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Evolution Of Rna Puf Protein Networks
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Book Synopsis Evolution of RNA-PUF Protein Networks by :
Download or read book Evolution of RNA-PUF Protein Networks written by and published by . This book was released on 2015 with total page 200 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins bind and control mRNAs, directing their localization, translation, and stability. Members of the PUF family of RNA-binding proteins control multiple mRNAs in a single cell, and play key roles in development, stem cell maintenance and memory formation. Here we demonstrate the conservation of PUF regulatory networks by bioinformatic analysis. We identified the mRNA targets of two Saccharomyces cerevisiae PUF proteins, Puf3p and Puf5p, and two Neurospora crassa PUF proteins, PUF3 and PUF5, by UV-crosslinking-affinity purification and high-throughput sequencing (HITS-CLIP). Taken together these data allowed us to elucidate a rewiring of a nulcear-endcoded circuit of mitochondrial related mRNAs. S. cerevisiae Puf5p associates with ~1,000 RNAs, suggesting that it is a broad spectrum regulator. The binding sites recognized by both Puf5 proteins are diverse, with variable spacer lengths between two specific sequences. S. cerevisiae Puf3p binds a group of RNAs significantly enriched for nuclear encoded RNAs that code for mitochondrial proteins. Many of these orthologous RNAs are bound by N. crassa PUF5. This constitutes a switch, from Puf3p to Puf5, regulation, when comparing S. cerevisiae and N. crassa PUF regulatory networks. Crystal structures of S. cerevisiae Puf5p-RNA complexes reveal that the protein scaffold presents an exceptionally flat and extended interaction surface relative to other PUF proteins. A single PUF protein repeat is sufficient to induce broadening of specificity. Changes in protein architecture, such as alterations in curvature, may have led to evolution of mRNA regulatory networks which we observe.
Book Synopsis Evolution and Coordination of Gene Expression Through RNA-protein Interactions by : Gregory John Hogan
Download or read book Evolution and Coordination of Gene Expression Through RNA-protein Interactions written by Gregory John Hogan and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Reprogramming of a gene's expression pattern by acquisition or loss of sequences recognized by specific regulatory RNA binding proteins has the potential to be a major mechanism in the evolution of biological regulatory programs. Systematic study of orthologous Puf3 proteins across eukaryotes revealed that the RNA binding specificity is highly conserved, yet the identity and functional commonalities of their RNA targets have extensively diverged. We identified six eukaryotic lineages within which RNA targets of Puf3 orthologs have been conserved over 250-500 million years of evolution. Focusing on Puf proteins and their targets across 80 fungi, we were able to construct a parsimonious model for their evolutionary history. This history entails changes in the number of Puf genes, modifications in the RNA binding specificity of the Puf proteins, and extensive and coordinated changes in the Puf targets and, in one remarkable case, switching of hundreds of mRNA targets from Puf3 to Puf4. Binding of Puf3 to more than 200 RNAs whose protein products are predominantly involved in the production and organization of mitochondrial complexes pre-dates the origin of budding yeasts and filamentous fungi and was maintained throughout the evolution of budding yeast. In filamentous fungi, more than 150 of the ancestral Puf3 targets were gained en masse by Puf4, with one lineage maintaining both Puf3 and Puf4 as regulators and another lineage losing Puf3 as a regulator of these RNAs. Gene expression profiling and sequence analysis suggest that the regulatory consequences of Puf4 in filamentous fungi are distinct from that of Puf3 for this set of RNAs in budding yeast. In filamentous fungi, Puf4 broadened its target set to include mitochondrial genes involved in the tricarboxylic acid (TCA) cycle among other functions, and Puf3 targets in these fungi diversified, notably gaining interactions with the mRNAs encoding the electron transport chain (ETC) complex I. These and many other changes involving just this handful of Puf proteins in fungi strongly support their role in coordinating gene expression through "RNA operons" and indicate an extensive involvement of RNA binding proteins and their RNA targets in the adaptation and reprogramming of gene expression. The timing and nature of these changes are distinct from those observed at the level of transcriptional control, suggesting that RNA-protein interactions provide an additional and rich infrastructure from which gene expression can be reconfigured. Beyond the static pictures of extant gene expression programs of currently employed model organisms, identifying the changes in gene expression programs throughout evolution will provide a unique window into the make-up, logic, and malleability of gene expression, ultimately contributing to our understanding of and ability to engineer this program.
