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Identifying Regulatory Elements Of Mrna Stability And Translation In The Nervous System
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Book Synopsis Identifying Regulatory Elements of MRNA Stability and Translation in the Nervous System by : Panid Sharifnia
Download or read book Identifying Regulatory Elements of MRNA Stability and Translation in the Nervous System written by Panid Sharifnia and published by . This book was released on 2015 with total page 14 pages. Available in PDF, EPUB and Kindle. Book excerpt: The mechanism from gene to protein, also known as the central dogma, has been one of the fundamental principles of biology. From the start of transcription, to the production of a mature RNA transcript, and to the translation of RNA into protein, regulatory steps control the entire process. Studies have revealed many layers of quality control, especially in regards to mRNA stability, decay, localization and translation. In the nervous system, the idea of mRNA regulation is tempting in regards to certain events, such as those that require quick responses to stimuli. Key experiments have identified ribosomes in dendrites of neurons. RNA binding proteins (RBPs) that localize cytoplasmically and sequences within the untranslated regions of mRNA that mediate binding of these RBPs that regulate its localization and stability. It has become apparent that both cis and trans elements contribute to this tightly controlled network of biology but few studies have examined this interaction in the nervous system of C. elegans. In the following chapters I will describe my studies using the model organism C. elegans to examine RBPs in the nervous system with specific regard to a transcription factor, cebp-1, whose 3'UTR has important roles in controlling its expression during development and adult stages, and two trans factors that may regulate cebp-1 through cebp-1's 3'UTR.
Book Synopsis Dynamic Regulation of RNA Stability During Drosophila Neurogenesis by :
Download or read book Dynamic Regulation of RNA Stability During Drosophila Neurogenesis written by and published by . This book was released on 2016 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: High-throughput gene expression and functional genomics technologies have revolutionized the study of gene expression during development. Yet traditional genome-wide approaches fail to address complex patterns of gene expression, which include both synthesis and decay. Post-transcriptional regulation is essential for temporal and spatial control of protein expression. Although candidate studies have revealed important mechanisms of post-transcriptional regulation of gene expression via mRNA decay, there is a lack of global information on mRNA decay during development. TU-decay technology allows measurement of genome-wide mRNA decay in intact Drosophila embryos, across all tissues and specifically in the nervous system. Using this approach neural-specific decay kinetics were observed, including stabilization of transcripts encoding regulators of axonogenesis and destabilization of transcripts encoding ribosomal proteins and histones. These data also demonstrate mRNA stability is correlated to physiologic properties of mRNAs; mRNAs that are predicted to be translated within axon growth cones or dendrites have long half-lives while mRNAs encoding transcription factors that regulate neurogenesis have short half-lives. Searches for candidate cis-regulatory elements identified enrichment of the Pumilio recognition element (PRE) in mRNAs encoding regulators of neurogenesis. Decreased expression of the RNA-binding protein, Pumilio, stabilizes predicted neural mRNA targets and presence of a 3'UTR PRE is sufficient to trigger mRNA decay in the nervous system. Clustering of mRNAs by codon content reveals a bias in codon usage related to physiological function and neural-specific mRNA decay kinetics; ribosomal proteins and histones have higher fractions of optimal codons while transcriptional regulators and mRNAs predicted to be localized to synapses have lower fractions of optimal codons. In Drosophila whole embryos, codon optimality is correlated with mRNA decay, while in the nervous system, codon-mediated effects on mRNA decay are attenuated. This work demonstrates a dynamic post-transcriptional program including mRNA decay allows fine-tuning of gene expression during neural development.
Book Synopsis Effects of Codon Usage on MRNA Translation and Decay by : Vladimir Presnyak
Download or read book Effects of Codon Usage on MRNA Translation and Decay written by Vladimir Presnyak and published by . This book was released on 2015 with total page 121 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene expression is a complex process regulated at many steps. One important step is the degradation of mRNA. The major pathways and enzymes in mRNA decay have been identified and described, but this has not yet led to a good understanding of the mechanisms for the observed differences in mRNA half-lives. Previous research has elucidated several examples of regulation through 3' UTR elements, but general mechanisms are not clear. The translation of mRNA is intricately linked to decay, thus the two processes must be evaluated together to uncover regulation that frequently affects both.We show that the choice of codons in the body of an mRNA can dictate the stability of the mRNA. Messages with a high percentage of optimal codons are relatively stable, whereas messages with a high percentage of non-optimal codons are relatively unstable. Reducing the optimal codon content of a stable message with naturally high occurrence of optimal codon leads to a reduction in stability, and conversely, increasing the optimal codon content of a naturally unstable message leads to an increase in stability. Similarly, inclusion of rare codons (a subset of non-optimal codons) in a message leads to a reduction in stability. Importantly, these effects appear to be dominant over previously-described 3' UTR regulatory elements. Finally, we show that optimal codon content is shared among groups of genes encoding proteins of related function, which have previously been found to have similar half-lives. Taken together, this evidence indicates that codon content can be an intrinsic regulatory feature of mRNAs affecting stability.Consistent with the role of codons in translation, we show that this method of regulation directly affects steps of translation. The reduction of mRNA stability caused by rare codon inclusion is dependent on translation. Concordantly, inclusion of non-optimal codons in reporters leads to reduction in protein output that is greater than the decrease in mRNA levels. These strongly suggest that translation is the primary target of this method of regulation. To determine the precise step affected, we demonstrate that the changes in optimal codon content have a direct effect on the rate of ribosome translocation on these messages. The coupling of translation to decay makes the changes in half-lives possible and further amplifies the effect of the regulation.This work demonstrates the powerful mechanisms of regulation possible through codon usage, suggesting that this may be an evolutionary feature that allows cells to regulate expression of proteins without changes to the sequence or the need for external control sequences. Additionally, it implicates the ribosome as the key point of regulation, not only for translation, but for mRNA stability as well.
Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Untranslated Gene Regions and Other Non-coding Elements by : Lucy W. Barrett
Download or read book Untranslated Gene Regions and Other Non-coding Elements written by Lucy W. Barrett and published by Springer Science & Business Media. This book was released on 2013-06-26 with total page 63 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Kaufman’s Atlas of Mouse Development Supplement by : Richard Baldock
Download or read book Kaufman’s Atlas of Mouse Development Supplement written by Richard Baldock and published by Academic Press. This book was released on 2015-09-23 with total page 343 pages. Available in PDF, EPUB and Kindle. Book excerpt: Kaufman's Atlas of Mouse Development: With Coronal Sections continues the stellar reputation of the original Atlas by providing updated, in-depth anatomical content and morphological views of organ systems.The publication offers written descriptions of the developmental origins of the organ systems alongside high-resolution images for needed visualization of developmental processes. Matt Kaufman himself has annotated the coronal images in the same clear, meticulous style of the original Atlas. Kaufman's Atlas of Mouse Development: With Coronal Sections follows the original Atlas as a continuation of the standard in the field for developmental biologists and researchers across biological and biomedical sciences studying mouse development. Provides high-resolution images for best visualization of key developmental processes and structures Offers in-depth anatomy and morphological views of organ systems Written descriptions convey developmental origins of the organ systems
Book Synopsis From Molecules to Networks by : Ruth Heidelberger
Download or read book From Molecules to Networks written by Ruth Heidelberger and published by Academic Press. This book was released on 2009-01-27 with total page 654 pages. Available in PDF, EPUB and Kindle. Book excerpt: An understanding of the nervous system at virtually any level of analysis requires an understanding of its basic building block, the neuron. From Molecules to Networks provides the solid foundation of the morphologic, biochemical, and biophysical properties of nerve cells. All chapters have been thoroughly revised for this second edition to reflect the significant advances of the past 5 years. The new edition expands on the network aspects of cellular neurobiology by adding a new chapter, Information Processing in Neural Networks, and on the relation of cell biological processes to various neurological diseases. The new concluding chapter illustrates how the great strides in understanding the biochemical and biophysical properties of nerve cells have led to fundamental insights into important aspects of neurodegenerative disease. - Written and edited by leading experts in the field, the second edition completely and comprehensively updates all chapters of this unique textbook - Discusses emerging new understanding of non-classical molecules that affect neuronal signaling - Full colour, professional graphics throughout - Includes two new chapters: Information Processing in Neural Networks - describes the principles of operation of neural networks and the key circuit motifs that are common to many networks in the nervous system. Molecular and Cellular Mechanisms of Neurodegenerative Disease - introduces the progress made in the last 20 years in elucidating the cellular and molecular mechanisms underlying brain disorders, including Amyotrophic Lateral Sclerosis (ALS), Parkinson disease, and Alzheimer's disease
Book Synopsis Serotonin Receptors in Neurobiology by : Amitabha Chattopadhyay
Download or read book Serotonin Receptors in Neurobiology written by Amitabha Chattopadhyay and published by CRC Press. This book was released on 2007-05-17 with total page 230 pages. Available in PDF, EPUB and Kindle. Book excerpt: A number of developments spanning a multitude of techniques makes this an exciting time for research in serotonin receptors. A comprehensive review of the subject from a multidisciplinary perspective, Serotonin Receptors in Neurobiology is among the first books to include information on serotonin receptor knockout studies. With contributions from l
Book Synopsis Biology of the NMDA Receptor by : Antonius M. VanDongen
Download or read book Biology of the NMDA Receptor written by Antonius M. VanDongen and published by CRC Press. This book was released on 2008-10-29 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: The NMDA receptor plays a critical role in the development of the central nervous system and in adult neuroplasticity, learning, and memory. Therefore, it is not surprising that this receptor has been widely studied. However, despite the importance of rhythms for the sustenance of life, this aspect of NMDAR function remains poorly studied. Written
Book Synopsis Acetylcholinesterase: Old Questions and New Developments by : Karl Tsim
Download or read book Acetylcholinesterase: Old Questions and New Developments written by Karl Tsim and published by Frontiers E-books. This book was released on with total page 120 pages. Available in PDF, EPUB and Kindle. Book excerpt: Acetylcholinesterase (AChE) is a primary regulator of cholinergic signaling within and out of the central nervous system. It has been studied extensively for several decades, yet many basic questions about its regulation, composition and functions remain open. Thus, neither the full impact of AChE’s activities on neuronal development, maintenance and functioning nor the reasons for why and how different AChE molecular forms are being synthesized and degraded are fully known yet, although recent evidence suggests the involvement of micro-RNA regulators in both of these aspects. The identification of the anchoring proteins, PRiMA and ColQ, stimulates studies on AChE’s assembly and its specific localization in the brain and muscle. Additionally, non-cholinergic function(s) of AChE has been proposed as relevant both for neuronal differentiation and cognitive functioning, whereas transgenic engineering, recombinant production and structure-function analyses of this enzyme’s variants with various inhibitors paved new avenues for the development of novel Alzheimer’s disease therapeutics, agricultural pesticides and prophylactics in anticipation of warfare agent exposure. The aims of this Research Topic is to provide a forum for experts in the field to critically discuss recent developments in AChE studies, initiate global critiques of the current views for resolving the fundamental questions in AChE research and promote the development of novel versions and uses of AChE-targeted agents. Topics of interest include but are not limited to: (i) post-transcriptional regulation of AChE; (ii) the non-cholinergic functions of AChE; and (iii) anti-AChE inhibitors and diseases.
