The Functions Of The Rna Polymerase Ii Ctd In Transcription And Rna Processing

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The Functions of the RNA Polymerase II CTD in Transcription and RNA Processing

Author :
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (926 download)

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Book Synopsis The Functions of the RNA Polymerase II CTD in Transcription and RNA Processing by :

Download or read book The Functions of the RNA Polymerase II CTD in Transcription and RNA Processing written by and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Finally, Chapter 4 describes what we have found the functions of CTD Tyr 1. Using the DT40-Rpb1 cells, I created stable cell lines expressing an Rpb1 with all Tyr residues mutated to phenylalanine (Phe). We found these cells were inviable, and the mutant Rpb1-Y1F was degraded to a CTD-less protein. Interestingly, the instability of Rpb1-Y1F was restored by reintroduction of one Tyr residue at the last heptad repeat. Further analysis provided evidence showing the involvement of Tyr phosphorylation in preventing Rpb1 from degradation by the 20S proteasome. Next, using ChIP assay, we showed Tyr phosphorylation was detected mostly at promoters, indicating a function of Tyr phosphorylation in transcription initiation. Indeed, transcription initiation defects were uncovered by assessing the recruitment of general transcription factors in cells with Y1F mutation. Extending this, we found an accumulation of upstream antisense RNAs in about one hundred reference genes by RNA-Seq analysis.

RNA Exosome

Author : Torben Heick Jensen
Publisher : Springer Science & Business Media
ISBN 13 : 1441978410
Total Pages : 161 pages
Book Rating : 4.4/5 (419 download)

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Book Synopsis RNA Exosome by : Torben Heick Jensen

Download or read book RNA Exosome written by Torben Heick Jensen and published by Springer Science & Business Media. This book was released on 2011-06-29 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Transcription and Splicing

Author : B. D. Hames
Publisher : Oxford University Press, USA
ISBN 13 :
Total Pages : 238 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Transcription and Splicing by : B. D. Hames

Download or read book Transcription and Splicing written by B. D. Hames and published by Oxford University Press, USA. This book was released on 1988 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book gives a co-ordinated review of our present knowledge of eukaryotic RNA synthesis.

The Role of RNA Polymerase II Phosphorylation in the Early Stages of Transcription

Author : Jonathan Donald Chesnut
Publisher :
ISBN 13 :
Total Pages : 280 pages
Book Rating : 4.:/5 (54 download)

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Book Synopsis The Role of RNA Polymerase II Phosphorylation in the Early Stages of Transcription by : Jonathan Donald Chesnut

Download or read book The Role of RNA Polymerase II Phosphorylation in the Early Stages of Transcription written by Jonathan Donald Chesnut and published by . This book was released on 1994 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Role of the RNA Polymerase II C-terminal Domain in Transcription Termination and Function of Spt5 in 3' RNA-processing Factor Recruitment

Download Role of the RNA Polymerase II C-terminal Domain in Transcription Termination and Function of Spt5 in 3' RNA-processing Factor Recruitment PDF Online Free

Author : Amelie Erna Schreieck
Publisher :
ISBN 13 :
Total Pages : 196 pages
Book Rating : 4.:/5 (881 download)

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Book Synopsis Role of the RNA Polymerase II C-terminal Domain in Transcription Termination and Function of Spt5 in 3' RNA-processing Factor Recruitment by : Amelie Erna Schreieck

Download or read book Role of the RNA Polymerase II C-terminal Domain in Transcription Termination and Function of Spt5 in 3' RNA-processing Factor Recruitment written by Amelie Erna Schreieck and published by . This book was released on 2013 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Structural Heterogeneity in the RNA Polymerase II C-Terminal Domain

Author : Bede Portz
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (1 download)

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Book Synopsis Structural Heterogeneity in the RNA Polymerase II C-Terminal Domain by : Bede Portz

