Download or read book Fine Tuning of RNA Functions by Modification and Editing written by Henri Grosjean and published by Springer. This book was released on 2010-02-12 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Naturally occurring RNA always contains numerous biochemically altered nucleotides. They are formed by enzymatic modification of the primary transcripts during the complex RNA maturation process designated RNA modification. A large number of enzymes catalyzing the formation of these modified nucleosides or converting one canonical base into another at the posttranscriptional level have been studied for many years, but only recently have systematic and comparative studies begun. The functions of individual enzymes and/or the modified/edited nucleosides in RNA, however, have remained largely ignored. This book provides advance information on RNA modification, including the associated editing machinery, while offering the reader some perspective on the significance of such modifications in fine-tuning the structure and functions of mature RNA molecules and hence the ability to influence the efficiency and accuracy of genetic expression. Outstanding scientists who are actively working on RNA modification/editing processes have provided up-to-date information on these intriguing cellular processes that have been generated over the course of millions of years in all living organisms. Each review has been written and illustrated for a large audience of readers, not only specialists in the field, but also for advanced students or researchers who want to learn more about recent progress in RNA modification and editing.
Download or read book RNA Modification written by and published by Academic Press. This book was released on 2017-06-21 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA Modification, Volume 41 examines the powerful ability to regulate the function of RNA molecules or modify the message transmitted by RNA molecules. Chapters in this newly released volume include The Importance of Being Modified: Modifications Shape RNA Function through Chemistry, Structure and Dynamics, The evolution of multi-substrate specificity by RNA modification enzymes, TrmD: a methyl transferase for tRNA methylation with m1G37, Structures and activities of the Elongator complex and its co-factors, RNA pseudouridylation: Mechanism and Function, The activity of 5'3' exonucleases on hypo modified tRNA substrates and other structured RNAs, and the Synthesis, heterogeneity and function of post-transcriptional nucleotide modifications in eukaryotic ribosomal RNAs. This field has recently seen a very rapid progress in the understanding of the mechanism and enzymes involved in RNA modification. This volume presents some of the most recent advances in the identification and function of enzymes involved in modifying RNA molecules. - Features authoritative expertise from recognized contributors to the field - Presents the most recent advances in the rapidly evolving field of RNA modification - Covers the identification and function of enzymes involved in modifying RNA molecules
Download or read book Modification and Editing of RNA written by Henri Grosjean and published by . This book was released on 1998 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This Comprehensive, current text explores the manifold ways in which living cells respond to genomic injury and alterations, including both spontaneous and environmentally induced DNA damage. With more than 4,000 complete references to primary research literature and over 380 color figures throughout, this book is an important text for all courses in DNA repair and mutagenesis. It will also serve as a major reference for all molecular biologists working in cancer biology, recombination, transcription and gene regulation, DNA replication, environmental studies, and biological evolution.
Download or read book DNA and RNA Modification Enzymes written by Henri Grosjean and published by CRC Press. This book was released on 2009 with total page 682 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a timely and comprehensive description of the many facets of DNA and RNA modification-editing processes and to some extent repair mechanisms. Each chapter offers fundamental principles as well as up to date information on recent advances in the field (up to end 2008) They ended by a short ‘conclusion and future prospect’ section and an exhaustive list of 35 to up to 257 references (in average 87) Contributors are geneticists, structural enzymologists and molecular biologists working at the forefront of this exciting, fast-moving and diverse field of researches. This book will be a major interest to PhD students and University teachers alike. It will also serve as an invaluable reference tool for new researchers in the field, as well as for specialists of RNA modification enzymes generally not well informed about what is going on in similar processes acting on DNA and vice-versa for specialists of the DNA modification-editing and repair processes usually not much acquainted with what is going on in the RNA maturation field. The book is subdivided into 41 chapters (740 pages) The common links between them are mainly the enzymatic aspects of the different modification-editing and repair machineries: structural, mechanistic, functional and evolutionary aspects. It starts with two general and historical overview of the discovery of modified nucleosides in DNA and RNA and corresponding modification-editing enzymes. Then follows eleven chapters on DNA modification and editing (mechanistic and functional aspects) Two additional chapters cover problems related to DNA/RNA repair and base editing by C-to-U deaminases, followed by three chapters on RNA editing by C-to-U and A-to-I type of deamination. Discussions about interplay between DNA and RNA modifications and the emergence of DNA are covered in two independent chapters, followed by twenty chapters on different but complementary aspects of RNA modification enzymes and their cellular implications. The last chapter concerns the description of the present state-of-the art for incorporating modified nucleosides by in vitro chemical synthesis. At the end of the book, six appendicies give useful details on modified nucleosides, modification-editing enzymes and nucleosides analogs. This information is usually difficult to obtain from current scientific literature.
