The Roles of RNA Secondary Structure and RNA-protein Interactions in the Expression and Function of Alu RNA PDF Download

Author: Ruth Elizabeth Ballard
Publisher:
ISBN:
Category :
Languages : en
Pages : 268

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Author: Christopher W.J. Smith
Publisher: Oxford University Press, UK
ISBN: 0191591629
Category :
Languages : en
Pages : 370

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Book Description
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. -

Author: Gisela Storz
Publisher: John Wiley & Sons
ISBN: 1683670248
Category : Medical
Languages : en
Pages : 400

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Book Description
Revealing the many roles of RNA in regulating gene expression For decades after the discoveries of messenger RNA, transfer RNA, and ribosomal RNA, it was largely assumed that the role of RNA in the cell was limited to shuttling the genomic message, chaperoning amino acids, and toiling in the ribosomes. Eventually, hints that RNA molecules might have regulatory roles began to appear. With the advent of genomics and bioinformatics, it became evident that numerous other RNA forms exist and have specific functions, including small RNAs (sRNA), RNA thermometers, and riboswitches to regulate core metabolic pathways, bacterial pathogenesis, iron homeostasis, quorum sensing, and biofilm formation. All of these functions, and more, are presented in Regulating with RNA in Bacteria and Archaea, written by RNA biologists from around the globe. Divided into eight sections-RNases and Helicases, Cis-Acting RNAs, Cis Encoded Base Pairing RNAs, Trans-Encoded Base Pairing RNAs, Protein Titration and Scaffolding, General Considerations, Emerging Topics, and Resources-this book serves as an excellent resource for established RNA biologists and for the many scientists who are studying regulated cellular systems. It is no longer a fair assumption that gene expression regulation is the provenance of proteins only or that control is exerted primarily at the level of transcription. This book makes clear that regulatory RNAs are key partners along with proteins in controlling the complex interactions and pathways found within prokaryotes.

Author: Elan A. Shatoff
Publisher:
ISBN:
Category : Molecular structure
Languages : en
Pages : 0

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Book Description
RNA is ubiquitous in the cellular environment, and it can function in innumerable ways with a variety of interaction partners. A RNA molecule's structure, in particular the set of base pairing interactions between the nucleotides of the molecule known as secondary structure, can help determine its function. Since most proteins can only bind to either single stranded or double stranded RNA, RNA secondary structure can also help determine where and how RNA-protein binding interactions occur. In this work I investigate computational models for RNA-protein interactions in a variety of different contexts. In Chapter 2 I probe the effect of single nucleotide variations on RNA-protein binding as mediated by RNA secondary structure. Single nucleotide variations are single nucleotide changes in an organism's genome that can often cause disease, and may do so through a number of different mechanisms. In this work we propose that sequence changes can affect accessibility to protein binding sites through changes in secondary structure, even when these sequence changes occur tens of nucleotides outside of protein binding sites. We find that single nucleotide variations can have a many fold effect on the binding affinity of proteins for RNA, and characterize the genome-wide effect of single nucleotide variations on HuR binding. HuR is a single-stranded RNA binding protein that binds to AU-rich sequences, and has links to diseases such as cancer. We also find an asymmetry in this effect for HuR, indicating that this effect may be under selection. Following the previous work, which utilizes a model incorporating single stranded RNA binding proteins into RNA secondary structure folding, I introduce a model for incorporating double stranded RNA binding proteins (dsRBPs) into RNA secondary structure partition function calculations in Chapter 3. The dsRBPs are an important but understudied class of proteins that have uses in a wide range of processes. We implement our model in the ViennaRNA package, and validate it by calculating a number of experimental observables for transactivation response element RNA-binding protein. We find that RNA secondary structure can have a many fold effect on the effective binding affinity of dsRBPs, and show that calculated affinities for pre-miRNA-like constructs correlate with experimentally measured processing rates. Our model provides a novel method for interrogating the interplay between dsRBPs and RNA secondary structure. In Chapter 4 I study RNA-protein interactions in a different context, and investigate the role of Shine-Dalgarno (SD) sequences in translation in the Bacteroidetes. The Bacteroidetes are a phylum of bacteria known to rarely use SD sequences, but after performing a survey of SD usage in the phylum we find that certain ribosomal protein genes utilize them, particularly rpsU. A cryo-electron microscopy structure of the ribosome from Flavobacterium johnsoniae, a member of the Bacteroidetes, also shows that S21, which is encoded by the ribosomal open reading frame rpsU, sequesters the anti-Shine-Dalgarno (ASD) sequence. In our survey of SD sequences we also find covariation between the SD sequence of rpsU and the ASD sequence. These observations suggest an autoregulatory model for S21 in the Bacteroidetes.

