Download or read book Post Transcriptional Gene Regulation by N6 Methyladenosine and Selective RNA Binding Proteins written by Ian A. Roundtree and published by . This book was released on 2017 with total page 137 pages. Available in PDF, EPUB and Kindle. Book excerpt: Regulation of genetic output is a complex biological phenomenon that allows cells with identical genetic material to enable diverse phenotypic outcomes. Epigenetics is the study of factors that change gene expression without perturbing the underlying genetic sequence. Mechanisms of epigenetics feature a multitude of chemical modifications to DNA as well as accompanying histone proteins, which tune the transcriptional output in a reversible manner. Recently, the concept of reversible RNA epigenetics has emerged as a mechanism to regulate gene expression post-transcriptionally. N6-methylasdenosein (m6A) is the most common internal modification in eukaryotic messenger RNA (mRNA). This RNA modification is recognized by m6A-selective RNA binding protein of the YTH family, which incorporate modified RNAs into canonical pathways for mRNA metabolism. In this work, we describe the function of the only nuclear YTH protein YTHDC1 in promoting the nuclear export of methylated mRNAs by interaction with the splicing and export adaptor protein SRSF3. We then turn to a biological example of rapid mRNA processing during progression through the cell cycle. We propose that m6A modifications serve roles in the dynamic regulation of the cellular transcriptome.
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 RNA Modifications Impact on Protein Binding Co transcriptional Regulation and Sequencing Signatures written by Katherine Ismei Zhou and published by . This book was released on 2018 with total page 195 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene expression is controlled by a complex and interconnected regulatory system. In this thesis, I explore how RNA modifications impact protein binding, co-transcriptional regulation, and sequencing signatures. The cellular functions of the abundant messenger RNA (mRNA) modification N6-methyladenosine (m6A) are mediated by m6A reader proteins. Some m6A reader proteins selectively bind m6A-modified RNAs by recognizing motifs that become accessible upon an m6A-induced change in RNA structure. In Chapter 2, I use biophysical methods to examine how m6A modification alters the structure of an RNA hairpin to enhance binding of the protein heterogeneous nuclear ribonucleoprotein C (hnRNPC). In Chapter 3, I describe the discovery of another m6A reader protein, hnRNPG, which binds to a motif that becomes exposed upon m6A modification of an RNA hairpin. Unlike hnRNPC, hnRNPG binds to a motif that includes the m6A site. Moreover, hnRNPG uses Arg-Gly-Gly (RGG) repeats in a low-complexity region to selectively bind to m6A-modified RNA. In Chapter 4, I explore the cellular functions of hnRNPG binding to m6A-modified RNAs. The hnRNPG protein binds to the phosphorylated C-terminal domain of RNA polymerase II and to nascent m6A-modified RNA for co-transcriptional, m6A-dependent gene regulation. In Chapter 5, I build on existing sequencing methods for the detection of another RNA modification, pseudouridine (Psi). This work spans a variety of perspectives on the impact of RNA modifications, from a biophysical study of the effect of m6 A on RNA structure and protein binding, to an investigation of the cellular functions of m6A in gene regulation, to method development for the detection of pseudouridines in high-throughput sequencing data. Together, these diverse perspectives demonstrate the widespread impact of RNA modifications.
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 2005-05-11 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 Post transcriptional Coordination by an RNA binding Protein written by Joshua Jaeger Wolf and published by . This book was released on 2010 with total page 148 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-binding proteins can regulate the stability, localization, and translation of their target mRNAs. Post-transcriptional regulation can orchestrate dynamic changes in gene expression, and can coordinate multiple cellular processes in response to various stimuli. Filamentous growth in Saccharomyces cerevisiae is a morphogenetic switch that occurs in response to nitrogen starvation and requires alterations in cell growth, cell cycle, and cell wall functions. Tyl element retrotransposition is also induced under conditions of nitrogen starvation. I describe a role for the RNA-binding protein Khdl in regulating these two responses to environmental stress through its mRNA targets. I identified the RNA targets of Khdl using in vivo crosslinking and immunoprecipitation (CLIP), combined with deep sequencing. This produced a high-resolution map of Khdl binding sites across the transcriptome, and provided unprecedented insight into its biological functions. Khdl regulates multiple post-transcriptional regulatory loops to coordinate the components of filamentous growth and Tyl retrotransposition. Although similar mechanisms were known to transcriptionally regulate these processes, the posttranscriptional coordination is a novel discovery. The feed-forward regulation that Khdl confers on FLO11, which encodes a protein required for filamentous growth, enables asymmetric expression between mother and daughter cells to switch between filamentous and yeast form growth. In this thesis, I describe regulation of gene expression by RNA-binding proteins, methods to identify their target transcripts and recognition sequences, the KH domain, known functions of Khdl, and the phenotypes it coordinates. My work represents the first application of CLIP to budding yeast, and the growing understanding of RNA-binding proteins in this organism facilitated the placement of Khdl into its posttranscriptional regulatory network. While many questions remain regarding the role Khdl plays in regulating cellular activities, this thesis addresses its direct role in key processes.
Download or read book Post transcriptional Gene Regulation by the Double Stranded RNA Binding Protein Staufen1 written by Bronwyn Ayla Lucas and published by . This book was released on 2019 with total page 155 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA binding proteins (RBPs) are key regulators of gene expression that, by interacting with specific RNAs, can impact their splicing, localization, translation and decay. Staufen proteins are RBPs that are conserved through metazoan evolution, and can simultaneously bind both double-stranded RNAs (dsRNAs) and diverse proteins. These properties, together with its presence in the nucleus, cytoplasm and at the endoplasmic reticulum (ER), has made it a versatile regulatory protein. In this thesis I explore three distinct contexts wherein Staufen1 has been co-opted during mammalian evolution to regulate gene expression. The first example pursues the Maquat-lab finding that mammalian Staufen1 (STAU1) binds dsRNA structures formed between primate-specific Alu short interspersed elements (SINEs) in humans and between rodent-specific B or ID (B/ID) SINEs in mice. When these duplexes are present in mRNA 3'-untranslated regions (3'-UTRs), STAU1 binding promotes Staufen-mediated decay (SMD). We hypothesized that gene regulation resulting from SINE insertion might have been similarly adaptive in separate mammalian lineages, leading to parallel evolution of the Staufen network by independent exaptation of SINEs. To explore this hypothesis, we identified and confirmed orthologous gene pairs with 3'-UTR SINEs that have been independently exapted in mouse and humans for SMD control of myoblast metabolism. Expanding to other species we demonstrated that SINE-directed SMD likely emerged in both primate and rodent lineages>25 million years ago. This work reveals a novel mechanism for the convergent evolution of post-transcriptional gene regulatory networks in mammals by species-specific SINE transposition and SMD. Another consequence of STAU1 binding to duplexes formed between inverted Alu repeats (IRAlus) in mRNA 3'-UTRs is to promote the escape from nuclear retention. While some mRNAs harboring 3'-UTR IRAlus can be retained in the nucleus by interaction with the paraspeckle protein p54nrb, other 3'-UTR IRAlus do not promote nuclear retention but do promote mRNA translation. The diverse consequences of 3'-UTR Alus imply the existence of different, as yet undefined subcategories. To reach a global understanding of the contribution of 3'-UTR Alus to mRNA localization, translation and decay we undertook to characterize the nucleocytoplasmic distribution, translation and abundance of the 3'-UTR Alu element-containing transcriptome using the isoform-specific RNA seq method, READS+. Using this method uncovered 3'-UTR features that correlate with mRNA localization and distinguish a subset of IRAlus-containing mRNAs, for which the mRNA export is regulated by STAU1. We made an additional and unexpected finding that 3'-UTR length is a determinant of mRNA localization, independent of Alu content. STAU1 also binds intramolecular duplexes in ER-localized mRNAs, including the ER stress-responsive transcript XBP1. Under ER stress, this transcript is known to undergo cytoplasmic cleavage and ligation resulting in a translational frameshift and production of a potent transcription factor that activates ER stress-responsive genes. I have show that knockdown of Staufen1 reduced the production of spliced XBP1 in response to ER stress without a concomitant increase in unspliced XBP1, which, together with my finding that STAU1 co-immunoprecipitates with the RNA ligase RTCB, implicates Staufen1 as a regulator of the ligation step, rather than the cleavage step, of XBP1 splicing. Depletion of Staufen1 also reduced the abundance of XBP1 mRNA in unstressed cells, signifying that STAU1 is additionally required for the maintenance of XBP1 mRNA, and as such the sensitivity to ER stress. This poses the possibility that STAU1 promotes the re-ligation by RTCB after cleavage of XBP1 mRNA at a single site. Interestingly, while the endonuclease that catalyzes the cleavage step of XBP1 mRNA splicing is conserved in eukaryotes, RTCB catalyzes the ligation step of XBP1 mRNA splicing only in metazoans, co-occurring with the emergence of Staufen proteins. Taken together, the capacity of STAU1 to bind to different dsRNA sequences and structures has enabled the convergent evolution of SINE-directed Staufen-mediated mRNA decay in human and mouse, promotes the expression of IRAlus-containing mRNAs and the cellular resilience to ER stress.
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 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.
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 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.
Download or read book Color Atlas of Immunology written by Gerd R. Burmester and published by Thieme. This book was released on 2011-01-01 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: A pocket atlas flexibook on this dynamic and wide-ranging field, indispensable for students of medicine and biology alike.Complex processes are well-illustrated in clear images that are not burdened with unnecessary details.Following an introductory part and a section on laboratory methods in immunology, the bulk of the book concentrates on the manifestations of immunological diseases in the human body, providing comprehensive capsule descriptions of all common immune diseases.