Book Synopsis RNA Regulatory Networks Diversified Through Curvature of the PUF Protein Scaffold by :
Download or read book RNA Regulatory Networks Diversified Through Curvature of the PUF Protein Scaffold written by and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins bind and control mRNAs, directing their localization, translation and stability. Members of the PUF family of RNA-binding proteins control multiple mRNAs in a single cell, and play key roles in development, stem cell maintenance and memory formation. Here we identified the mRNA targets of a S. cerevisiae PUF protein, Puf5p, by ultraviolet-crosslinking-affinity purification and high-throughput sequencing (HITS-CLIP). The binding sites recognized by Puf5p are diverse, with variable spacer lengths between two specific sequences. Each length of site correlates with a distinct biological function. Crystal structures of Puf5p-RNA complexes reveal that the protein scaffold presents an exceptionally flat and extended interaction surface relative to other PUF proteins. In complexes with RNAs of different lengths, the protein is unchanged. A single PUF protein repeat is sufficient to induce broadening of specificity. Changes in protein architecture, such as alterations in curvature, may lead to evolution of mRNA regulatory networks.
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 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.
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 Evolution of Gene Regulatory Networks in Plant Development by : Federico Valverde
Download or read book Evolution of Gene Regulatory Networks in Plant Development written by Federico Valverde and published by Frontiers Media SA. This book was released on 2018-02-15 with total page 252 pages. Available in PDF, EPUB and Kindle. Book excerpt: During their life cycle plants undergo a wide variety of morphological and developmental changes. Impinging these developmental processes there is a layer of gene, protein and metabolic networks that are responsible for the initiation of the correct developmental transitions at the right time of the year to ensure plant life success. New omic technologies are allowing the acquisition of massive amount of data to develop holistic and integrative analysis to understand complex processes. Among them, Microarray, Next-generation Sequencing (NGS) and Proteomics are providing enormous amount of data from different plant species and developmental stages, thus allowing the analysis of gene networks globally. Besides, the comparison of molecular networks from different species is providing information on their evolutionary history, shedding light on the origin of many key genes/proteins. Moreover, developmental processes are not only genetically programed but are also affected by internal and external signals. Metabolism, light, hormone action, temperature, biotic and abiotic stresses, etc. have a deep effect on developmental programs. The interface and interplay between these internal and external circuits with developmental programs can be unraveled through the integration of systematic experimentation with the computational analysis of the generated omics data (Molecular Systems Biology). This Research Topic intends to deepen in the different plant developmental pathways and how the corresponding gene networks evolved from a Molecular Systems Biology perspective. Global approaches for photoperiod, circadian clock and hormone regulated processes; pattern formation, phase-transitions, organ development, etc. will provide new insights on how plant complexity was built during evolution. Understanding the interface and interplay between different regulatory networks will also provide fundamental information on plant biology and focus on those traits that may be important for next-generation agriculture.
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.
Book Synopsis Cancer RNome: Nature & Evolution by : Mansi Arora
Download or read book Cancer RNome: Nature & Evolution written by Mansi Arora and published by Springer. This book was released on 2018-11-02 with total page 313 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the last decade, researchers working in the field of cancer biology have shifted their focus from genetic defects to epigenetic dysregulation, especially that of non-coding RNAs (ncRNAs). This book encompasses a comprehensive review of the transcriptional landscape of the cell and its involvement in the cancer pathophysiology. The first two chapters elucidate the basics of biosynthesis, mechanism of action and modulation of the epigenetic regulation of gene expression by coding as well as non-coding RNAs. The third chapter discusses the aberrant expression of the cellular RNome in the cancer cells and highlights its role in the orchestration of processes involved in evolution as well as the sustenance of cancer cells. The fourth chapter describes the recent advances in the field of translating the transcriptome into diagnostic/prognostic biomarkers and as targets for novel anti-cancer therapies. The final chapter then reviews the emerging experimental approaches to screen, identify and explore the functions of ncRNAs. Providing valuable insights into the field of RNome in the context of cancer, this book is helpful to students, researchers and clinicians..
Download or read book RNA Tagging written by Manfred Heinlein and published by Humana. This book was released on 2021-08-08 with total page 490 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a compendium of state-of-the-art methods for the labeling, detection, and purification of RNA and RNA-protein complexes and thereby constitutes an important toolbox for researchers interested in understanding the complex roles of RNA molecules in development, signaling, and disease. Beginning with a section on in situ detection of RNA molecules using FISH techniques, the volume continues with parts exploring in vivo imaging of RNA transport and localization, imaging and analysis of RNA uptake and transport between cells, identification and analysis of RNA-binding proteins, guide RNAs in genome editing, as well as other specific analytical techniques. 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 Tagging: Methods and Protocols serves as a vital reference for researchers looking to further the increasingly important research in RNA biology.