Download or read book Structural Heterogeneity in the RNA Polymerase II C-Terminal Domain written by Bede Portz and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA polymerase II contains a repetitive and intrinsically disordered C-Terminal Domain (CTD) composed of heptad repeats of the consensus sequence YSPTSPS. The CTD can be heavily phosphorylated and serves as a scaffold, interacting with factors involved in transcription initiation, elongation, termination, RNA processing and chromatin modification. Despite its role as a nexus of eukaryotic gene regulation, the structure of the CTD and the structural implications of CTD phosphorylation, are poorly understood. Additionally, there is an increasing awareness of the importance of intrinsically disordered proteins (IDPs) that function without adopting a stably folded structure. Here I present a biophysical and biochemical interrogation of the structure of the full-length CTD of D. melanogaster, which I conclude is a compact random coil. I find that the repetitive CTD is structurally heterogeneous as evidenced by a discontinuous pattern of cutting in limited proteolysis assays. Small Angle X-Ray scattering (SAXS) is a method ideally suited for the structural interrogation of large IDPs and can be employed to measure the size of a protein and to monitor structural changes in response to post-translational modification. Using SAXS I determined that phosphorylation by the kinase P-TEFb caused an increase in CTD radius and stiffness. Limited proteolysis of the phosphorylated CTD showed these gross structural changes are accompanied by increased protease accessibility and an alteration in relative protease accessibility across the length of the CTD.Additionally, we show that the human CTD is also structurally heterogeneous and able to substitute for the Drosophila melanogaster CTD in supporting the development of flies to adulthood. These finding implicate conserved structural organization, not a precise array of heptad motifs, as important to CTD function.The CTD is attached to the catalytic core of Pol II via a linker. I show that this linker is more compact than the CTD repeats and serves as an independent structural unit. The phosphorylated linker-CTD remains flexible relative to the phosphorylated CTD alone. Together, these results support a mechanism by which phosphorylation reduces the conformational entropy of the CTD, generating a more binding competent dock for CTD:protein interactions, with the linker region maintaining the ability of CTD bound factors to sample the 3-dimensional space which may be required for RNA processing and histone modification.The data described herein represent the most thorough structural characterization to date of the full length CTD on the global and local scales, examining both the overall size and local structural organization of the CTD. These studies establish the Drosophila CTD as an attractive model for the biophysical, biochemical and genetic interrogation of the structure and function of the CTD from a developmentally complex organism.

RNA Processing

Author : Paula Grabowski
Publisher : BoD – Books on Demand
ISBN 13 : 9533075570
Total Pages : 262 pages
Book Rating : 4.5/5 (33 download)

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Book Synopsis RNA Processing by : Paula Grabowski

Download or read book RNA Processing written by Paula Grabowski and published by BoD – Books on Demand. This book was released on 2011-08-29 with total page 262 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA functions broadly as informational molecule, genome, enzyme and machinery for RNA processing. While these functions reflect ancient activities, they also remain vital components of contemporary biochemical pathways. In eukaryotic cells RNA processing impacts the biogenesis of RNA molecules of essentially every shape and function. The collection of articles in this volume describes the current state of understanding of the broad array of RNA processing events in animal and plant cells, key unanswered questions, and cutting edge approaches available to address these questions. Some questions discussed in this volume include, how viruses subvert the RNA processing machinery of the host cell, how the coordination of co-transcriptional RNA processing is regulated at the level of chromatin, the status of RNA processing in plant organelles, and how micro RNA machinery is biosynthesized and regulated.

Protein Phosphorylation in Human Health

Author : Cai Huang
Publisher : BoD – Books on Demand
ISBN 13 : 9535107372
Total Pages : 482 pages
Book Rating : 4.5/5 (351 download)

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Book Synopsis Protein Phosphorylation in Human Health by : Cai Huang

Download or read book Protein Phosphorylation in Human Health written by Cai Huang and published by BoD – Books on Demand. This book was released on 2012-09-06 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: 15 chapters on protein phosphorylation and human health written by expert scientists. Covers most important research hot points, such as Akt, AMPK and mTOR. Bridges the basic protein phosphorylation pathways with human health and diseases. Detailed and comprehensive text with excellent figure illustration.

Introduction to Epigenetics

Author : Renato Paro
Publisher : Springer Nature
ISBN 13 : 3030686701
Total Pages : 215 pages
Book Rating : 4.0/5 (36 download)

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Book Synopsis Introduction to Epigenetics by : Renato Paro

Download or read book Introduction to Epigenetics written by Renato Paro and published by Springer Nature. This book was released on 2021-03-23 with total page 215 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access textbook leads the reader from basic concepts of chromatin structure and function and RNA mechanisms to the understanding of epigenetics, imprinting, regeneration and reprogramming. The textbook treats epigenetic phenomena in animals, as well as plants. Written by four internationally known experts and senior lecturers in this field, it provides a valuable tool for Master- and PhD- students who need to comprehend the principles of epigenetics, or wish to gain a deeper knowledge in this field. After reading this book, the student will: Have an understanding of the basic toolbox of epigenetic regulation Know how genetic and epigenetic information layers are interconnected Be able to explain complex epigenetic phenomena by understanding the structures and principles of the underlying molecular mechanisms Understand how misregulated epigenetic mechanisms can lead to disease

HIV-1 Latency

Author : Guido Silvestri
Publisher : Springer
ISBN 13 : 303002816X
Total Pages : 253 pages
Book Rating : 4.0/5 (3 download)

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Book Synopsis HIV-1 Latency by : Guido Silvestri

Download or read book HIV-1 Latency written by Guido Silvestri and published by Springer. This book was released on 2018-10-11 with total page 253 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume summarizes recent advances in understanding the mechanisms of HIV-1 latency, in characterizing residual viral reservoirs, and in developing targeted interventions to reduce HIV-1 persistence during antiretroviral therapy. Specific chapters address the molecular mechanisms that govern and regulate HIV-1 transcription and latency; assays and technical approaches to quantify viral reservoirs in humans and animal models; the complex interchange between viral reservoirs and the host immune system; computational strategies to model viral reservoir dynamics; and the development of therapeutic approaches that target viral reservoir cells. With contributions from an interdisciplinary group of investigators that cover a broad spectrum of subjects, from molecular virology to proof-of-principle clinical trials, this book is a valuable resource for basic scientists, translational investigators, infectious-disease physicians, individuals living with HIV/AIDS and the general public.

Spliceosomal Pre-mRNA Splicing

Author : Klemens J. Hertel
Publisher : Humana
ISBN 13 : 9781627039796
Total Pages : 0 pages
Book Rating : 4.0/5 (397 download)

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Book Synopsis Spliceosomal Pre-mRNA Splicing by : Klemens J. Hertel

Download or read book Spliceosomal Pre-mRNA Splicing written by Klemens J. Hertel and published by Humana. This book was released on 2014-02-21 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing a guide to classical experimental approaches to decipher splicing mechanisms and experimental strategies that rely on novel multi-disciplinary approaches, Spliceosomal Pre-mRNA Splicing: Methods and Protocols describes the theory of alternative pre-mRNA splicing in seven introductory chapters and then introduces protocols and their theoretical background relevant for a variety of experimental research. These protocol chapters cover basic methods to detect splicing events, analyses of alternative pre-mRNA splicing in vitro and in vivo manipulation of splicing events and high-throughput and bioinformatic analyses of alternative splicing. 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 protocols and tips on troubleshooting and avoiding known pitfalls. Comprehensive and practical, Spliceosomal Pre-mRNA Splicing: Methods and Protocols will aid newcomers and seasoned molecular biologists in understanding the fascinating world of alternative splicing with the ultimate goal of paving the way for many new discoveries to come.

RNA Polymerase II Controls Transcription Dynamics

Author :
Publisher :
ISBN 13 :
Total Pages : 261 pages
Book Rating : 4.:/5 (849 download)

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Book Synopsis RNA Polymerase II Controls Transcription Dynamics by :

Download or read book RNA Polymerase II Controls Transcription Dynamics written by and published by . This book was released on 2013 with total page 261 pages. Available in PDF, EPUB and Kindle. Book excerpt: The C-terminal domain (CTD) of RNA polymerase II (Pol II) consists of conserved heptapeptide repeats that are subject to sequential waves of posttranslational modifications during specific stages of the transcription cycle. These patterned modifications have led to the postulation of the CTD code hypothesis, where stage-specific patterns define a spatiotemporal code that is recognized by the appropriate interacting partners. This thesis summarizes our efforts to define the CTD code, identify the writers and erasers, and explore the function of the code during transcription. We examined the genome-wide distributions of the phospho-serine modifications. We found unique profile clusters for the "early" serine 5 phosphorylation (Ser5-P), the "mid" serine 7 phosphorylation (Ser7-P), and the "late" serine 2 phosphorylation (Ser2-P). We also identified gene class-specific patterns and find widespread co-occurrence of the CTD marks. These phosphorylation marks are placed by an array of phospho-serine kinases. We identified Kin28 (CDK7) as a Ser7-P kinase, and specific inhibition of Kin28 caused a significant decrease in Ser7-P levels at promoters. However, the promoter-distal Ser7-P marks are not remnants of early phosphorylation by Kin28. Instead, we find that Bur1 (CDK9) is positioned to phosphorylate Ser7 within the coding regions. Next, we investigated the phosphatases that erase the CTD code. The importance of these enzymes is emphasized by our observation that an inability to remove Ser7-P marks is lethal. We identified Ssu72 as a Ser7-P phosphatase, and inactivation of Ssu72 triggers a drastic remodeling of Ser7-P distributions across protein-coding and non-coding genes. Furthermore, we report that removal of all phospho-CTD marks during transcription termination is mechanistically coupled. An inability to remove these marks prevents Pol II from terminating efficiently at both gene classes and also impedes proper transcription initiation. Interestingly, Ssu72 seems to be enriched within introns, peaking at the 3' splice site. Interestingly, we do not find polymerase pausing at the 3' splice site or at the terminal exons, as has been previously reported. Instead, we believe Ssu72 may be involved in facilitating the cotranscriptional recruitment of splicing factors by establishing a chromatin state accommodating to splicing.

