Read Books Online and Download eBooks, EPub, PDF, Mobi, Kindle, Text Full Free.
Studying The Basis For Sequence Specific Rna Recognition By A New Class Of Rna Binding Proteins
Download Studying The Basis For Sequence Specific Rna Recognition By A New Class Of Rna Binding Proteins full books in PDF, epub, and Kindle. Read online Studying The Basis For Sequence Specific Rna Recognition By A New Class Of Rna Binding Proteins ebook anywhere anytime directly on your device. Fast Download speed and no annoying ads. We cannot guarantee that every ebooks is available!
Book Synopsis Studying the Basis for Sequence Specific RNA Recognition by a New Class of RNA Binding Proteins by : Sean Thomas Saxton
Download or read book Studying the Basis for Sequence Specific RNA Recognition by a New Class of RNA Binding Proteins written by Sean Thomas Saxton and published by . This book was released on 2008 with total page 68 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis RNA-Protein Interactions : A Practical Approach by : Christopher W.J. Smith
Download or read book RNA-Protein Interactions : A Practical Approach written by Christopher W.J. Smith and published by Oxford University Press, UK. This book was released on 1998-07-09 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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. -
Book Synopsis RNA Binding Proteins by : Zdravko Lorkovic
Download or read book RNA Binding Proteins written by Zdravko Lorkovic and published by CRC Press. This book was released on 2012-08-10 with total page 174 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Book Synopsis Systems Biology of RNA Binding Proteins by : Gene W. Yeo
Download or read book Systems Biology of RNA Binding Proteins written by Gene W. Yeo and published by Springer. This book was released on 2014-09-08 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis RNA'Protein Interaction Protocols by : Susan R. Haynes
Download or read book RNA'Protein Interaction Protocols written by Susan R. Haynes and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 485 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book RNA Processing written by Gene W. Yeo and published by Springer. This book was released on 2016-06-02 with total page 335 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ribonucleic acid (RNA) binding proteins currently number in the thousands and defects in their function are at the heart of diseases such as cancer and neurodegeneration. RNA binding proteins have become implicated in the intricate control of surprisingly diverse biological settings, such as circadian rhythm, stem cell self-renewal, oncogenesis and germ cell development. This book surveys a range of genome-wide and systems approaches to studying RNA binding proteins, the importance of RNA binding proteins in development, cancer and circadian rhythm.
Book Synopsis High-Resolution Profiling of Protein-RNA Interactions by : Mathias Munschauer
Download or read book High-Resolution Profiling of Protein-RNA Interactions written by Mathias Munschauer and published by Springer. This book was released on 2015-03-14 with total page 140 pages. Available in PDF, EPUB and Kindle. Book excerpt: The work reported in this book represents an excellent example of how creative experimentation and technology development, complemented by computational data analysis, can yield important insights that further our understanding of biological entities from a systems perspective. The book describes how the study of a single RNA-binding protein and its interaction sites led to the development of the novel ‘protein occupancy profiling’ technology that for the first time captured the mRNA sequence space contacted by the ensemble of expressed RNA binders. Application of protein occupancy profiling to eukaryotic cells revealed that extensive sequence stretches in 3’ UTRs can be contacted by RBPs and that evolutionary conservation as well as negative selection act on protein-RNA contact sites, suggesting functional importance. Comparative analysis of the RBP-bound sequence space has the potential to unravel putative cis-acting RNA elements without a priori knowledge of the bound regulators. Here, Dr. Munschauer provides a comprehensive introduction to the field of post-transcriptional gene regulation, examines state-of-the-art technologies, and combines the conclusions from several journal articles into a coherent and logical story from the frontiers of systems-biology inspired life science. This thesis, submitted to the Department of Biology, Chemistry and Pharmacy at Freie Universität Berlin, was selected as outstanding work by the Berlin Institute for Medical Systems Biology at the Max-Delbrueck Center for Molecular Medicine, Germany.
