. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. In addition to the functional annotation of unknown genes, RNAi technology has been applied to the genetic engineering of important plant metabolites including starches, oils, and storage proteins. RNAi has been used to engineer plants resistant to plant viruses and also to nematodes and insects. RNAi and Plant Gene Function Analysis: Methods and Protocols will provide both professionals and novices of plant biotechnology and breeding research with essential tips for designing experiments meant to explore plant gene function.
RNAi and Small Regulatory RNAs in Stem Cells
by Baohong ZhangThis detailed collection provides an accessible compendium of up-to-date methods focused on the study of RNAi and small regulatory miRNAs in stem cells. Beginning with a brief introductory section, the volume continues by exploring methods and protocols for RNAi screening, transfection, and the knockdown of specific genes and pathways in several animal species, including humans and mice, recently developed methods for miRNA expression and functional analysis, as well as usage of CRISPR/Cas 9 to knockout an individual gene for functional studies. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, list of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and authoritative, RNAi and Small Regulatory RNAs in Stem Cells: Methods and Protocols aims to accelerate progress in this crucial field by reducing the time required to decipher and put into practice procedures published in the literature.
RNAi for Plant Improvement and Protection
by Bruno Mezzetti, Jeremy Sweet & Lorenzo BurgosRNA interference (RNAi) has the potential to make major contributions towards sustainable crop production and protection with minimal environmental impacts compared to other technologies. RNAi is being developed and exploited both within plants (i.e. host-induced gene silencing, HIGS) and/or as topical applications (e.g. spray-induced gene silencing, SIGS) for targeting pest and pathogen genes and for manipulating endogenous gene expression in plants. Chapters by international experts review current knowledge on RNAi, methods for developing RNAi systems in GM plants and applications for crop improvement, crop production and crop protection. Chapters examine both endogenous systems in GM plants and exogenous systems where interfering RNAs are applied to target plants, pests and pathogens. The biosafety of these different systems is examined and methods for risk assessment for food, feed and environmental safety are discussed. Finally, aspects of the regulation of technologies exploiting RNAi and the socio-economic impacts of RNAi technologies are discussed.
RNAi Strategies for Pest Management: Methods and Protocols (Methods in Molecular Biology #2360)
by Luis María VaschettoThis volume explores the latest techniques used for sustainable development of eco-friendly pest management systems. Chapters in this book look at the design of novel RNAi-mediated pest control strategies and related issues. Some of the topics covered in this book are identification and characterization of differentially expressed non-coding RNAs in insect genomes; functional small RNA design; analysis of endogenous RNAi pathways; RNAi screening; plant models of RNAi-mediated pest control; and dsRNA delivery. 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. Cutting-edge and comprehensive, RNAi Strategies for Pest Management: Methods and Protocols is a valuable resource for any scientist or researcher interested in learning more about this exciting and developing field. Chapter 18 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
RNA Amplification and Analysis: Methods and Protocols (Methods in Molecular Biology #2822)
by Mekbib AstatkeThis volume provides methods to analyze RNA and gain insight to a number of critical cellular functions. Chapters detail RNA isolation and enrichment, RNA amplification and detection, RNA sequencing, analysis of RNA modification, RNA delivery approaches, and analysis of RNA binding and catalytic activity. 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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA Amplifications and Analysis: Methods and Protocols aims to present researchers with cutting-edge technologies with detailed explanations of critical steps, while providing a clear understanding of the overall protocol.
RNA and Cancer
by Jane Y. WuAccumulating evidence supports the role of defects in post-transcriptional gene regulation in the development of cancer. RNA and Cancer examines the recent advances in our understanding of post-transcriptional gene regulation, especially RNA processing and its role in cancer development and treatment. A particular focus is mRNA splicing, but other topics such as microRNAs, mRNA stability, the perinucleolar compartment, and oligonucleotide therapeutics are also covered in detail. All chapters have been written by internationally renowned experts. The book is intended for all with an interest in gene regulation and cancer biology, and especially for those not directly working on RNA biology, including clinicians and medical students. It is hoped that it will stimulate further innovative research collaborations between RNA biologists and cancer researchers to the benefit of patients.
