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Dysfunction of nuclear-cytoplasmic transport systems has been associated with many human diseases. Thus, understanding of how functional this transport system maintains, or through dysfunction fails to maintain remains the core question in cell biology. In eukaryotic cells, the nuclear envelope (NE) separates the genetic transcription in the nucleus from the translational machinery in the cytoplasm. Thousands of nuclear pore complexes (NPCs) embedded on the NE selectively mediate the bidirectional trafficking of macromolecules such as RNAs and proteins between these two cellular compartments. In this book, the authors integrate recent progress on the structure of NPC and the mechanism of nuclear-cytoplasmic transport system in vitro and in vivo.
This detailed volume provides a collection of protocols for the study of miRNA functions in plants. Beginning with coverage of miRNA function, biogenesis, activity, and evolution in plants, the book continues by guiding readers through methods on the identification and detection of plant miRNAs, bioinformatic analyses, and strategies for functional analyses of miRNAs. Written in the highly successful Methods in Molecular Biology series format, 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 cutting-edge, Plant MicroRNAs: Method and Protocols aims to ensure successful results in the further study of this vital area of plant science.
The diversity of RNAs inside living cells is amazing. We have known of the more “classic” RNA species: mRNA, tRNA, rRNA, snRNA and snoRNA for some time now, but in a steady stream new types of molecules are being described as it is becoming clear that most of the genomic information of cells ends up in RNA. To deal with the enormous load of resulting RNA processing and degradation reactions, cells need adequate and efficient molecular machines. The RNA exosome is arising as a major facilitator to this effect. Structural and functional data gathered over the last decade have illustrated the biochemical importance of this multimeric complex and its many co-factors, revealing its enormous regulatory power. By gathering some of the most prominent researchers in the exosome field, it is the aim of this volume to introduce this fascinating protein complex as well as to give a timely and rich account of its many functions. The exosome was discovered more than a decade ago by Phil Mitchell and David Tollervey by its ability to trim the 3’end of yeast, S. cerevisiae, 5. 8S rRNA. In a historic account they laid out the events surrounding this identification and the subsequent birth of the research field. In the chapter by Kurt Januszyk and Christopher Lima the structural organization of eukaryotic exosomes and their evolutionary counterparts in bacteria and archaea are discussed in large part through presentation of structures.
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.
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. - Covers the nonsense-mediated mRNA decay (NMD) or mRNA surveillance pathway - Expert researchers introduce the most advanced technologies and techniques to identify mRNA processing, transport, localization and turnover, which are central to the process of gene expression - Offers step-by-step lab instructions, including necessary equipment and reagents
Since the 1996 publication of Translational Control, there has been fresh interest in protein synthesis and recognition of the key role of translation control mechanisms in regulating gene expression. This new monograph updates and expands the scope of the earlier book but it also takes a fresh look at the field. In a new format, the first eight chapters provide broad overviews, while each of the additional twenty-eight has a focus on a research topic of more specific interest. The result is a thoroughly up-to-date account of initiation, elongation, and termination of translation, control mechanisms in development in response to extracellular stimuli, and the effects on the translation machinery of virus infection and disease. This book is essential reading for students entering the field and an invaluable resource for investigators of gene expression and its control.
This is the first comprehensive review of mRNA stability and its implications for regulation of gene expression. Written by experts in the field, Control of Messenger RNA Stability serves both as a reference for specialists in regulation of mRNA stability and as a general introduction for a broader community of scientists. Provides perspectives from both prokaryotic and eukaryotic systems Offers a timely, comprehensive review of mRNA degradation, its regulation, and its significance in the control of gene expression Discusses the mechanisms, RNA structural determinants, and cellular factors that control mRNA degradation Evaluates experimental procedures for studying mRNA degradation
There is now compelling evidence that the complexity of higher organisms correlates with the relative amount of non-coding RNA rather than the number of protein-coding genes. Previously dismissed as “junk DNA”, it is the non-coding regions of the genome that are responsible for regulation, facilitating complex temporal and spatial gene expression through the combinatorial effect of numerous mechanisms and interactions working together to fine-tune gene expression. The major regions involved in regulation of a particular gene are the 5’ and 3’ untranslated regions and introns. In addition, pervasive transcription of complex genomes produces a variety of non-coding transcripts that interact with these regions and contribute to regulation. This book discusses recent insights into the regulatory roles of the untranslated gene regions and non-coding RNAs in the control of complex gene expression, as well as the implications of this in terms of organism complexity and evolution.​