Book Synopsis Engineering RNA-binding Proteins by : Muhammad Fazril Mohamad Razif
Download or read book Engineering RNA-binding Proteins written by Muhammad Fazril Mohamad Razif and published by . This book was released on 2012 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-protein interactions have key roles in the regulation of gene expression and are vital for many cellular processes and complex developmental programs in eukaryotes. Proteins that have the ability to bind RNAs tend to do so in various modes that are often difficult to predict, limiting the ability to engineer these RNA-binding proteins for medical and biotechnological use. Hence, engineering proteins that can bind a specific RNA sequence has many potential applications, analogous to that of siRNAs and miRNAs, with even more potential benefits. The ability to fuse RNA-binding proteins to any desired effector domain, in turn enabling the manipulation of any aspect of the target RNA's metabolism makes engineering these proteins highly appealing. Here, the recognition of PUF repeats beyond adenine, guanine and uracil has been achieved through directed evolution, enabling them to specifically bind cytosine. With this code, PUF domains capable of selectively binding RNA targets of diverse sequence and structure can be designed. Unlike the PUFs, the basis for nucleotide RNA recognition by pentatricopeptide repeat (PPR) proteins, another RNA-binding protein, remains ambiguous. Here, computational methods have been used to create a stable, highly reduced PPR architecture for the study of RNA-binding specificity and the design of specific tools to manipulate RNA metabolism. We used these synthetic PPRs to examine the amino acid codes for nucleotide recognition by PPRs, which also revealed that PPRs have a modular recognition mechanism similar to that of PUFs. These findings provide a significant step towards predicting native binding sites of the vast number of PPR proteins found in nature. It also highlights the possibility of a PPR scaffold to be engineered for new functions and sequence specificities.
Book Synopsis Strategies for Specific Recognition of RNA Using Hydrogen Bonding by : Alan C. Cheng
Download or read book Strategies for Specific Recognition of RNA Using Hydrogen Bonding written by Alan C. Cheng and published by . This book was released on 2002 with total page 386 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis RNA Binding Proteins by : Kathryn Sandberg
Download or read book RNA Binding Proteins written by Kathryn Sandberg and published by Springer. This book was released on 2001-12-31 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Structural Studies of RNA Recognition by the Splicing Regulator Sex-lethal by : Scott Michael Crowder
Download or read book Structural Studies of RNA Recognition by the Splicing Regulator Sex-lethal written by Scott Michael Crowder and published by . This book was released on 1999 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Non-Protein Coding RNAs by : Nils Walter
Download or read book Non-Protein Coding RNAs written by Nils Walter and published by Springer Science & Business Media. This book was released on 2008-11-18 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, Andrew Fire and Craig Mello. This prize, which follows “RNA” Nobels for splicing and RNA catalysis, highlights just one class of recently discovered non-protein coding RNAs. Remarkably, non-coding RNAs are thought to outnumber protein coding genes in mammals by perhaps as much as four-fold. In fact, it appears that the complexity of an organism correlates with the fraction of its genome devoted to non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic tra- posons, higher-level organization of eukaryotic chromosomes, and gene expression are found to be largely directed by non-protein coding RNAs. Currently, bioinformatic, high-throughput sequencing, and biochemical approaches are identifying an increasing number of these RNAs. Unfortunately, our ability to characterize the molecular details of these RNAs is significantly lacking. The biophysical study of these RNAs is an emergent field that is unraveling the molecular underpinnings of how RNA fulfills its multitude of roles in sustaining cellular life. The resulting understanding of the physical and chemical processes at the molecular level is critical to our ability to harness RNA for use in biotechnology and human therapy, a prospect that has recently spawned a multi-billion dollar industry.