RNA and DNA Diagnostics
by Volker A. Erdmann Stefan Jurga Jan BarciszewskiThe aim of molecular diagnostics is preferentially to detect a developing disease before any symptoms appear. There has been a significant increase, fueled by technologies from the human genome project, in the availability of nucleic acid sequence information for all living organisms including bacteria and viruses. When combined with a different type of instrumentation applied, the resulting diagnostics is specific and sensitive. Nucleic acid-based medical diagnosis detects specific DNAs or RNAs from the infecting organism or virus and a specific gene or the expression of a gene associated with a disease. Nucleic acid approaches also stimulate a basic science by opening lines of inquiry that will lead to greater understanding of the molecules at the center of life. One can follow Richard Feynman's famous statement "What I cannot create, I do not understand. "
RNA and DNA Editing
by Ruslan AphasizhevThe recent expansion in diversity of RNA and DNA editing types has stimulated the development of many unique genetic, molecular, biochemical, and computational approaches to biological issues. In RNA and DNA Editing: Methods and Protocols, leading experts in the field introduce methods developed over the last few years to study editing substrates, mechanisms of specificity, and functions of RNA and DNA editing enzymes and complexes. Sections of the book are dedicated to state-of-the art techniques which enable investigation of uracil insertion/deletion RNA editing in mitochondrion of Trypanosoma brucei, adenosine to inosine RNA editing, cytidine to uracil RNA and DNA editing, as well as tRNA editing and RNA modifications. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA and DNA Editing: Methods and Protocols seeks to inspire the further development of these vital and powerful techniques.
RNA'Protein Interaction Protocols
by Susan R. HaynesHighly skilled experimentalists provide a comprehensive series of commonly used, as well as specialized, techniques for analyzing how proteins and RNA interact. Richly detailed and readily reproducible, these methods enable researchers to analyze the structural details of an RNA-protein interaction, to determine in detail what parts of the protein and RNA are in close contact, and to isolate RNP complexes from cells. There are also in vitro and in vivo methods and protocols for assaying the effects of proteins and RNP complexes on mRNA metabolism. The methods assume only a knowledge of basic molecular biology, biochemistry, and cell culture, and can be readily adapted to other systems. RNA-Protein Interaction Protocols offers a wide-ranging collection of up-to-date experimental methods that will assure productive and reproducible results for all investigators in the field.
RNA Binding Proteins
by Zdravko LorkovicGene expression in eukaryotes is regulated at different levels, which need to be coordinated to implement the information in the genome. Now it is clear that post-transcriptional regulation of gene expression such as pre-mRNA splicing, mRNA transport, editing, turnover and translation are as important as the control of transcription. In all aspects
RNA Bioinformatics
by Ernesto PicardiThis volume provides an overview of RNA bioinformatics methodologies, including basic strategies to predict secondary and tertiary structures, and novel algorithms based on massive RNA sequencing. Interest in RNA bioinformatics has rapidly increased thanks to the recent high-throughput sequencing technologies allowing scientists to investigate complete transcriptomes at single nucleotide resolution. Adopting advanced computational technics, scientists are now able to conduct more in-depth studies and present them to you in this book. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and equipment, step-by-step, readily reproducible bioinformatics protocols, and key tips to avoid known pitfalls. Authoritative and practical, RNA Bioinformatics seeks to aid scientists in the further study of bioinformatics and computational biology of RNA.
RNA Bioinformatics (Methods in Molecular Biology #2284)
by Ernesto PicardiThis detailed book aims to provide an overview of novel bioinformatics resources for exploring diverse aspects of RNA biology. This edition focuses on methods dealing with non-coding RNA (miRNAs, circRNAs or lncRNAs), RNA modifications (m6A or RNA editing), single cell RNA-seq and statistical models to handle count data from RNA-seq experiments. The book also includes chapters based on the classical RNA bioinformatics methods, such as those for deciphering secondary and tertiary RNA structures; however, they are revised to take into account deep sequencing data. Finally, chapters describing methods to analyze RNA sequencing data from emerging third generation sequencing technologies that could provide interesting insights into the transcriptional process and its regulation are also included. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of expert implementation advice that encourages quality results. Comprehensive and up-to-date, RNA Bioinformatics, Second Edition serves as an ideal guide for researchers digging ever-deeper into the depths of the study of RNAs.The chapter 'RNA-Seq Data Analysis in Galaxy' is open access under a CC BY 4.0 license.
