Specificity And Manipulation Of Puf Rna Interactions

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Specificity and Manipulation of PUF-RNA Interactions

Author :
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (935 download)

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Book Synopsis Specificity and Manipulation of PUF-RNA Interactions by :

Download or read book Specificity and Manipulation of PUF-RNA Interactions written by and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Post-transcriptional control is essential for biological processes. RNA-binding factors are critical for eliciting mRNA-specific control. The Pumilio and Fem-3 binding factor (PUF) family of proteins is a single-stranded RNA-binding family conserved throughout eukaryotes. PUF proteins bind mRNAs with high specificity in order to control their translation, localization and stability. PUF regulation is dependent upon specific RNA recognition through protein-RNA contacts within the PUF RNA-binding domain (RBD). In these studies, we have elucidated mechanisms governing PUF-RNA interactions and determined binding properties of manipulated PUF scaffolds. We performed structure-based mutational analyses of PUF binding to RNA across several PUF scaffolds. This work led to the identification of critical PUF-RNA interactions and uncovered a binding pattern applicable across PUF proteins. We discovered a mechanism that determines alternate RNA base-flipping patterns observed in Saccharomyces cerevisiae Puf4p and Caenorhabditis elegans FBF-2 crystal structures, and we determined overlapping in vivo regulatory targets of S. cerevisiae Puf4p and Puf5p. Modularity of PUF RBDs allows for their engineered specificity. Three important amino acids, termed the tripartite recognition motif (TRM), impart RNA base specificity for each PUF repeat. We showed the generality of a TRM recognition code across PUF RBD scaffolds and PUF repeats, demonstrating the use of specific TRM combinations to target desired RNA sequences. We also found that additional PUF-RNA contacts do not substantially increase binding affinity or specificity by testing RNA-binding of extended PUF RBDs. Together, these data have furthered our knowledge of how PUF proteins recognize target mRNAs, uncovered details of in vivo PUF regulation, and further developed the PUF RBD as a scaffold for engineered RNA-targeting.

Target Selection by Natural and Redesigned PUF Proteins

Author : Douglas F. Porter
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (988 download)

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Book Synopsis Target Selection by Natural and Redesigned PUF Proteins by : Douglas F. Porter

Download or read book Target Selection by Natural and Redesigned PUF Proteins written by Douglas F. Porter and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-binding proteins define extensive, subtle networks of regulation in Eukaryotes. RNA-binding proteins control the amount of protein produced from mRNA, the location of translation and the protein isoform produced. Pumilio/PUF proteins are a family of RNA-binding protein families present in humans, as well as Eukaryotes in general, one of a limited number of such families. Pumilio/PUF proteins bind specific sequences in single-stranded RNA. The modular nature of the PUF-RNA interaction has led to the use of Pumilio/PUF proteins in reengineering RNA-binding proteins to recognize new RNA motifs. S. cerevisiae possesses a Pumilio/PUF protein representing a special subfamily we term the Puf2p family. The Puf2p family recognizes the unusual cognate motif of UAAU in RNA. We identify the RNA-binding map of S. cerevisiae Puf2p, determining that Puf2p binds roughly a fifth of the yeast genome and binds through clusters of UAAU motifs in 3'UTRs. In addition, we find that regions outside the PUF domain affect binding. Next, we reengineered Puf2p to recognize a UAAG site, and identified that the reengineered Puf2p binds its novel site in RNA with the same specificity as wild-type or greater. We evaluate the prediction of the RNA-binding map of a redesigned protein, and find that PUF-RNA interactions involve many factors beyond the binding site. We find that Puf2p is a repressor, and that reengineered Puf2p represses a novel RNA network. Our results suggest that direct RNA-binding by PUF proteins has small effects on many RNAs and large effects on a few RNAs. We find that, when redesigned to a new specificity, redesigned PUF proteins conserve targets, partly by finding new sites in the same mRNAs. Next, we identified the RNA binding specificity of the conserved stem cell regulator and PUF protein FBF in C. elegans. We find that FBF binds predominantly in mRNA 3'UTRs at its cognate motif, but that it also binds an alternative 7-mer site in the cell and that many FBF interaction sites are 'secondary' interactions near a stronger, primary interaction. Our results suggest a method for improving our understanding of RNA-protein interactions.

RNA-protein Interactions

Author : Kiyoshi Nagai
Publisher : Oxford University Press, USA
ISBN 13 :
Total Pages : 302 pages
Book Rating : 4.3/5 (91 download)

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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.