Book Synopsis Innovative Medicine by : Kazuwa Nakao
Download or read book Innovative Medicine written by Kazuwa Nakao and published by Springer. This book was released on 2015-10-13 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is devoted to innovative medicine, comprising the proceedings of the Uehara Memorial Foundation Symposium 2014. It remains extremely rare for the findings of basic research to be developed into clinical applications, and it takes a long time for the process to be achieved. The task of advancing the development of basic research into clinical reality lies with translational science, yet the field seems to struggle to find a way to move forward. To create innovative medical technology, many steps need to be taken: development and analysis of optimal animal models of human diseases, elucidation of genomic and epidemiological data, and establishment of “proof of concept”. There is also considerable demand for progress in drug research, new surgical procedures, and new clinical devices and equipment. While the original research target may be rare diseases, it is also important to apply those findings more broadly to common diseases. The book covers a wide range of topics and is organized into three complementary parts. The first part is basic research for innovative medicine, the second is translational research for innovative medicine, and the third is new technology for innovative medicine. This book helps to understand innovative medicine and to make progress in its realization.
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.
Book Synopsis Hierarchy in Natural and Social Sciences by : Denise Pumain
Download or read book Hierarchy in Natural and Social Sciences written by Denise Pumain and published by Springer Science & Business Media. This book was released on 2006-02-09 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: Hierarchy is a form of organisation of complex systems that rely on or produce a strong differentiation in capacity (power and size) between the parts of the system. It is frequently observed within the natural living world as well as in social institutions. According to the authors, hierarchy results from random processes, follows an intentional design, or is the result of the organisation which ensures an optimal circulation of energy for information. This book reviews ancient and modern representations and explanations of hierarchies, and compares their relevance in a variety of fields, such as language, societies, cities, and living species. It throws light on concepts and models such as scaling laws, fractals and self-organisation that are fundamental in the dynamics and morphology of complex systems. At a time when networks are celebrated for their efficiency, flexibility and better social acceptance, much can be learned about the persistent universality and adaptability of hierarchies, and from the analogies and differences between biological and social organisation and processes. This book addresses a wide audience of biologists and social scientists, as well as managers and executives in a variety of institutions.
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.
Download or read book The Genetic Gods written by John C. Avise and published by Harvard University Press. This book was released on 2009-06-30 with total page 289 pages. Available in PDF, EPUB and Kindle. Book excerpt: They mastermind our lives, shaping our features, our health, and our behavior, even in the sacrosanct realms of love and sex, religion, aging, and death. Yet we are the ones who house, perpetuate, and give the promise of immortality to these biological agents, our genetic gods. The link between genes and gods is hardly arbitrary, as the distinguished evolutionary geneticist John Avise reveals in this compelling book. In clear, straightforward terms, Avise reviews recent discoveries in molecular biology, evolutionary genetics, and human genetic engineering, and discusses the relevance of these findings to issues of ultimate concern traditionally reserved for mythology, theology, and religious faith. The book explains how the genetic gods figure in our development--not just our metabolism and physiology, but even our emotional disposition, personality, ethical leanings, and, indeed, religiosity. Yet genes are physical rather than metaphysical entities. Having arisen via an amoral evolutionary process--natural selection--genes have no consciousness, no sentient code of conduct, no reflective concern about the consequences of their actions. It is Avise's contention that current genetic knowledge can inform our attempts to answer typically religious questions--about origins, fate, and meaning. The Genetic Gods challenges us to make the necessary connection between what we know, what we believe, and what we embody. Table of Contents: Preface Prologue 1. The Doctrines of Biological Science 2. Geneses 3. Genetic Maladies 4. Genetic Beneficence 5. Strategies of the Genes 6. Genetic Sovereignty 7. New Lords of Our Genes? 8. Meaning Epilogue Notes Glossary Index Reviews of this book: Our genes, [Avise] says, are responsible not only for how we got here and exist day to day, but also for the core of our being--our personalities and morals. It is our genetic make-up that allows for and formulates our religious belief systems, he argues. Avise does not eschew spirituality but seeks a more informed, less confrontational approach between science and the pulpit. --Science News Reviews of this book: For the general scientific reader, the book is an excellent distillation of a broad and increasingly important field, a course of causation that cannot be ignored. From advising expectant parents to getting innocent people off death row, genetics increasingly dominates our lives. The sections on genetics are expertly written, particularly for those readers without in-depth knowledge. The author explains slowly and carefully just how genetics operates, using multiple metaphors. His genetic discourse proceeds in a neighborly fashion, as one might tell stories while sitting in a rocking chair at a country store. He seems to be invigorated by genes and just can't wait to tell about them. --David W. Hodo, Journal of the American Medical Association Reviews of this book: As a whole, this book is quite informative and stimulating, and sections of it are beautifully written. Indeed, Professor Avise has a real gift for prose and scientific expositions, and I would suspect that he must be a formidable lecturer...At its core, [The Genetic Gods] is a survey, and a very nice one at that, of evolutionary genetics, the field of the author's major research interests. There is a strong sociobiological cast to the arguments, and the work and ideas of E. O. Wilson figure prominently. The presentation of evolutionary genetics is imbedded in a more general discussion of modern human and molecular genetics...However, this book is, most of all, a philosophical treatise that attempts, admittedly with the bias of a biologist, to examine the intersection of the fundamental premises of evolution and religion. Professor Avise has given us plenty to think about in this book [and]...it was a real pleasure to wrestle with the ideas he was presenting. I would suggest that other readers give it a try. --Charles J. Epstein, Trends in Genetics Reviews of this book: [Avise's] account of the role genes play in shaping the human condition is wholly involving, paying particular attention to issues of reproduction, aging and death. In addition to presenting ample biological information in a form accessible to the nonspecialist, Avise does a superb job of discussing many of the ethical implications that have arisen from our growing knowledge of human genetics. Just a few of the topics covered are genetic engineering, the patenting of life, genetic screening, abortion, human cloning, gene therapy and insurance-related controversies. --Publishers Weekly Reviews of this book: Avise explains thoroughly how evolution operates on a genetic level. His goal is to show that humans can look to this information as a way to answer fundamental questions of life instead of looking to traditional religious beliefs...Avise includes some very interesting discussions of ethical concerns related to genetic issues. --Eric D. Albright, Library Journal This is a splendid account of a subject that affects us all: the breathtaking increase in understanding of human genetics and the insight it provides into human evolution. John Avise speaks with authority of molecular evolutionary genetics and with affecting compassion of what it might mean. --Douglas J. Futuyma, State University of New York at Stony Brook The Genetic Gods is many things. It is a wonderful introduction to modern molecular biology, by a man who knows his subject backwards. It is a stimulating account of the ways in which genetics impinges on human nature--our thinking and our behavior. It is a remarkably level-headed and sympathetic account of the implications of our new findings for traditional and not-so-traditional issues in philosophy and religion. In an age of genetic counseling, cloning, construction of new life forms, the book is worth its weight in gold for this alone. But most of all, it is a huge amount of fun to read--you want to applaud or argue with the author on nigh every page. Highly recommended! --Michael Ruse, University of Guelph The Genetic Gods makes a valuable contribution to the on-going task of sorting out the implications of evolutionary biology and genetics for human self-understanding. Avise addresses, with authority and grace, the most consequential intellectual issues of our time. A challenging and insightful book. --Loyal Rue, Harvard University A wonderfully informative and engaging book. Avise offers a lucid, accessible primer on our genes, angelic and demonic, and examines religious and ethical issues, all too human, now confronted by genetic science. He makes a compelling case that anyone seeking to 'Know Thyself' should study the DNA molecular scriptures, our most ancient and universal legacy. --Dudley Herschbach, Harvard University, Nobel Laureate in Chemistry
Book Synopsis Prokaryotic Metabolism and Physiology by : Byung Hong Kim
Download or read book Prokaryotic Metabolism and Physiology written by Byung Hong Kim and published by Cambridge University Press. This book was released on 2019-05-16 with total page 509 pages. Available in PDF, EPUB and Kindle. Book excerpt: Extensive and up-to-date review of key metabolic processes in bacteria and archaea and how metabolism is regulated under various conditions.
Book Synopsis An Introduction to Ecological Genomics by : Nico M. van Straalen
Download or read book An Introduction to Ecological Genomics written by Nico M. van Straalen and published by Oxford University Press. This book was released on 2012 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: The authors also provide a comparative survey of the properties of genomes (genome size, gene families, synteny, and polymorphism) for prokaryotes as well as the main eukaryotic models.