RNA Chaperones: Methods and Protocols (Methods in Molecular Biology #2106)
by Tilman HeiseThis book provides a wide spectrum of methods to study RNA chaperones in vitro, at the single molecule level, and protocols useful for cell-based assays. Beginning with a section on a number of bacterial proteins for study, the volume also explores proteins from eukaryotic cells and how to delve into the complex interactions between RNA chaperones and the folding and unfolding of proteins. Written for the highly successful Methods in Molecular Biology series, 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 practical, RNA Chaperones: Methods and Protocols serves as an ideal guide for scientists and students interested in RNA biology and RNA chaperones.Chapter 3 is available Open Access under a Creative Commons Attribution 4.0 International License via link.springer.com.
RNA Damage and Repair
by Ioly Kotta-LoizouRibonucleic acid (RNA) is a macromolecule that plays a central role in cell physiology: RNA molecules act as intermediates between the deoxyribonucleic acid (DNA), where genetic information is stored, and proteins, which perform the necessary functions within the cell. Traditionally, the structural and functional properties of RNA are closely linked to gene expression. However, RNA-based enzymes, called ribozymes, are also involved in catalysis and small RNAs regulate key cellular processes, such as cell growth, division, differentiation, aging and death. RNA is a sensitive macromolecule that can be easily damaged by environmental conditions (ultraviolet radiation, oxidative stress) and biological factors (ribonucleases, ribotoxins, CRISPR-Cas systems). Therefore, cells have developed mechanisms to protect and/or repair RNA molecules. This book presents an overview of the biology of RNA damage, protection and repair in prokaryotes and eukaryotes. Individual chapters cover the expression regulation, enzymology and physiological role of such systems, and link them to important human diseases such as cancer and degenerative diseases.
RNA Delivery Function for Anticancer Therapeutics (Nanotechnology for Drugs, Vaccines and Smart Delivery Systems)
by Loutfy H. MadkourThis book presents an overview of the current status of translating the RNAi cancer therapeutics in the clinic, a brief description of the biological barriers in drug delivery, and the roles of imaging in aspects of administration route, systemic circulation, and cellular barriers for the clinical translation of RNAi cancer therapeutics, and with partial content for discussing the safety concerns. It then focuses on imaging-guided delivery of RNAi therapeutics in preclinical development, including the basic principles of different imaging modalities, and their advantages and limitations for biological imaging. With growing number of RNAi therapeutics entering the clinic, various imaging methods will play an important role in facilitating the translation of RNAi cancer therapeutics from bench to bedside. RNAi technique has become a powerful tool for basic research to selectively knock down gene expression in vitro and in vivo. Our scientific and industrial communities have started to develop RNAi therapeutics as the next class of drugs for treating a variety of genetic disorders, such as cancer and other diseases that are particularly hard to address with current treatment strategies. Key Features Provides insight into the current advances and hurdles of RNAi therapeutics. Accelerates RNAi, miRNAs, and siRNA drug development for cancer therapy from bench to bedside. Addresses various modifications and novel delivery strategies for miRNAs, piRNAs and siRNA delivery in anticancer therapeutics. Explores the need for the interaction of hematologists,cell biologists, immunologists, and material scientists in the development of novel cancer therapies. Describes the current status of clinical trials related to miRNA and siRNA-based cancer therapy Presents remaining issues that need to be overcome to establish successful therapies.
RNA Design: Methods and Protocols (Methods in Molecular Biology #2847)
by Alexander Churkin Danny BarashThis volume provides comprehensive methods on RNA design. Chapters details traditional RNA design in secondary structure, RNA design in tertiary structure, and RNA design applications and assessments. 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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA Design: Methods and Protocols aims to ensure successful results in the further study of this vital field.