Nucleic Acids

Author : Victor A. Bloomfield
Publisher : Sterling Publishing Company
ISBN 13 : 9780935702491
Total Pages : 854 pages
Book Rating : 4.7/5 (24 download)

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Book Synopsis Nucleic Acids by : Victor A. Bloomfield

Download or read book Nucleic Acids written by Victor A. Bloomfield and published by Sterling Publishing Company. This book was released on 2000-04-17 with total page 854 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing a comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function, this text has been organized to meet the needs of those who have only a basic understanding of physical chemistry and molecular biology.

Protein-Nucleic Acid Interactions

Author : Phoebe A. Rice
Publisher : Royal Society of Chemistry
ISBN 13 : 0854042725
Total Pages : 417 pages
Book Rating : 4.8/5 (54 download)

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Book Synopsis Protein-Nucleic Acid Interactions by : Phoebe A. Rice

Download or read book Protein-Nucleic Acid Interactions written by Phoebe A. Rice and published by Royal Society of Chemistry. This book was released on 2008-05-22 with total page 417 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

How Tobacco Smoke Causes Disease

Author : United States. Public Health Service. Office of the Surgeon General
Publisher :
ISBN 13 :
Total Pages : 728 pages
Book Rating : 4.:/5 (318 download)

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Book Synopsis How Tobacco Smoke Causes Disease by : United States. Public Health Service. Office of the Surgeon General

Download or read book How Tobacco Smoke Causes Disease written by United States. Public Health Service. Office of the Surgeon General and published by . This book was released on 2010 with total page 728 pages. Available in PDF, EPUB and Kindle. Book excerpt: This report considers the biological and behavioral mechanisms that may underlie the pathogenicity of tobacco smoke. Many Surgeon General's reports have considered research findings on mechanisms in assessing the biological plausibility of associations observed in epidemiologic studies. Mechanisms of disease are important because they may provide plausibility, which is one of the guideline criteria for assessing evidence on causation. This report specifically reviews the evidence on the potential mechanisms by which smoking causes diseases and considers whether a mechanism is likely to be operative in the production of human disease by tobacco smoke. This evidence is relevant to understanding how smoking causes disease, to identifying those who may be particularly susceptible, and to assessing the potential risks of tobacco products.

Plant RNA Biology

Author : Dóra Szakonyi
Publisher : Frontiers Media SA
ISBN 13 : 2889630250
Total Pages : 167 pages
Book Rating : 4.8/5 (896 download)

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Book Synopsis Plant RNA Biology by : Dóra Szakonyi

Download or read book Plant RNA Biology written by Dóra Szakonyi and published by Frontiers Media SA. This book was released on 2019-11-18 with total page 167 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discoveries from the past decades revealed that RNA molecules are much more than inert intermediates between the coding DNA sequences and their functional products, proteins. Today, RNAs are recognized as active regulatory molecules influencing gene expression, chromatin organization and genome stability, thus impacting all aspects of plant life including development, growth, reproduction and stress tolerance. Innovations in methodologies, the expanding application of next-generation sequencing technologies, and the creation of public datasets and databases have exposed a new universe of RNA-based mechanisms and led to the discovery of new families of non-coding RNAs, uncovered the large extent of alternative splicing events, and highlighted the potential roles of RNA modifications and RNA secondary structures. Furthermore, considerable advances have been made in identifying RNA-binding and processing factors involved in the synthesis and maturation of different forms of RNA molecules as well as in RNA processing, biochemical modifications or degradation. This Research Topic showcases the broad biological significance of RNAs in plant systems and contains eight original research articles, one review and four mini-reviews, covering various RNA-based mechanisms in higher plants. Emerging new technologies and novel multidisciplinary approaches are empowering the scientific community and will expectedly bring novel insights into our understanding of the mechanisms through which RNA is regulated and regulates biological processes in plant cells.

Systems Biology of RNA Binding Proteins

Author : Gene W. Yeo
Publisher : Springer
ISBN 13 : 1493912216
Total Pages : 474 pages
Book Rating : 4.4/5 (939 download)

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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.

Epigenetic Mechanisms of Neurogenesis in the Developing Neocortex

Author : Magdalena Götz
Publisher : Frontiers Media SA
ISBN 13 : 288971778X
Total Pages : 139 pages
Book Rating : 4.8/5 (897 download)

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Book Synopsis Epigenetic Mechanisms of Neurogenesis in the Developing Neocortex by : Magdalena Götz

Download or read book Epigenetic Mechanisms of Neurogenesis in the Developing Neocortex written by Magdalena Götz and published by Frontiers Media SA. This book was released on 2021-11-30 with total page 139 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Post-Transcriptional Gene Regulation

Author : Jeffrey Wilusz
Publisher : Springer Science & Business Media
ISBN 13 : 1588297837
Total Pages : 330 pages
Book Rating : 4.5/5 (882 download)

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Book Synopsis Post-Transcriptional Gene Regulation by : Jeffrey Wilusz

Download or read book Post-Transcriptional Gene Regulation written by Jeffrey Wilusz and published by Springer Science & Business Media. This book was released on 2008 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: Step-by-step instructions that ensure successful results.

Quadruplex Nucleic Acids

Author : Stephen Neidle
Publisher : Royal Society of Chemistry
ISBN 13 : 1847555292
Total Pages : 317 pages
Book Rating : 4.8/5 (475 download)

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Book Synopsis Quadruplex Nucleic Acids by : Stephen Neidle

Download or read book Quadruplex Nucleic Acids written by Stephen Neidle and published by Royal Society of Chemistry. This book was released on 2007-10-31 with total page 317 pages. Available in PDF, EPUB and Kindle. Book excerpt: Guanine rich DNA has been known for decades to form unusual structures, although their biological relevance was little understood. Recent advances have demonstrated that quadruplex structures can play a role in gene expression and provide opportunities for a new class of anticancer therapeutics. A number of quadruplex-specific proteins have also been discovered. Quadruplex Nucleic Acids discusses all aspects of the fundamentals of quadruplex structures, including their structure in solution and the crystalline state, the kinetics of quadruplex folding, and the role of cations in structure and stability. The biology of quadruplexes and G-rich genomic regions and G-quartets in supramolecular chemistry and nanoscience are also considered. Surveying the current state of knowledge, and with contributions from leading experts, this is the first comprehensive review of this rapidly growing area. Quadruplex Nucleic Acids is ideal for researchers interested in areas related to chemistry, chemical biology, medicinal chemistry, molecular pharmacology, and structural and molecular biology.

Applied RNA Bioscience

Author : Seiji Masuda
Publisher : Springer
ISBN 13 : 981108372X
Total Pages : 286 pages
Book Rating : 4.8/5 (11 download)

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Book Synopsis Applied RNA Bioscience by : Seiji Masuda

Download or read book Applied RNA Bioscience written by Seiji Masuda and published by Springer. This book was released on 2018-04-10 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt: The focus of this book is to introduce up-to-date information on applications and practical use of RNA for agriculture, biotechnology and medicine. It provides unique ideas, tools, and methods in detail from a variety of scientific and technical disciplines. RNA science has progressed enormously in recent decades, and vast amounts of information on RNA functions and their regulatory mechanisms are becoming available. Such a progress opened the door to an age of practical application of RNA in many fields including agriculture, plant science, medical science, brewing and fermentation technology, and material production. This book inspires its readership and contributes to not only expansion in application of RNA but also to basic research.

Introduction to Epigenetics

Author : Renato Paro
Publisher : Springer Nature
ISBN 13 : 3030686701
Total Pages : 215 pages
Book Rating : 4.0/5 (36 download)

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Book Synopsis Introduction to Epigenetics by : Renato Paro

Download or read book Introduction to Epigenetics written by Renato Paro and published by Springer Nature. This book was released on 2021-03-23 with total page 215 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access textbook leads the reader from basic concepts of chromatin structure and function and RNA mechanisms to the understanding of epigenetics, imprinting, regeneration and reprogramming. The textbook treats epigenetic phenomena in animals, as well as plants. Written by four internationally known experts and senior lecturers in this field, it provides a valuable tool for Master- and PhD- students who need to comprehend the principles of epigenetics, or wish to gain a deeper knowledge in this field. After reading this book, the student will: Have an understanding of the basic toolbox of epigenetic regulation Know how genetic and epigenetic information layers are interconnected Be able to explain complex epigenetic phenomena by understanding the structures and principles of the underlying molecular mechanisms Understand how misregulated epigenetic mechanisms can lead to disease

Clinical Case Studies for the Family Nurse Practitioner

Author : Leslie Neal-Boylan
Publisher : John Wiley & Sons
ISBN 13 : 1118277856
Total Pages : 432 pages
Book Rating : 4.1/5 (182 download)

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Book Synopsis Clinical Case Studies for the Family Nurse Practitioner by : Leslie Neal-Boylan

Download or read book Clinical Case Studies for the Family Nurse Practitioner written by Leslie Neal-Boylan and published by John Wiley & Sons. This book was released on 2011-11-28 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: Clinical Case Studies for the Family Nurse Practitioner is a key resource for advanced practice nurses and graduate students seeking to test their skills in assessing, diagnosing, and managing cases in family and primary care. Composed of more than 70 cases ranging from common to unique, the book compiles years of experience from experts in the field. It is organized chronologically, presenting cases from neonatal to geriatric care in a standard approach built on the SOAP format. This includes differential diagnosis and a series of critical thinking questions ideal for self-assessment or classroom use.

Germline Stem Cells

Author : Steven X. Hou
Publisher : Humana Press
ISBN 13 : 9781617378805
Total Pages : 0 pages
Book Rating : 4.3/5 (788 download)

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Book Synopsis Germline Stem Cells by : Steven X. Hou

Download or read book Germline Stem Cells written by Steven X. Hou and published by Humana Press. This book was released on 2014-10-15 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this comprehensive and cutting-edge book, leading experts explore the parameters that define germline stem cells and the mechanisms that regulate the cell behavior in order to better isolate, characterize and maintain them. The volume begins by providing protocols for germline stem cell identification and regulation in model organisms, and concludes with detailed chapters covering current techniques involving in vitro culture and the applications of the cells.

Temporomandibular Disorders

Author : National Academies of Sciences, Engineering, and Medicine
Publisher : National Academies Press
ISBN 13 : 0309670489
Total Pages : 427 pages
Book Rating : 4.3/5 (96 download)

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Book Synopsis Temporomandibular Disorders by : National Academies of Sciences, Engineering, and Medicine

Download or read book Temporomandibular Disorders written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2020-07-01 with total page 427 pages. Available in PDF, EPUB and Kindle. Book excerpt: Temporomandibular disorders (TMDs), are a set of more than 30 health disorders associated with both the temporomandibular joints and the muscles and tissues of the jaw. TMDs have a range of causes and often co-occur with a number of overlapping medical conditions, including headaches, fibromyalgia, back pain and irritable bowel syndrome. TMDs can be transient or long-lasting and may be associated with problems that range from an occasional click of the jaw to severe chronic pain involving the entire orofacial region. Everyday activities, including eating and talking, are often difficult for people with TMDs, and many of them suffer with severe chronic pain due to this condition. Common social activities that most people take for granted, such as smiling, laughing, and kissing, can become unbearable. This dysfunction and pain, and its associated suffering, take a terrible toll on affected individuals, their families, and their friends. Individuals with TMDs often feel stigmatized and invalidated in their experiences by their family, friends, and, often, the health care community. Misjudgments and a failure to understand the nature and depths of TMDs can have severe consequences - more pain and more suffering - for individuals, their families and our society. Temporomandibular Disorders: Priorities for Research and Care calls on a number of stakeholders - across medicine, dentistry, and other fields - to improve the health and well-being of individuals with a TMD. This report addresses the current state of knowledge regarding TMD research, education and training, safety and efficacy of clinical treatments of TMDs, and burden and costs associated with TMDs. The recommendations of Temporomandibular Disorders focus on the actions that many organizations and agencies should take to improve TMD research and care and improve the overall health and well-being of individuals with a TMD.

RNA Metabolism in Neurodegenerative Diseases

Author : Rita Sattler
Publisher : Springer
ISBN 13 : 331989689X
Total Pages : 310 pages
Book Rating : 4.3/5 (198 download)

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Book Synopsis RNA Metabolism in Neurodegenerative Diseases by : Rita Sattler

Download or read book RNA Metabolism in Neurodegenerative Diseases written by Rita Sattler and published by Springer. This book was released on 2018-06-18 with total page 310 pages. Available in PDF, EPUB and Kindle. Book excerpt: It has become evident over the last years that abnormalities in RNA processing play a fundamental part in the pathogenesis of neurodegenerative diseases. Cellular viability depends on proper regulation of RNA metabolism and subsequent protein synthesis, which requires the interplay of many processes including transcription, pre--‐mRNA splicing, mRNA editing as well as mRNA stability, transport and translation. Dysfunction in any of these processes, often caused by mutations in the coding and non--‐ coding RNAs, can be very destructive to the cellular environment and consequently impair neural viability. The result of this RNA toxicity can lead to a toxic gain of function or a loss of function, depending on the nature of the mutation. For example, in repeat expansion disorders, such as the newly discovered hexanucleotide repeat expansion in theC9orf72 gene found in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), a toxic gain of function leads to the formation of RNA foci and the sequestration of RNA binding proteins (RBPs). This in return leads to a loss of function of those RBPs, which is hypothesized to play a significant part in the disease progression of ALS and FTD. Other toxicities arising from repeat expansions are the formation of RNA foci, bi--‐directional transcription and production of repeat associated non--‐ATG (RAN) translation products. This book will touch upon most of these disease mechanisms triggered by aberrant RNA metabolism and will therefore provide a broad perspective of the role of RNA processing and its dysfunction in a variety of neurodegenerative disorders, including ALS, FTD, Alzheimer’s disease, Huntington’s disease, spinal muscular atrophy, myotonic dystrophy and ataxias. The proposed authors are leading scientists in the field and are expected to not only discuss their own work, but to be inclusive of historic as well as late breaking discoveries. The compiled chapters will therefore provide a unique collection of novel studies and hypotheses aimed to describe the consequences of altered RNA processing events and its newest molecular players and pathways.