Book Synopsis RNA Recognition by SAM Domains by : Tzvi Aviv
Download or read book RNA Recognition by SAM Domains written by Tzvi Aviv and published by . This book was released on 2006 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt: Anteroposterior patterning in Drosophila melanogaster is dependent upon the sequence-specific RNA binding protein Smaug, which binds to and regulates the translation of nanos mRNA. In this thesis, I demonstrate that the s & barbelow;terile-a & barbelow;lpha m & barbelow;otif (SAM) domain of Smaug functions as an RNA recognition domain. This represents a new function for the SAM domain family, which is well characterized for mediating protein-protein interactions. Using homology modeling and site-directed mutagenesis, I have localized the RNA binding surface of the Smaug SAM domain. The conservation of these surface residues in a group of SAM domain containing proteins present from yeast to human suggested that these proteins share a common RNA binding function. I proved this point by demonstrating that the SAM domain of the Smaug homolog in Saccharomyces cerevisiae (Vts1) binds RNA hairpins with essentially the same affinity and sequence specificity as Smaug. In addition, I solved the crystal structures of the Vts1 SAM domain in its unliganded state and in complex with an RNA hairpin. The two structures are essentially identical, implying that no major structural rearrangements occur upon RNA binding. Specificity of hairpin binding arises from the association of a guanosine base of the hairpin loop with a shallow pocket on the SAM domain and from multiple contacts made to the unique backbone structure of the hairpin. Using a reporter gene, I demonstrated that Vts1 induces transcript degradation through a mechanism involving the cytoplasmic deadenylase CCR4. Subsequentially, I validated NNF1 as an endogenous target of Vts1 among 79 transcripts that co-purify with epitope tagged Vts1. Together my work uncovers the molecular details of sequence-specific RNA recognition by a conserved subfamily of SAM domains and define a class of post-transcriptional regulators that act in part through a common RNA binding mechanism.
Book Synopsis Development of the Yeast Three-hybrid System in Studying RNA-protein Interactions by : Beilin Zhang
Download or read book Development of the Yeast Three-hybrid System in Studying RNA-protein Interactions written by Beilin Zhang and published by . This book was released on 1999 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis RNA-protein Interactions by : Kiyoshi Nagai
Download or read book RNA-protein Interactions written by Kiyoshi Nagai and published by Oxford University Press, USA. This book was released on 1994 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Exploring the Code for Specific Binding by the RNA Recognition Motif Domain by : Markus Blatter
Download or read book Exploring the Code for Specific Binding by the RNA Recognition Motif Domain written by Markus Blatter and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein-binding and RNA-binding Properties of RNA-binding Proteins FBF and RBM39 by : Joann Wu
Download or read book Protein-binding and RNA-binding Properties of RNA-binding Proteins FBF and RBM39 written by Joann Wu and published by . This book was released on 2012 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: Post-transcriptional regulation of gene expression is critical in the development, physiology, and reproduction of multicellular organisms. Large dynamic multi-protein complexes formed through extensive protein*protein and protein*RNA interactions control mRNA processing, splicing, nuclear transport, localization, stability, and translation. However, despite the biological importance of these regulatory complexes, there is sparse molecular information describing the interactions involved in their assembly. In these studies, two categories of RNA-binding proteins that act as foundations for these complexes are examined: the Pu milio and F[barbelow]BF (PUF) proteins and R[barbelow]NA r[barbelow]ecognition m[barbelow]otif (RRM) domain-containing proteins. While there is a wealth of knowledge for PUF protein interactions with RNA, there is limited information describing the equally essential interactions between PUF proteins and their protein binding partners. Defined in these studies are the molecular bases for the developmentally essential interactions between Caenorhabditis elegans PUF protein f[barbelow]em-3 b[barbelow]inding f[barbelow]actor (FBF) and the two protein binding partners: g[barbelow]erml[barbelow]ine d[barbelow]evelopment defective-3[barbelow] (GLD-3) and c[barbelow]ytoplasmic p[barbelow]olyadenylation element b[barbelow]inding-1 (CPB-1). Short specific sequences in unstructured regions of the GLD-3 and CPB-1 proteins are critical for interaction with FBF, while a loop connecting PUF repeats R7 and R8 in FBF is essential for association with both GLD-3 and CPB-1. The PUF protein*binding partner complex FBF*GLD-3 is capable of forming a stable complex on RNA FBF regulatory elements in the 3' u[barbelow]nt[barbelow]ranslated r[barbelow]egions (UTR) of specific germline developmental mRNAs, and may control their expression through several proposed mechanisms. Although the RRM domains that characterize RRM-containing proteins adopt the same vary greatly in: amino acid sequence; DNA, RNA, and protein-binding abilities; and mode of interaction with these biological molecules. These studies potentially identify the first member of a unique class of RRMs that bind to RNA in a manner similar to RRMs that interact with proteins. These studies characterizing the protein- and RNA-binding properties of these RNA-binding proteins provide insight into the biologically essential molecular complexes involved in post-transcriptional gene regulation.