Download or read book RNA Interference Editing and Modification written by Jonatha M. Gott and published by Springer Science & Business Media. This book was released on 2008-02-05 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a comprehensive collection of cuttingedge methods for elucidating the function of new genes and altering gene expression. These readily reproducible techniques can be used either in transient and stable gene splicing applied to worms, flies, trypanosomes, mammals, and plants, or in studying RNA editing mechanisms in a wide range of organisms, including systems that involve the conversion of one base to another and insertion/deletion editing. Topics of interest include stable and transient RNA interference, gene silencing, RNA editing, bioinformatics, small noncoding RNAs, and RNomics. Special attention is given to methods for the identification and characterization of small RNAs involved in RNA interference or modification. Readily reproducible protocols for discovering new genes or altering gene expression.
Download or read book RNA and DNA Editing written by Ruslan Aphasizhev and published by Humana Press. This book was released on 2016-08-23 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: The recent expansion in diversity of RNA and DNA editing types has stimulated the development of many unique genetic, molecular, biochemical, and computational approaches to biological issues. In RNA and DNA Editing: Methods and Protocols, leading experts in the field introduce methods developed over the last few years to study editing substrates, mechanisms of specificity, and functions of RNA and DNA editing enzymes and complexes. Sections of the book are dedicated to state-of-the art techniques which enable investigation of uracil insertion/deletion RNA editing in mitochondrion of Trypanosoma brucei, adenosine to inosine RNA editing, cytidine to uracil RNA and DNA editing, as well as tRNA editing and RNA modifications. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA and DNA Editing: Methods and Protocols seeks to inspire the further development of these vital and powerful techniques.
Download or read book RNA and DNA Editing written by Harold C. Smith and published by John Wiley & Sons. This book was released on 2008-04-25 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA and DNA Editing assembles a team of leading experts who present the latest discoveries in the field alongside the latest models and methodology. In addition, the authors set forth the many open questions and suggest routes for further investigation. Overall, the book serves as a practical guide for professionals in the field who need to understand the interrelationship of RNA and DNA editing with other chemical and biological processes.
Download or read book RNA Editing written by H. Ulrich Göringer and published by Springer Science & Business Media. This book was released on 2008-01-12 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: Goringer’s brilliant new work dedicates a chapter to each of the main types of RNA editing – the very first volume to do so. All of the sections here have been written by experts in the various research areas and a specific focus is put on the correlation between RNA structure and function, as well as on the complex cellular machineries that catalyze the different editing reactions. This leads to a "state of the art" compendium of our current knowledge on RNA editing.
Download or read book RNA Modification Enzymes written by and published by Academic Press. This book was released on 2021-09-11 with total page 476 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA Modification Enzymes, Volume 659 in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of related topics, including Locating chemical modifications in RNA sequences through ribonucleases and LC-MS based analysis, Development of RNA modification mapping pipelines for high-throughput sequencing approaches, AlkAniline-Seq for high-resolution mapping RNA m7G and m3C modifications, Facile detection of RNA phospho-methylation in cells, Detection and analysis of glycosylated queuosine modifications, A comprehensive pipeline for analysis of RNA 3’-end modification, Analysis of the epitranscriptome with ion-pairing reagent free oligonucleotide mass spectrometry, and more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology series Updated release includes the latest information on the RNA Modification Enzymes
Download or read book RNA Modification written by and published by Elsevier. This book was released on 2007-09-13 with total page 476 pages. Available in PDF, EPUB and Kindle. Book excerpt: The presence of modified nucleotides in cellular RNAs has been known for decades and over 100 distinct RNA modifications have been characterized to date. While the exact role of many of these modifications is still unclear, many are highly conserved across evolution and most contribute to the overall fitness of the organism. In recent years, new methods and bioinformatics approaches have been developed for the dissection of modification pathways and functions. These methods intersect a number of related fields, ranging from RNA processing to comparative genomics and systems biology. In addition, many of the techniques described in this volume have broad applicability, particularly in regards to the isolation, characterization, and reconstitution of ribonucleoprotein complexes, expanding the experimental repertoire available to all RNA researchers.