Protein Conformational Dynamics

Author : Ke-li Han
Publisher : Springer Science & Business Media
ISBN 13 : 3319029703
Total Pages : 488 pages
Book Rating : 4.3/5 (19 download)

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Book Synopsis Protein Conformational Dynamics by : Ke-li Han

Download or read book Protein Conformational Dynamics written by Ke-li Han and published by Springer Science & Business Media. This book was released on 2014-01-20 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.

Long Noncoding RNAs in Plants

Author : Santosh Kumar Upadhyay
Publisher : Academic Press
ISBN 13 : 0128214635
Total Pages : 390 pages
Book Rating : 4.1/5 (282 download)

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Book Synopsis Long Noncoding RNAs in Plants by : Santosh Kumar Upadhyay

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 390 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

The Nature of RNA Polymerase II Interactions Mediated by the CTD in the Assembly of Transcription Complexes

Author : Mona Eunsung Kang
Publisher :
ISBN 13 :
Total Pages : 304 pages
Book Rating : 4.:/5 (56 download)

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Book Synopsis The Nature of RNA Polymerase II Interactions Mediated by the CTD in the Assembly of Transcription Complexes by : Mona Eunsung Kang

Download or read book The Nature of RNA Polymerase II Interactions Mediated by the CTD in the Assembly of Transcription Complexes written by Mona Eunsung Kang and published by . This book was released on 1995 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Medical Biochemistry

Author : Antonio Blanco
Publisher : Academic Press
ISBN 13 : 0323916007
Total Pages : 910 pages
Book Rating : 4.3/5 (239 download)

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Book Synopsis Medical Biochemistry by : Antonio Blanco

Download or read book Medical Biochemistry written by Antonio Blanco and published by Academic Press. This book was released on 2022-03-23 with total page 910 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second edition of Medical Biochemistry is supported by more than 45 years of teaching experience, providing coverage of basic biochemical topics, including the structural, physical, and chemical properties of water, carbohydrates, lipids, proteins, and nucleic acids. In addition, the general aspects of thermodynamics, enzymes, bioenergetics, and metabolism are presented in straightforward and easy-to-comprehend language. This book ties these concepts into more complex aspects of biochemistry using a systems approach, dedicating chapters to the integral study of biological phenomena, including cell membrane structure and function, gene expression and regulation, protein synthesis and post-translational modifications, metabolism in specific organs and tissues, autophagy, cell receptors, signal transduction pathways, biochemical bases of endocrinology, immunity, vitamins and minerals, and hemostasis. The field of biochemistry is continuing to grow at a fast pace. This edition has been revised and expanded with all-new sections on the cell plasma membrane, the human microbiome, autophagy, noncoding, small and long RNAs, epigenetics, genetic diseases, virology and vaccines, cell signaling, and different modes of programmed cell death. The book has also been updated with full-color figures, new tables, chapter summaries, and further medical examples to improve learning and better illustrate the concepts described and their clinical significance. Integrates basic biochemistry principles with molecular biology and molecular physiology Illustrates basic biochemical concepts through medical and physiological examples Utilizes a systems approach to understanding biological phenomena Fully updated for recent studies and expanded to include clinically relevant examples and succinct chapter summaries

Macromolecular Protein Complexes II: Structure and Function

Author : J. Robin Harris
Publisher : Springer Nature
ISBN 13 : 3030281515
Total Pages : 657 pages
Book Rating : 4.0/5 (32 download)

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Book Synopsis Macromolecular Protein Complexes II: Structure and Function by : J. Robin Harris

Download or read book Macromolecular Protein Complexes II: Structure and Function written by J. Robin Harris and published by Springer Nature. This book was released on 2020-01-14 with total page 657 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book follows on from Volume 83 in the SCBI series (“Macromolecular Protein Complexes”), and addresses several important topics (such as the Proteasome, Anaphase Promoting Complex, Ribosome and Apoptosome) that were not previously included, together with a number of additional exciting topics in this rapidly expanding field of study. Although the first SCBI Protein Complex book focused on soluble protein complexes, the second (Vol. 87)addressed Membrane Complexes, and the third (Vol. 88) put the spotlight on Viral Protein and Nucleoprotein Complexes, a number of membrane, virus and even fibrillar protein complexes have been be considered for inclusion in the present book. A further book is also under preparation that follows the same pattern, in an attempt to provide a thorough coverage of the subject. Chapter 9 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.