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Gene 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
Systems Biology of RNA Binding Proteins by Gene W. Yeo Pdf
After transcription in the nucleus, RNA binding proteins (RBPs) recognize cis-regulatory RNA elements within pre-mRNA sequence to form mRNA-protein (mRNP) complexes. Similarly to DNA binding proteins such as transcription factors that regulate gene expression by binding to DNA elements in the promoters of genes, RBPs regulate the fate of target RNAs by interacting with specific sequences or RNA secondary structural features within the transcribed RNA molecule. The set of functional RNA elements recognized by RBPs within target RNAs and which control the temporal, functional and spatial dynamics of the target RNA define a putative “mRNP code”. These cis-regulatory RNA elements can be found in the 5’ and 3’ untranslated regions (UTRs), introns, and exons of all protein-coding genes. RNA elements in 5’ and 3’ UTRs are frequently involved in targeting RNA to specific cellular compartments, affecting 3’ end formation, controlling RNA stability and regulating mRNA translation. RNA elements in introns and exons are known to function as splicing enhancers or silencers during the splicing process from pre-mRNA to mature mRNA. This book provides case studies of RNA binding proteins that regulate aspects of RNA processing that are important for fundamental understanding of diseases and development. Chapters include systems-level perspectives, mechanistic insights into RNA processing and RNA Binding proteins in genetic variation, development and disease. The content focuses on systems biology and genomics of RNA Binding proteins and their relation to human diseases.
RNA Binding Proteins by Kathryn Sandberg,Susan E. Mulroney Pdf
RNA binding proteins are an exciting area of research in gene regulation. A multitude of RNA-protein interactions are used to regulate gene expression including pre-mRNA splicing, polyadenylation, editing, transport, cytoplasmic targeting, translation and mRNA turnover. In addition to these post-transcriptional processes, RNA-protein interactions play a key role in transcription as illustrated by the life cycle of retroviruses. Unlike DNA, the structure of RNA is highly variable and conformationally flexible, thus creating a number of unique binding sites and the potential for complex regulation by RNA binding proteins. Although there is a wide range of topics included in this volume, general themes have been repeated, highlighting the overall integrative nature of RNA binding proteins. The chapters have been separated into three different sections: Translational Control; mRNA Metabolism; and Hormonal and Homeostatic Regulation. The chapters of this volume were written with the seasoned investigator and student in mind. Summaries of key concepts are reviewed within each chapter as well as guiding questions that can be used to stimulate class discussions. The Editors of this volume hope that this compendium educates, enthralls, and stimulates the readers to look to the future possibilities in this rapidly evolving field.
RNA-Protein Interactions : A Practical Approach by Christopher W.J. Smith Pdf
RNA-protein interactions play a fundamental role in gene expression and protein synthesis. Recent research into the role of RNA in cells has elucidated many more vital interactions with proteins. This book provides an up-to-date and comprehensive guide to a wide range of laboratory procedures to investigate the interactions between RNA and proteins. - ;RNA-protein interactions play a vital role in gene transcription and protein expression. Interactions such as the synthesis of mRNA by RNA polymerases, to the essential modification of RNA by the proteins of the spliceosome complex, and the highly catalytic action of the ribosome in protein synthesis, are established as being fundamental to the function of RNA. Recent research into, for example, the role of RNA as a catalyst, has elucidated many more interactions with proteins that are vital to cell function. RNA - Protein Interactions: A Practical Approach provides a clear and comprehensive guide to the experimental procedures used in studying RNA - protein interactions. The approaches covered range from those initially used to detect a novel RNA-protein interaction, various biochemical and genetic approaches to purifying and cloning RNA binding proteins, through to methods for an in depth analysis of the structural basis of the interaction. The volume includes a number of procedures that have not previously been covered in this type of manual. These include the production of site-specifically modified RNAs by enzymatic and chemical methods and in vivo screening for novel RNA - protein interactions in yeast and E. coli . This is the first volume to gather in one place this wide array of approaches for studying RNA - protein interactions. As is customary for the Practical Approach series, the writing is characterized by a clear explanatory style with many detailed protocols. This informative book will be a valuable aid to laboratory workers in biochemistry and molecular biology - graduate students, postdoctoral and senior scientists - whose research encompasses this field. -
RNA-Binding Proteins: Advances in Research and Application: 2011 Edition by Anonim Pdf
RNA-Binding Proteins: Advances in Research and Application: 2011 Edition is a ScholarlyBrief™ that delivers timely, authoritative, comprehensive, and specialized information about RNA-Binding Proteins in a concise format. The editors have built RNA-Binding Proteins: Advances in Research and Application: 2011 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about RNA-Binding Proteins in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of RNA-Binding Proteins: Advances in Research and Application: 2011 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.
RNA-protein Interactions by Kiyoshi Nagai,Iain W. Mattaj Pdf
The study of RNA-protein interactions is crucial to understanding the mechanisms and control of gene expression and protein synthesis. The realization that RNAs are often far more biologically active than was previously appreciated has stimulated a great deal of new research in this field. Uniquely, in this book, the world's leading researchers have collaborated to produce a comprehensive and current review of RNA-protein interactions for all scientists working in this area. Timely, comprehensive, and authoritative, this new Frontiers title will be invaluable for all researchers in molecular biology, biochemistry and structural biology.
RNA'Protein Interaction Protocols by Susan R. Haynes Pdf
The molecular characterization of RNA and its interactions with proteins is an important and exciting area of current research. Organisms utilize a variety of RNA–protein interactions to regulate the expression of their genes. This is particularly true for eukaryotes, since newly synthesized messenger RNA must be extensively modified and transported to the cytoplasm before it can be used for protein synthesis. The realization that posttranscriptional processes are critical components of gene regulation has sparked an explosion of interest in both stable ribonucleoprotein (RNP) complexes and transient RNA–protein interactions. RNA is conformationally flexible and can adopt complex structures that provide diverse surfaces for interactions with proteins. The fact that short RNA molecules (aptamers; see Chapter 16) can be selected to bind many different types of molecules is evidence of the structural variability of RNA. RNA molecules are rarely entirely single- or double-stranded, but usually contain multiple short duplexes interrupted by single-stranded loops and bulges; in some RNAs, such as tRNAs, the short duplexes stack on each other. Further variability is generated by the presence of non-Watson-Crick base pairs, modified nucleotides, and more complex structures, such as pseudoknots and triple-strand interactions.
Protein-Nucleic Acid Interactions by Phoebe A. Rice,Carl C. Correll Pdf
This book provides both in-depth background and up-to-date information in this area. The chapters are organized by general themes and principles, written by experts who illustrate topics with current findings. Topics covered include: - the role of ions and hydration in protein-nucleic acid interactions - transcription factors and combinatorial specificity - indirect readout of DNA sequence - single-stranded nucleic acid binding proteins - nucleic acid junctions and proteins, - RNA protein recognition - recognition of DNA damage. It will be a key reference for both advanced students and established scientists wishing to broaden their horizons.
RNA-Binding Proteins—Advances in Research and Application: 2012 Edition by Anonim Pdf
RNA-Binding Proteins—Advances in Research and Application: 2012 Edition is a ScholarlyBrief™ that delivers timely, authoritative, comprehensive, and specialized information about RNA-Binding Proteins in a concise format. The editors have built RNA-Binding Proteins—Advances in Research and Application: 2012 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about RNA-Binding Proteins in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of RNA-Binding Proteins—Advances in Research and Application: 2012 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.
RNA Binding Proteins in Development and Disease by Robert B. Denman Pdf
Introduction - The circle of life is a philosophical construct, for want of a better term that posits the interconnectedness of all living things. In the movie The Lion King which brought the term to the consciousness of the Western mind, Mufasa tries to explain the concept to his heir-apparent, Simba, by saying, we eat the antelope, but when we die, we become the grass that they eat . While the circle of life has an uncanny resonance with something deep within, especially for children, being Disney marketing magic it is never spelled out what actually connects us. I would submit to you that what this book demonstrates is that RNA binding proteins (RBPs) are some of the stuff connecting the circle of life. They are ageless, they are ubiquitous, and they are diverse. Found in all kingdoms, phyla and subphyla they impinge on all aspects of cellular metabolism from the transcription and splicing of messenger RNAs, to the formation of ribosomal RNA (see Aveilla et al. Chapter 11), from the translation of messenger RNAs (see Zhong et al. Chapter 1), to the timing of their translation and their degradation (see Pelletier et al. Chapter 2 and Vessey et al. Chapter 5). They are chaperones and repressors. More broadly they are regulators, which are in turn are regulated by a host of post-translational modifications (see Gopal et al. Chapter 3 and Kobarg Chapter 4). They play important roles in the differentiation of the nervous system (see Kawahara et al. Chapter 6), in muscle development (see Denman Chapter 7) and in germ line development (see Vessey et al. Chapter 5). Correspondingly, as befits a central role in metabolism, their loss or mutation can have profound organismal affects, from outright lethality to cancer (see Noubissi et al. Chapter 8), muscular disorders (see Meola et al. Chapter 9), eye disorders (see Schreuder et al. Chapter 10), bone marrow failure (see Aveilla et al. Chapter 11) epilepsy and mental retardation (Zhong et al. Chapter 1). Quite simply, they are RNA binding proteins . I would therefore invite the interested reader on an abbreviated tour of the circle of life that is contained in this slender tome. Of course, the very enterprise of making a book places constraints on what is included and what is not. As there are currently more than 30,000 papers on PubMed dealing with RNA binding proteins it is probable that many a would-be-reader will not find his or her favorite RBP reviewed here. Nevertheless, I would commend this book as a representative sampling of those articles, and therefore a worthwhile read for several reasons. First, the modular architecture of RBPs produces diversity via the mixing of a limited set of RNA binding motifs. Doubtless, one of the motifs the would-be reader is familiar with is discussed in these pages. Therefore, this book would offer a unique view of this motif operating in a different context. Second, the most common problem attended to within the field of RNA binding proteins is, What RNAs bind to a particular RBP and how do we know they are bona fide? By reading this book you will see how others have dealt with, or are dealing with this problem providing you the reader with the insight needed to attack this problem on another front. Finally, the dynamism of RBP-RNA interactions, coupled with their propensity to form larger aggregates make it likely that the RBP most familiar to a would-be reader associates with one or more of the RBPs reviewed here. If so, I would say, in order to know thyself, know thy neighbor . It is after all the circle of life.
RNA-Based Regulation in Human Health and Disease by Anonim Pdf
RNA-based Regulation in Human Health and Disease offers an in-depth exploration of RNA mediated genome regulation at different hierarchies. Beginning with multitude of canonical and non-canonical RNA populations, especially noncoding RNA in human physiology and evolution, further sections examine the various classes of RNAs (from small to large noncoding and extracellular RNAs), functional categories of RNA regulation (RNA-binding proteins, alternative splicing, RNA editing, antisense transcripts and RNA G-quadruplexes), dynamic aspects of RNA regulation modulating physiological homeostasis (aging), role of RNA beyond humans, tools and technologies for RNA research (wet lab and computational) and future prospects for RNA-based diagnostics and therapeutics. One of the core strengths of the book includes spectrum of disease-specific chapters from experts in the field highlighting RNA-based regulation in metabolic & neurodegenerative disorders, cancer, inflammatory disease, viral and bacterial infections. We hope the book helps researchers, students and clinicians appreciate the role of RNA-based regulation in genome regulation, aiding the development of useful biomarkers for prognosis, diagnosis, and novel RNA-based therapeutics. Comprehensive information of non-canonical RNA-based genome regulation modulating human health and disease Defines RNA classes with special emphasis on unexplored world of noncoding RNA at different hierarchies Disease specific role of RNA - causal, prognostic, diagnostic and therapeutic Features contributions from leading experts in the field
MicroRNAs (miRNAs) are RNA molecules, conserved by evolution, that regulate gene expressions and their recent discovery is revolutionising both basic biomedical research and drug discovery. Expression levels of MiRNAs have been found to vary between tissues and with developmental stages and hence evaluation of the global expression of miRNAs potentially provides opportunities to identify regulatory points for many different biological processes. This wide-ranging reference work, written by leading experts from both academia and industry, will be an invaluable resource for all those wishing to use miRNA techniques in their own research, from graduate students, post-docs and researchers in academia to those working in R&D in biotechnology and pharmaceutical companies who need to understand this emerging technology. From the discovery of miRNAs and their functions to their detection and role in disease biology, this volume uniquely integrates the basic science with industry application towards drug validation, diagnostic and therapeutic development. Forewords by: Sidney Altman, Yale University, Winner of the Nobel Prize in Chemistry, 1989 and Victor R. Ambros, Dartmouth Medical School, Co-discoverer of MicroRNAs
Biophysics of RNA-Protein Interactions by Chirlmin Joo,David Rueda Pdf
RNA molecules play key roles in all aspects of cellular life, but to do so efficiently, they must work in synergism with proteins. This book addresses how proteins and RNA interact to carry out biological functions such as protein synthesis, regulation of gene expression, genome defense, liquid phase separation and more. The topics addressed in this volume will appeal to researchers in biophysics, biochemistry and structural biology. The book is a useful resource for anybody interested in elucidating the molecular mechanisms and discrete properties of RNA-protein complexes. Included are reviews of key systems such as microRNA and CRISPR/Cas that exemplify how RNA and proteins work together to perform their biological function. Also covered are techniques ranging from single molecule fluorescence and force spectroscopy to crystallography, cryo-EM microscopy, and kinetic modeling.
The Role of Protein Post-Translational Modifications in Protein-RNA Interactions and RNP Assemblies by Roberto Giambruno,Dorothee Dormann,Nicolas Lux Fawzi,Ewa Anna Grzybowska Pdf
Dr. Nicolas Lux Fawzi is a member of the Scientific Advisory Board of Dewpoint Therapeutics LLC. All other Topic Editors declare no competing interests with regards to the Research Topic.