Download or read book Insights Into the Functions of RNA Post transcriptional Modifications Gained Through Studies in Cellular Stress written by Kevin Charles Baldridge and published by . This book was released on 2017 with total page 478 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, the explosion of knowledge regarding functional roles for RNA in biology have uncovered the need for detailed molecular understanding of the relationship between the chemistry of RNA and its function. Post-transcriptional modifications in RNA are changes to the chemistry of the four basic RNA nucleotides, which can be thought of as expansions to the genetic alphabet of RNA. By subtly changing the chemistry of the standard RNA nucleotides, post-transcriptional modifications (PTMs) can act to modulate RNA function through a variety of mechanisms ranging from altering the basic physicochemical properties of an RNA molecule to fine-tuning complex regulation processes in higher organisms such as humans. While a number of functions have been ascribed to RNA post-transcriptional modifications, we still lack a comprehensive picture of how subtle changes in RNA chemistry can alter cellular function. Therefore, my dissertation focuses on applying cellular stress models as a way to interrogate how RNA post-transcriptional modifications can modulate RNA function. First, I provide a thorough discussion of how ribosomal RNA methylations help Escherichia coli adapt to stressful environmental conditions by protecting the vital protein translation process. Furthermore, by performing a targeted meta-analysis of publicly available stress-induced gene expression data, I identify specific ribosomal RNA methylations which may be important for E. coli adaptation to particular stresses including oxidative, heat, and cold stresses. Next, I examined the question of how RNA chemistry is affected directly by an external stress using a model system for simulated air pollution exposure with human lung cell cultures to demonstrate that cellular RNA oxidation is a reliable consistent indicator of oxidative stress from air pollution exposure. Building upon this air pollution exposure model system, I further explored how chemical oxidation of RNAs can be specifically enriched in certain RNA transcripts under oxidative stress induced by air pollution exposure. This work highlights specific oxidation of mRNAs involved in regulatory pathways as a possible mechanism for air-pollution related disease, suggesting that accumulation of oxidized mRNAs might interfere with processing or gene regulation. Additionally, examination of specific RNA oxidation associated with pre- and post-stress differential gene expression after exposure to air pollution highlights the potential that the oxidized RNA base 8-oxoguanosine might function as an epitranscriptomic mark affecting transcription. Lastly, I characterized how RNA modification machinery can contribute to cellular stress associated with expression of engineered transfer RNAs for applications in expanding the genetic code in E. coli. Using a suite of suppressor tRNAs designed by directed evolution, I demonstrated that the evolved lower expression level minimizes the impact of stress caused by interactions with E. coli post-transcriptional modification machinery, resulting in high performing tRNAs that remain functional regardless of their interactions with host PTM machinery. Collectively, the studies described in this dissertation demonstrate the power of employing cellular stress models to interrogate functional roles of RNA post-transcriptional modifications and highlight the myriad roles that PTMs can play in responding to and contributing to cellular stress
Download or read book RNA Editing and Modification in Development and Diseases written by Yanqiang Li and published by Frontiers Media SA. This book was released on 2022-11-14 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Role of RNA Modification in Disease written by Emanuele Buratti and published by Frontiers Media SA. This book was released on 2020-02-03 with total page 77 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Epitranscriptomics written by Stefan Jurga and published by Springer Nature. This book was released on 2021-07-28 with total page 632 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews a novel and exciting field of cellular and molecular biology called epitranscriptomics, which focuses on changes in an organism’s cells resulting from the posttranscriptional modification of cellular RNA. RNA-binding proteins (RBPs) play a crucial role in these posttranscriptional modifications and also support several cellular processes necessary for maintaining RNA homeostasis. Exploring the mechanisms underlying RNA modifications and RBP function is an emerging area of biomedical research, taking the study of gene regulation a step beyond epigenetics. This book reveals that the RNA molecule is not just an information-carrying molecule with some secondary structures. Accordingly, how RNA is modified, regulated, packaged, and controlled is an important aspect. Leading experts address questions such as where the over 170 distinct posttranscriptional RNA modifications are located on the genome, what percentage of mRNAs and noncoding RNAs these modifications include, and how an RNA modification impacts a person’s biology. In closing, the book reviews the role of RNA modifications and RBPs in a variety of diseases and their pathogenesis. Addressing some of the most exciting challenges in epitranscriptomics, this book provides a valuable and engaging resource for researchers in academia and industry studying the phenomena of RNA modification.
Download or read book DNA and RNA Modification Enzymes written by Henri Grosjean and published by CRC Press. This book was released on 2009-06-11 with total page 682 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a timely and comprehensive description of the many facets of DNA and RNA modification-editing processes and to some extent repair mechanisms. Each chapter offers fundamental principles as well as up to date information on recent advances in the field (up to end 2008). They ended by a shortconclusion and future prospect' section and
Download or read book Modified Nucleic Acids in Biology and Medicine written by Stefan Jurga and published by Springer. This book was released on 2016-07-29 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is comprised of 18 chapters, covering various aspects of DNA modification and RNA modified bases. It also discusses in detail circular RNA, therapeutic oligonucleotides and their different properties. The chemical nature of DNA, RNA, protein and lipids makes these macromolecules easily modifiable, but they are also susceptible to damage from both endogenous and exogenous agents. Alkylation and oxidation show a potential to disrupt the cellular redox equilibrium and cause cellular damage leading to inflammation and even chronic disease. Furthermore, DNA damage can drive mutagenesis and the resulting DNA sequence changes can induce carcinogenesis and cancer progression. Modified nucleosides can occur as a result of oxidative DNA damage and RNA turnover, and are used as markers for various diseases. To function properly some RNA needs to be chemically modified post-transcriptionally. Dysregulation of the RNA-modification pattern or of the levels of the enzymes that catalyze these modifications alters RNA functionality and can result in complex phenotypes, likely due to defects in protein translation. While modifications are best characterized in noncoding ribonucleic acids like tRNA and rRNA, coding mRNAs have also been found to contain modified nucleosides. This book is a valuable resource, not only for graduate students but also researchers in the fields of molecular medicine and molecular biology.
Download or read book RNA Modifications and Epitranscriptomics written by Xiao Han and published by Frontiers Media SA. This book was released on 2022-05-05 with total page 387 pages. Available in PDF, EPUB and Kindle. Book excerpt:
