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Investigating Phase Separation Mechanisms For Transcriptional Control
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Book Synopsis Investigating Phase Separation Mechanisms for Transcriptional Control by : Marc Böhning
Download or read book Investigating Phase Separation Mechanisms for Transcriptional Control written by Marc Böhning and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription of protein-coding genes by RNA polymerase (Pol) II is a highly coordinated process. In metazoan cells, transcription is regulated both at the initiation step by recruitment of the Pol II machinery as well as during early elongation by promoter-proximal pausing. Prior to transcription initiation, Pol II forms short-lived clusters near active gene promoters, but the underlying molecular basis has remained unknown. Pol II possesses a disordered C-terminal heptad repeat domain (CTD) that is essential for factor recruitment during the transcription cycle. CTD length is organism-spe...
Book Synopsis Enhancers and Phase Separation in the Control of Gene Expression by : John C. Manteiga
Download or read book Enhancers and Phase Separation in the Control of Gene Expression written by John C. Manteiga and published by . This book was released on 2020 with total page 148 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene regulation underlies the control of cell identity, development, and disease. Transcription of genes is regulated by DNA elements called enhancers, which are bound by transcription factors and coactivators, leading to the recruitment of RNA polymerase II and the production of RNA. Enhancers are thought to loop to specific gene promoters to stimulate transcription, but the mechanisms that cause enhancers to selectively loop to specific gene promoters is not well understood. In this thesis, I first describe new insights into enhancer-promoter loop specificity from studies examining the mechanisms that allow tumor-specific super-enhancers to loop to the MYC oncogene in diverse cancer types (Schuijers and Manteiga et al., 2018). While conducting these studies, it was proposed that super-enhancers and the factors associated with them form liquid-liquid phase-separated condensates. Following this proposal, I contributed to collaborative studies that strongly supported this model (Boija et al., 2018; Sabari et al., 2018, see Appendix I and II of this thesis). This model of transcription led me to ask how key transcriptional components could be recruited into super-enhancer condensates. I performed studies showing that the interaction of RNA polymerase II with these condensates involves the large heptapeptide repeat of the C-terminal domain (CTD) of the enzyme. Furthermore, these studies provided evidence that phosphorylation of the CTD, which is associated with the initiation to elongation transition, weakens these interactions, thus facilitating the transition of RNA polymerase II into different condensates involved in co-transcriptional splicing of the nascent transcript (Guo and Manteiga et al., 2019). These studies provide new insights into the mechanisms of enhancer-promoter interaction, roles for the RNA polymerase II CTD in the enzyme’s partitioning into nuclear condensates, and a role for phosphorylation in switching the nuclear condensate partitioning behavior of RNA polymerase II.
Book Synopsis Dynamical Heterogeneities in Glasses, Colloids, and Granular Media by : Ludovic Berthier
Download or read book Dynamical Heterogeneities in Glasses, Colloids, and Granular Media written by Ludovic Berthier and published by OUP Oxford. This book was released on 2011-07-14 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: Most of the solid materials we use in everyday life, from plastics to cosmetic gels exist under a non-crystalline, amorphous form: they are glasses. Yet, we are still seeking a fundamental explanation as to what glasses really are and to why they form. In this book, we survey the most recent theoretical and experimental research dealing with glassy physics, from molecular to colloidal glasses and granular media. Leading experts in this field present broad and original perspectives on one of the deepest mysteries of condensed matter physics, with an emphasis on the key role played by heterogeneities in the dynamics of glassiness.
Book Synopsis Mechanisms in Transcriptional Regulation by : Albert J. Courey
Download or read book Mechanisms in Transcriptional Regulation written by Albert J. Courey and published by John Wiley & Sons. This book was released on 2009-01-22 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mechanisms in Transcriptional Regulation provides a concisediscussion of the fundamental concepts in transcription and itsregulation. Covers RNA polymerases, transcriptional machinery, mechanismsof transcriptional activation, the histone code hypothesis, theepigenetic control of transcription, and combinatorial control insignaling and development Features over 80 figures available to download online Chapters include comprehensive reading lists, boxeshighlighting theoretical concepts and experimental methods andproblems designed to build and test understanding
Book Synopsis Differentiation of Embryonic Stem Cells by :
Download or read book Differentiation of Embryonic Stem Cells written by and published by Elsevier. This book was released on 2003-12-18 with total page 577 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume covers all aspects of embryonic stem cell differentiation, including mouse embryonic stem cells, mouse embryonic germ cells, monkey and human embryonic stem cells, and gene discovery. * Early commitment steps and generation of chimeric mice* Differentiation to mesoderm derivatives* Gene discovery by manipulation of mouse embryonic stem cells
Book Synopsis Disentangling Mechanisms of Genomic Regulation of Cell Functions at the Gene Level by : Hans Binder
Download or read book Disentangling Mechanisms of Genomic Regulation of Cell Functions at the Gene Level written by Hans Binder and published by MDPI. This book was released on 2021-04-22 with total page 132 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this Special Issue, we have several papers related to fuel-cell-based cogeneration systems; the management and control of fuel cell systems; the analysis, simulation, and operation of different types of fuel cells; modelling and online experimental validation; and the environment assessment of cathode materials in lithium-ion battery energy generation systems. A paper which gives a comprehensive review with technical guidelines for the design and operation of fuel cells, especially in a cogeneration system setup, which can be an important source of references for the optimal design and operation of various types of fuel cells in cogeneration systems, can also be found in this Special Issue.
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.
Book Synopsis Molecular Biology of The Cell by : Bruce Alberts
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Alternative Splicing and Disease by : Philippe Jeanteur
Download or read book Alternative Splicing and Disease written by Philippe Jeanteur and published by Springer Science & Business Media. This book was released on 2006-10-04 with total page 265 pages. Available in PDF, EPUB and Kindle. Book excerpt: Splicing of primary RNA transcript is a quasi-systematic step of gene expression in higher organisms. This is the first book to highlight the medical implications, i.e. diseases, caused by alternative splicing. Alternative splicing not only vastly increases protein diversity but also offers numerous opportunities for aberrant splicing events with pathological consequences. The book also outlines possible targets for therapy.
Book Synopsis Investigating Promoter-driven MRNA Localization and Translational Control During Stress by : Yang S. Chen
Download or read book Investigating Promoter-driven MRNA Localization and Translational Control During Stress written by Yang S. Chen and published by . This book was released on 2021 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: During times of unpredictable stress, organisms must adapt their gene expression to maximize survival. Along with changes in transcription, one conserved means of gene regulation during conditions that quickly represses translation is the formation of cytoplasmic phase-separated mRNP (messenger ribonucleoprotein) granules. Two well-known stress-induced mRNP granules are processing bodies (P-bodies) and stress granules. Previously, we identified that distinct steps in gene expression can be coupled during glucose starvation stress as promoter sequences in the nucleus are able to direct the subcellular localization to or excluded from the phase-separated granules and translatability of mRNAs in the cytosol. During my Ph.D., I have been investigating the underlying mechanisms of how promoter dictates the cytoplasmic fate of mRNAs during glucose starvation. Chapter 1 is a background introduction of the questions I asked. In chapter 2, I led a discovery of a promoter-directed mechanism mediated by AAA+ proteins Rvb1/Rvb2 that couple the transcription, mRNA cytoplasmic localization, and translation of select genes during glucose starvation. In chapter 3, colleagues and I reviewed recent findings regarding stress-related phase-separated granules and shared our insights. Chapter 4 describes 3 projects that aimed to answer the promoter-dictation question from other perspectives, such as expression timing and promoter motifs. Finally, Chapter 5 discusses insights and future directions for my thesis work. I anticipate that these studies will provide us with more insights into complex gene regulation during stressful and pathological conditions.
Download or read book Histone Genes written by Gary S. Stein and published by Wiley-Interscience. This book was released on 1984 with total page 520 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis HiC-Pro: an Optimized and Flexible Pipeline for Hi-C Data Processing by : Oldenburg Oldenburg Press
Download or read book HiC-Pro: an Optimized and Flexible Pipeline for Hi-C Data Processing written by Oldenburg Oldenburg Press and published by . This book was released on 2016-01-29 with total page 40 pages. Available in PDF, EPUB and Kindle. Book excerpt: HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps. In addition, HiC-Pro can use phased genotype data to build allele-specific contact maps. We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available at http://github.com/nservant/HiC-Pro.
Download or read book Fuzziness written by Monika Fuxreiter and published by Springer Science & Business Media. This book was released on 2012-03-07 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: Detailed characterization of fuzzy interactions will be of central importance for understanding the diverse biological functions of intrinsically disordered proteins in complex eukaryotic signaling networks. In this volume, Peter Tompa and Monika Fuxreiter have assembled a series of papers that address the issue of fuzziness in molecular interactions. These papers provide a broad overview of the phenomenon of fuzziness and provide compelling examples of the central role played by fuzzy interactions in regulation of cellular signaling processes and in viral infectivity. These contributions summarize the current state of knowledge in this new field and will undoubtedly stimulate future research that will further advance our understanding of fuzziness and its role in biomolecular interactions.
Download or read book C. Elegans II written by Donald L. Riddle and published by Firefly Books. This book was released on 1997 with total page 1252 pages. Available in PDF, EPUB and Kindle. Book excerpt: Defines the current status of research in the genetics, anatomy, and development of the nematode C. elegans, providing a detailed molecular explanation of how development is regulated and how the nervous system specifies varied aspects of behavior. Contains sections on the genome, development, neural networks and behavior, and life history and evolution. Appendices offer genetic nomenclature, a list of laboratory strain and allele designations, skeleton genetic maps, a list of characterized genes, a table of neurotransmitter assignments for specific neurons, and information on codon usage. Includes bandw photos. For researchers in worm studies, as well as the wider community of researchers in cell and molecular biology. Annotation copyrighted by Book News, Inc., Portland, OR
Book Synopsis Protein-Nucleic Acid Interactions by : Phoebe A. Rice
Download or read book Protein-Nucleic Acid Interactions written by Phoebe A. Rice and published by Royal Society of Chemistry. This book was released on 2008-05-22 with total page 417 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides both in-depth background and up-to-date information in this area. The chapters are organized by general themes and principles, written by experts who illustrate topics with current findings. Topics covered include: - the role of ions and hydration in protein-nucleic acid interactions - transcription factors and combinatorial specificity - indirect readout of DNA sequence - single-stranded nucleic acid binding proteins - nucleic acid junctions and proteins, - RNA protein recognition - recognition of DNA damage. It will be a key reference for both advanced students and established scientists wishing to broaden their horizons.
Download or read book RNA Tagging written by Manfred Heinlein and published by Humana. This book was released on 2021-08-08 with total page 490 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a compendium of state-of-the-art methods for the labeling, detection, and purification of RNA and RNA-protein complexes and thereby constitutes an important toolbox for researchers interested in understanding the complex roles of RNA molecules in development, signaling, and disease. Beginning with a section on in situ detection of RNA molecules using FISH techniques, the volume continues with parts exploring in vivo imaging of RNA transport and localization, imaging and analysis of RNA uptake and transport between cells, identification and analysis of RNA-binding proteins, guide RNAs in genome editing, as well as other specific analytical techniques. 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 Tagging: Methods and Protocols serves as a vital reference for researchers looking to further the increasingly important research in RNA biology.
Author :National Academies of Sciences, Engineering, and Medicine Publisher :National Academies Press ISBN 13 :0309437873 Total Pages :231 pages Book Rating :4.3/5 (94 download)
Book Synopsis Gene Drives on the Horizon by : National Academies of Sciences, Engineering, and Medicine
Download or read book Gene Drives on the Horizon written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2016-08-28 with total page 231 pages. Available in PDF, EPUB and Kindle. Book excerpt: Research on gene drive systems is rapidly advancing. Many proposed applications of gene drive research aim to solve environmental and public health challenges, including the reduction of poverty and the burden of vector-borne diseases, such as malaria and dengue, which disproportionately impact low and middle income countries. However, due to their intrinsic qualities of rapid spread and irreversibility, gene drive systems raise many questions with respect to their safety relative to public and environmental health. Because gene drive systems are designed to alter the environments we share in ways that will be hard to anticipate and impossible to completely roll back, questions about the ethics surrounding use of this research are complex and will require very careful exploration. Gene Drives on the Horizon outlines the state of knowledge relative to the science, ethics, public engagement, and risk assessment as they pertain to research directions of gene drive systems and governance of the research process. This report offers principles for responsible practices of gene drive research and related applications for use by investigators, their institutions, the research funders, and regulators.