Download or read book Unsupervised Feature Extraction Applied to Bioinformatics written by Y-h. Taguchi and published by Springer Nature. This book was released on 2019-08-23 with total page 321 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book proposes applications of tensor decomposition to unsupervised feature extraction and feature selection. The author posits that although supervised methods including deep learning have become popular, unsupervised methods have their own advantages. He argues that this is the case because unsupervised methods are easy to learn since tensor decomposition is a conventional linear methodology. This book starts from very basic linear algebra and reaches the cutting edge methodologies applied to difficult situations when there are many features (variables) while only small number of samples are available. The author includes advanced descriptions about tensor decomposition including Tucker decomposition using high order singular value decomposition as well as higher order orthogonal iteration, and train tenor decomposition. The author concludes by showing unsupervised methods and their application to a wide range of topics. Allows readers to analyze data sets with small samples and many features; Provides a fast algorithm, based upon linear algebra, to analyze big data; Includes several applications to multi-view data analyses, with a focus on bioinformatics.
Download or read book Epigenetics in Plants of Agronomic Importance Fundamentals and Applications written by Raúl Alvarez-Venegas and published by Springer. This book was released on 2014-07-22 with total page 158 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the past decades, chromatin remodelling has emerged as an important regulator of gene expression and plant defense. This book provides a detailed understanding of the epigenetic mechanisms involved in plants of agronomic importance. The information presented here is significant because it is expected to provide the knowledge needed to develop in the future treatments to manipulate and selectively activate/inhibit proteins and metabolic pathways to counter pathogens, to treat important diseases and to increase crop productivity. New approaches of this kind and the development of new technologies will certainly increase our knowledge of currently known post-translational modifications and facilitate the understanding of their roles in, for example, host-pathogen interactions and crop productivity. Furthermore, we provide important insight on how the plant epigenome changes in response to developmental or environmental stimuli, how chromatin modifications are established and maintained, to which degree they are used throughout the genome, and how chromatin modifications influence each another.
Download or read book The DNA RNA and Histone Methylomes written by Stefan Jurga and published by Springer Nature. This book was released on 2019-08-28 with total page 624 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews the chemical, regulatory, and physiological mechanisms of protein arginine and lysine methyltransferases, as well as nucleic acid methylations and methylating enzymes. Protein and nucleic acid methylation play key and diverse roles in cellular signalling and regulating macromolecular cell functions. Protein arginine and lysine methyltransferases are the predominant enzymes that catalyse S-adenosylmethionine (SAM)-dependent methylation of protein substrates. These enzymes catalyse a nucleophilic substitution of a methyl group to an arginine or lysine side chain nitrogen (N) atom. Cells also have additional protein methyltransferases, which target other amino acids in peptidyl side chains or N-termini and C-termini, such as glutamate, glutamine, and histidine. All these protein methyltransferases use a similar mechanism. In contrast, nucleic acids (DNA and RNA) are substrates for methylating enzymes, which employ various chemical mechanisms to methylate nucleosides at nitrogen (N), oxygen (O), and carbon (C) atoms. This book illustrates how, thanks to there ability to expand their repertoire of functions to the modified substrates, protein and nucleic acid methylation processes play a key role in cells.
Download or read book Nuclear pre mRNA Processing in Plants written by A. S. N. Reddy and published by Springer Science & Business Media. This book was released on 2008-04-16 with total page 323 pages. Available in PDF, EPUB and Kindle. Book excerpt: During the last few years, tremendous progress has been made in understanding various aspects of pre-mRNA processing. This book, with contributions from leading scientists in this area, summarizes recent advances in nuclear pre-mRNA processing in plants. It provides researchers in the field, as well as those in related areas, with an up-to-date and comprehensive, yet concise, overview of the current status and future potential of this research in understanding plant biology.
Download or read book Long Noncoding RNAs in Plants written by Santosh Kumar Upadhyay and published by Academic Press. This book was released on 2020-11-13 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: The growth of human population has increased the demand for improved yield and quality of crops and horticultural plants. However, plant productivity continues to be threatened by stresses such as heat, cold, drought, heavy metals, UV radiations, bacterial and fungal pathogens, and insect pests. Long noncoding RNAs are associated with various developmental pathways, regulatory systems, abiotic and biotic stress responses and signaling, and can provide an alternative strategy for stress management in plants. Long Noncoding RNAs in Plants: Roles in development and stress provides the most recent advances in LncRNAs, including identification, characterization, and their potential applications and uses. Introductory chapters include the basic features and brief history of development of lncRNAs studies in plants. The book then provides the knowledge about the lncRNAs in various important agricultural and horticultural crops such as cereals, legumes, fruits, vegetables, and fiber crop cotton, and their roles and applications in abiotic and biotic stress management. - Includes the latest advances and research in long noncoding RNAs in plants - Provides alternative strategies for abiotic and biotic stress management in horticultural plants and agricultural crops - Focuses on the application and uses of long noncoding RNAs
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.
