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The Many Faces of RNA is the subject for the eighth SmithKline Beecham Pharmaceuticals Research Symposia. It highlights a rapidly developing area of scientific investigation. The style and format are deliberately designed to promote in-depth presentations and discussions and to facilitate the forging of collaborations between academic and industrial partners.This symposium focuses on several of the many fundamental, advancing strategies for exploring RNA and its functions. It emphasizes the interplay between biology, chemistry, genomics, and molecular biology which is leading to exc
RNA --- Ribonucleases --- RNA-protein interactions --- Antibiotics --- Therapeutic use --- Physiological effect --- Anti-infective agents --- Microbial metabolites --- Allelopathic agents --- Antibiosis --- Pharmaceutical microbiology --- Phytoncides --- Interactions, RNA-protein --- Protein-RNA interactions --- RNA-protein binding --- Protein binding --- RNases --- Nucleases --- Ribonucleic acid --- Ribose nucleic acid --- Nucleic acids --- Ribose
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After transcription in the nucleus, RNA binding proteins (RBPs) recognize cis-regulatory RNA elements within pre-mRNA sequence to form mRNA-protein (mRNP) complexes. Similarly to DNA binding proteins such as transcription factors that regulate gene expression by binding to DNA elements in the promoters of genes, RBPs regulate the fate of target RNAs by interacting with specific sequences or RNA secondary structural features within the transcribed RNA molecule. The set of functional RNA elements recognized by RBPs within target RNAs and which control the temporal, functional and spatial dynamics of the target RNA define a putative “mRNP code”. These cis-regulatory RNA elements can be found in the 5’ and 3’ untranslated regions (UTRs), introns, and exons of all protein-coding genes. RNA elements in 5’ and 3’ UTRs are frequently involved in targeting RNA to specific cellular compartments, affecting 3’ end formation, controlling RNA stability and regulating mRNA translation. RNA elements in introns and exons are known to function as splicing enhancers or silencers during the splicing process from pre-mRNA to mature mRNA. This book provides case studies of RNA binding proteins that regulate aspects of RNA processing that are important for fundamental understanding of diseases and development. Chapters include systems-level perspectives, mechanistic insights into RNA processing and RNA Binding proteins in genetic variation, development and disease. The content focuses on systems biology and genomics of RNA Binding proteins and their relation to human diseases.
RNA-protein interactions. --- Life sciences. --- Gene expression. --- Proteins. --- Systems biology. --- Life Sciences. --- Systems Biology. --- Protein Science. --- Gene Expression. --- Computational biology --- Bioinformatics --- Biological systems --- Molecular biology --- Proteids --- Biomolecules --- Polypeptides --- Proteomics --- Genes --- Genetic regulation --- Biosciences --- Sciences, Life --- Science --- Expression --- Interactions, RNA-protein --- Protein-RNA interactions --- RNA-protein binding --- Protein binding --- Biological models. --- Biochemistry. --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Biology --- Chemistry --- Medical sciences --- Models, Biological --- Composition --- Proteins .
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The work described in this book is an excellent example of interdisciplinary research in systems biology. It shows how concepts and approaches from the field of physics can be efficiently used to answer biological questions, and reports on a novel methodology involving creative computer-based analyses of high-throughput biological data. Many of the findings described in the book, which are the result of collaborations between the author (a theoretical scientist) and experimental biologists, and between different laboratories, have been published in high-quality peer-reviewed journals such as Molecular Cell and Nature. However, while those publications address different aspects of post-transcriptional gene regulation, this book provides readers with a complete, coherent and logical view of the research project as a whole. The introduction presents post-transcriptional gene regulation from a distinct angle, highlighting aspects of information theory and evolution, and laying the groundwork for the questions addressed in the subsequent chapters, which concern the regulation of the transcriptome as the primary functional carrier of active genetic information.
Engineering. --- Gene expression. --- Biochemistry. --- Systems biology. --- Biological systems. --- Computational intelligence. --- Computational Intelligence. --- Biological Networks, Systems Biology. --- Gene Expression. --- Biochemistry, general. --- Intelligence, Computational --- Artificial intelligence --- Soft computing --- Biosystems --- Systems, Biological --- Biology --- System theory --- Systems biology --- Computational biology --- Bioinformatics --- Biological systems --- Molecular biology --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Chemistry --- Medical sciences --- Genes --- Genetic regulation --- Construction --- Industrial arts --- Technology --- Philosophy --- Composition --- Expression --- RNA-protein interactions. --- Interactions, RNA-protein --- Protein-RNA interactions --- RNA-protein binding --- Protein binding --- Systems Biology.
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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.
Biochemical engineering. --- Biochemistry. --- Analytical biochemistry. --- Biological and Medical Physics, Biophysics. --- Biochemical Engineering. --- Protein Science. --- Analytical Chemistry. --- Analytic biochemistry --- Biochemistry --- Chemistry, Analytic --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Biology --- Chemistry --- Medical sciences --- Bio-process engineering --- Bioprocess engineering --- Biotechnology --- Chemical engineering --- Composition --- RNA-protein interactions. --- Interactions, RNA-protein --- Protein-RNA interactions --- RNA-protein binding --- Protein binding --- Bioanalytic chemistry --- Bioanalytical chemistry --- Analytical chemistry --- Biophysics. --- Biological physics. --- Proteins . --- Analytical chemistry. --- Analysis, Chemical --- Analytic chemistry --- Chemical analysis --- Proteids --- Biomolecules --- Polypeptides --- Proteomics --- Biological physics --- Physics
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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. .
Engineering. --- Biomedical Engineering. --- Systems Biology. --- Computational Biology/Bioinformatics. --- Bioinformatics. --- Biological models. --- Biomedical engineering. --- Ingénierie --- Bio-informatique --- Modèles biologiques --- Génie biomédical --- Health & Biological Sciences --- Biomedical Engineering --- RNA-protein interactions. --- RNA polymerases. --- DNA-dependent RNA polymerases --- DNA-directed RNA polymerases --- Polymerases, RNA --- Ribonucleate nucleotidyltransferases --- RNA nucleotidyltransferases --- Interactions, RNA-protein --- Protein-RNA interactions --- RNA-protein binding --- Systems biology. --- Protein binding --- Transferases --- Biomedical Engineering and Bioengineering. --- Bio-informatics --- Biological informatics --- Biology --- Information science --- Computational biology --- Systems biology --- Models, Biological --- Clinical engineering --- Medical engineering --- Bioengineering --- Biophysics --- Engineering --- Medicine --- Data processing --- Bioinformatics --- Biological systems --- Molecular biology
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In RNA-Protein Interaction Protocols, highly skilled experimentalists provide a comprehensive series of commonly used, as well as specialized, techniques for analyzing how proteins and RNA interact. Richly detailed and readily reproducible, these methods enable researchers to analyze the structural details of an RNA-protein interaction, to determine in detail what parts of the protein and RNA are in close contact, and to isolate RNP complexes from cells. There are also in vitro and in vivo methods and protocols for assaying the effects of proteins and RNP complexes on mRNA metabolism. The methods assume only a knowledge of basic molecular biology, biochemistry, and cell culture, and can be readily adapted to other systems. Providing an excellent standard resource for today's bench scientists studying many types of RNA-protein interactions, RNA-Protein Interaction Protocols offers a wide-ranging collection of up-to-date experimental methods that distill a great deal of wisdom and experience into productive, reproducible, step-by-step techniques for all investigators in the field.
RNA-protein interactions --- Interactions ARN-protéines --- Laboratory manuals. --- Manuels de laboratoire --- 57.088 --- 577.2 --- Special methods and techniques for studing biological molecules. Separation. Centrifuging. X-ray study. Radioisotope methods --- Molecular bases of life. Molecular biology --- 577.2 Molecular bases of life. Molecular biology --- 57.088 Special methods and techniques for studing biological molecules. Separation. Centrifuging. X-ray study. Radioisotope methods --- Interactions ARN-protéines --- Interactions, RNA-protein --- Protein-RNA interactions --- RNA-protein binding --- Protein binding --- Laboratory manuals --- Molecular biology. --- Molecular biochemistry --- Molecular biophysics --- Biochemistry --- Biophysics --- Biomolecules --- Systems biology --- Cytology. --- Cell Biology. --- Cell biology --- Cellular biology --- Biology --- Cells --- Cytologists
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Specific complexes of protein and RNA carry out many essential biological functions, including RNA processing, RNA turnover, RNA folding, as well as the translation of genetic information from mRNA into protein sequences. Messenger RNA (mRNA) decay is now emerging as an important control point and a major contributor to gene expression. Continuing identification of the protein factors and cofactors, and mRNA instability elements, responsible for mRNA decay allow researchers to build a comprehensive picture of the highly orchestrated processes involved in mRNA decay and its regulation.
RNA-protein interactions. --- Messenger RNA. --- Genetic regulation. --- Prokaryotes. --- Cell organelles. --- Interactions ARN-protéines --- ARN messager --- Régulation génétique --- Procaryotes --- Organites cellulaires --- Bacteria. --- Organelles,. --- RNA Stability. --- RNA, Archaeal. --- RNA, Bacterial. --- RNA, Bacterial --- RNA, Archaeal --- Organelles --- mRNA Cleavage and Polyadenylation Factors --- RNA Stability --- RNA --- RNA-Binding Proteins --- Biochemical Phenomena --- Cytoplasmic Structures --- Cytoplasm --- Nucleic Acids --- Nucleoproteins --- Carrier Proteins --- Chemical Phenomena --- Intracellular Space --- Nucleic Acids, Nucleotides, and Nucleosides --- Proteins --- Phenomena and Processes --- Cellular Structures --- Chemicals and Drugs --- Amino Acids, Peptides, and Proteins --- Cells --- Anatomy --- Animal Biochemistry --- Human Anatomy & Physiology --- Health & Biological Sciences --- Interactions ARN-protéines --- Régulation génétique --- Organelles, Cell --- Germs --- Microbes --- Gene expression --- Gene expression regulation --- Gene regulation --- Informational RNA --- Messenger ribonucleic acid --- mRNA --- Protein transcript --- Protein transcripts --- Template RNA --- Interactions, RNA-protein --- Protein-RNA interactions --- RNA-protein binding --- Regulation --- Prokaryotes --- Biosynthesis --- Cellular control mechanisms --- Molecular genetics --- Protein binding
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Successful chromosome replication is vital for maintaining the integrity of the genetic material in all forms of cellular life. In humans, there are clear links between chromosome replication defects and genome instability, genetic disease and cancer, making a detailed understanding of the molecular mechanisms of genome duplication vital for future advances in diagnosis and treatment. Inspired by recent exciting breakthroughs in protein structure determination and written by leading experts in the field, The Eukaryotic Replisome: a guide to protein structure and function takes the reader on a guided journey through the intricate molecular machinery of eukaryotic chromosomal DNA replication, from replication origin recognition and the assembly of the pre-replicative complexes in G1 through to the final processing of Okazaki fragments at the end of S-phase. This extensively illustrated book is an invaluable source of information, ideas and inspiration for all those with an interest in chromosome replication, whether from a basic science, translational biology and medical research perspective.
Cell cycle. --- Chromosome replication. --- Eukaryotic cells. --- Molecular biology. --- Oncology. --- Chromosome replication --- Biochemical Processes --- Macromolecular Substances --- Genetic Processes --- Biochemical Phenomena --- Chemicals and Drugs --- Genetic Phenomena --- Chemical Processes --- Phenomena and Processes --- Chemical Phenomena --- Multiprotein Complexes --- DNA Replication --- Biology --- Health & Biological Sciences --- Cytology --- DNA --- RNA-protein interactions. --- Synthesis. --- Interactions, RNA-protein --- Protein-RNA interactions --- RNA-protein binding --- Deoxyribonucleic acid synthesis --- Medicine. --- Cancer research. --- Biochemistry. --- Nucleic acids. --- Proteins. --- Biomedicine. --- Biomedicine general. --- Biochemistry, general. --- Protein Science. --- Protein Structure. --- Nucleic Acid Chemistry. --- Cancer Research. --- Protein binding --- Tumors --- Polynucleotides --- Biomolecules --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Chemistry --- Medical sciences --- Clinical sciences --- Medical profession --- Human biology --- Life sciences --- Pathology --- Physicians --- Composition --- Health Workforce --- Proteins . --- Biomedicine, general. --- Cancer research --- Proteids --- Polypeptides --- Proteomics --- Medicine --- Biomaterials. --- Cancer. --- Biomedical Research. --- Protein Biochemistry. --- Nucleic Acid. --- Cancer Biology. --- Research. --- Cancers --- Carcinoma --- Malignancy (Cancer) --- Malignant tumors --- Biological research --- Biomedical research
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This book assembles chapters from experts in the Biophysics of RNA to provide a broadly accessible snapshot of the current status of this rapidly expanding field. The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, highlighting just one example of a large number of non-protein coding RNAs. Because non-protein coding RNAs outnumber protein coding genes in mammals and other higher eukaryotes, it is now thought that the complexity of organisms is correlated with the fraction of their genome that encodes non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic transposons, higher-level organization of eukaryotic chromosomes, and gene expression itself are found to largely be directed by non-protein coding RNAs. The biophysical study of these RNAs employs X-ray crystallography, NMR, ensemble and single molecule fluorescence spectroscopy, optical tweezers, cryo-electron microscopy, and other quantitative tools. This emerging field has begun to unravel the molecular underpinnings of how RNAs fulfill their multitude of roles in sustaining cellular life. The physical and chemical understanding of RNA biology that results from biophysical studies is critical to our ability to harness RNAs for use in biotechnology and human therapy, a prospect that has recently spawned a multi-billion dollar industry.
Biochemistry. --- Bioinformatics. --- Biomedical Engineering. --- Cytology. --- Medicine. --- Non-coding RNA. --- Physics. --- RNA-protein interactions. --- Molecular Probe Techniques --- Amino Acids, Peptides, and Proteins --- RNA --- Investigative Techniques --- Nucleic Acids --- Chemicals and Drugs --- Nucleic Acids, Nucleotides, and Nucleosides --- Analytical, Diagnostic and Therapeutic Techniques and Equipment --- Proteins --- Protein Interaction Mapping --- RNA, Untranslated --- Human Anatomy & Physiology --- Biology --- Health & Biological Sciences --- Animal Biochemistry --- Biophysics --- Interactions, RNA-protein --- Protein-RNA interactions --- RNA-protein binding --- fRNA --- Functional RNA --- ncRNA --- nmRNA --- Non-messenger RNA --- Non-translated RNA --- Noncoding RNA --- Nontranslated RNA --- Small non-messenger RNA --- Small RNA --- snmRNA --- sRNA --- Untranslated RNA --- Life sciences. --- Human physiology. --- Molecular biology. --- Cell biology. --- Biophysics. --- Biological physics. --- Life Sciences. --- Biochemistry, general. --- Biophysics and Biological Physics. --- Human Physiology. --- Cell Biology. --- Molecular Medicine. --- Protein binding --- Biological and Medical Physics, Biophysics. --- Clinical sciences --- Medical profession --- Human biology --- Life sciences --- Medical sciences --- Pathology --- Physicians --- Cell biology --- Cellular biology --- Cells --- Cytologists --- Bio-informatics --- Biological informatics --- Information science --- Computational biology --- Systems biology --- Physiology --- Human body --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Chemistry --- Data processing --- Composition --- Health Workforce --- Molecular biochemistry --- Molecular biophysics --- Biochemistry --- Biomolecules --- Biological physics --- Physics
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This book aims to bring to the forefront a field that has been developing since the late 1990s called the STAR pathway for Signal Transduction and Activation of RNA. It is a signaling pathway that targets RNA directly; in contrast to the canonical signal - kinase cascade - transcription factor - DNA - RNA. It is proposed to allow quick responses to environment changes such as those necessary in many biological phenomenon such as the nervous system and during development.
Cellular signal transduction. --- RNA --Metabolism --Regulation. --- RNA-protein interactions. --- RNA-protein interactions --- RNA --- Cellular signal transduction --- Embryonic and Fetal Development --- Biochemical Processes --- Biological Science Disciplines --- Carrier Proteins --- Nucleoproteins --- Metabolic Phenomena --- Gene Expression Regulation --- Cell Physiological Processes --- Reproduction --- Biochemical Phenomena --- Morphogenesis --- Chemical Processes --- Proteins --- Genetic Processes --- Natural Science Disciplines --- Phenomena and Processes --- Cell Physiological Phenomena --- Amino Acids, Peptides, and Proteins --- Genetic Phenomena --- Chemical Phenomena --- Reproductive Physiological Processes --- Disciplines and Occupations --- Growth and Development --- Chemicals and Drugs --- Reproductive Physiological Phenomena --- Physiological Processes --- Physiological Phenomena --- Reproductive and Urinary Physiological Phenomena --- RNA Processing, Post-Transcriptional --- Transcriptional Activation --- Embryonic Development --- Metabolism --- Signal Transduction --- Physiology --- RNA-Binding Proteins --- Human Anatomy & Physiology --- Health & Biological Sciences --- Pharmacy, Therapeutics, & Pharmacology --- Animal Biochemistry --- Regulation --- Regulation. --- Cellular information transduction --- Information transduction, Cellular --- Signal transduction, Cellular --- Ribonucleic acid --- Ribose nucleic acid --- Interactions, RNA-protein --- Protein-RNA interactions --- RNA-protein binding --- Medicine. --- Neurosciences. --- Pharmacology. --- Biomedicine. --- Pharmacology/Toxicology. --- Drug effects --- Medical pharmacology --- Medical sciences --- Chemicals --- Chemotherapy --- Drugs --- Pharmacy --- Neural sciences --- Neurological sciences --- Neuroscience --- Nervous system --- Clinical sciences --- Medical profession --- Human biology --- Life sciences --- Pathology --- Physicians --- Physiological effect --- Bioenergetics --- Cellular control mechanisms --- Information theory in biology --- Nucleic acids --- Ribose --- Protein binding --- Toxicology. --- Medicine --- Pharmacology --- Poisoning --- Poisons --- Toxicology
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