Book Synopsis Regulation of Gene Expression by Small RNAs by : Rajesh K. Gaur
Download or read book Regulation of Gene Expression by Small RNAs written by Rajesh K. Gaur and published by CRC Press. This book was released on 2009-04-27 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: New Findings Revolutionize Concepts of Gene FunctionEndogenous small RNAs have been found in various organisms, including humans, mice, flies, worms, fungi, and bacteria. Furthermore, it's been shown that microRNAs acting as cellular rheostats have the ability to modulate gene expression. In higher eukaryotes, microRNAs may regulate as much as 50 p
Book Synopsis Biology for AP ® Courses by : Julianne Zedalis
Download or read book Biology for AP ® Courses written by Julianne Zedalis and published by . This book was released on 2017-10-16 with total page 1923 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biology for AP® courses covers the scope and sequence requirements of a typical two-semester Advanced Placement® biology course. The text provides comprehensive coverage of foundational research and core biology concepts through an evolutionary lens. Biology for AP® Courses was designed to meet and exceed the requirements of the College Board’s AP® Biology framework while allowing significant flexibility for instructors. Each section of the book includes an introduction based on the AP® curriculum and includes rich features that engage students in scientific practice and AP® test preparation; it also highlights careers and research opportunities in biological sciences.
Book Synopsis Gene Therapy of the Central Nervous System: From Bench to Bedside by : Michael G. Kaplitt
Download or read book Gene Therapy of the Central Nervous System: From Bench to Bedside written by Michael G. Kaplitt and published by Elsevier. This book was released on 2005-11-11 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Few areas of biomedical research provide greater opportunities for radically new therapies for devastating diseases that have evaded treatment so far than gene therapy. This is particularly true for the brain and nervous system, where gene transfer has become a key technology for basic research and has recently been translated to human therapy in several landmark clinical trials. Gene Therapy of the Central Nervous System: From Bench to Bedside represents the first definitive volume on this subject. Edited by two pioneers of neurological gene therapy, this volume contains contributions by leaders who helped create this field and are expanding the promise of gene therapy for the future of basic and clinical neuroscience. Drawing upon this extensive collective experience, this book provides clear and informative reviews on a variety of subjects of interest to anyone exploring or using gene therapy for neurobiological applications in research and clinical praxis.* Presents gene transfer technologies with particular emphases upon novel vehicles, immunological issues and the role of gene therapy in stem cells* Discusses preclinical areas that are likely to translate into clinical studies in the near future, including epilepsy, pain and amyotrophic lateral sclerosis* Includes "insider" information on technological and regulatory issues which can often limit effective translation of even the most promising idea into clinical use
Book Synopsis Localized RNAs by : Howard D. Lipshitz
Download or read book Localized RNAs written by Howard D. Lipshitz and published by R G Landes Company. This book was released on 1995 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book RNA Chaperones written by Tilman Heise and published by . This book was released on 2020 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a wide spectrum of methods to study RNA chaperones in vitro, at the single molecule level, and protocols useful for cell-based assays. Beginning with a section on a number of bacterial proteins for study, the volume also explores proteins from eukaryotic cells and how to delve into the complex interactions between RNA chaperones and the folding and unfolding of proteins. 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 Chaperones: Methods and Protocols serves as an ideal guide for scientists and students interested in RNA biology and RNA chaperones. Chapter 3 is available Open Access under a CC-BY 4.0 license via link.springer.com.
Book Synopsis Unsupervised Feature Extraction Applied to Bioinformatics by : Y-h. Taguchi
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.
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.