Author: Kiyoshi Nagai
Publisher: Oxford University Press, USA
ISBN:
Category : Medical
Languages : en
Pages : 302

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Book Description
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.

Author: Chirlmin Joo
Publisher: Springer
ISBN: 9781493997244
Category : Science
Languages : en
Pages : 249

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Book Description
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.

Author: Susan R. Haynes
Publisher: Springer Science & Business Media
ISBN: 1592596762
Category : Science
Languages : en
Pages : 485

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Book Description
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.

Author: Kathryn Sandberg
Publisher: Springer
ISBN: 9781441949356
Category : Medical
Languages : en
Pages : 0

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Book Description
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.

Author: Astrid Sigel
Publisher: Walter de Gruyter GmbH & Co KG
ISBN: 3110436647
Category : Science
Languages : en
Pages : 424

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The discovery of ribozymes nearly 30 years ago triggered a huge interest in the chemistry and biology of RNAs. Much of the recently made progress focusing on metal ions is addressed in MILS 9. This book, written by 28 internationally recognized experts from 8 nations, provides a most up-to-date view and is thus of special relevance for colleagues teaching courses in biological inorganic chemistry and for researchers dealing, e.g., with nucleic acids, gene expression, and enzymology, but also for those in analytical and bioinorganic chemistry or biophysics. Structural and Catalytic Roles of Metal Ions in RNA describes in an authoritative and timely manner in 12 stimulating chapters, supported by nearly 1600 references, 13 tables, and 75 illustrations, mostly in color, metal ion-binding motifs, methods to detect and characterize metal ion-binding sites, and the role of metal ions in folding and catalysis. It deals with diffuse metal ion binding, RNA quadruplexes, the regulation of riboswitches, metal ions and ribozymes, including artificial ribozymes. The spliceosome, the ribosome, ribozymes involving redox cofactors as well as the binding of kinetically inert metal ions to RNA are also covered.

Author: Bibekanand Mallick
Publisher: Springer Science & Business Media
ISBN: 3642225160
Category : Science
Languages : en
Pages : 549

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Book Description
Recent progress in high-throughput technologies and genome wide transcriptome studies have lead to a significant scientific milestone of discovering non-coding RNAs (ncRNAs) which spans through a major portion of the genome. These RNAs most often act as riboregulators, and actively participate in the regulation of important cellular functions at the transcriptional and/or post-transcriptional levels rather than simply being an intermediated messenger between DNA and proteins. As the appreciation for the importance of ncRNAs continues to emerge, it is also increasingly clear that these play critical roles in gene regulatory processes during development and differentiation. Further, regulatory RNAs are useful biomarkers for diagnosis of diseases. Hence these RNA regulators are essential to the development of therapeutics. This book on “Regulatory RNAs” offers a comprehensive view on our current understanding of these regulatory RNAs viz. siRNA, miRNA, piRNA, snoRNA, long non-coding RNA, small RNA etc. It addresses both the biogenesis and mechanism of action of regulatory RNAs with a primary focus on their annotation, experimental methodologies (microarray, next-gen sequencing etc.) for their discovery, computational tools for their prediction, and above all, applications of these revolutionary regulatory molecules in understanding biological systems and diseases, including therapeutics. This comprehensive volume is intended for readers with research or teaching interests in ncRNA biology and will provide a major information resource on current research in the fast-moving fields of RNA and gene expression regulation. Cutting-edge and concise, “Regulatory RNAs: Basics, Methods and Applications” promises to support vital research in the field of regulatory RNAs, ever-continuing to grow rapidly and gain increasing importance in basic and translational biology.