Download or read book Structure and Dynamics of Modified Nucleosomes Under Epigenetic Regulation written by Havva Kohestani and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Chromatin Regulation and Dynamics written by Anita Göndör and published by Academic Press. This book was released on 2016-10-25 with total page 498 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chromatin Regulation and Dynamics integrates knowledge on the dynamic regulation of primary chromatin fiber with the 3D nuclear architecture, then connects related processes to circadian regulation of cellular metabolic states, representing a paradigm of adaptation to environmental changes. The final chapters discuss the many ways chromatin dynamics can synergize to fundamentally contribute to the development of complex diseases. Chromatin dynamics, which is strategically positioned at the gene-environment interface, is at the core of disease development. As such, Chromatin Regulation and Dynamics, part of the Translational Epigenetics series, facilitates the flow of information between research areas such as chromatin regulation, developmental biology, and epidemiology by focusing on recent findings of the fast-moving field of chromatin regulation. Presents and discusses novel principles of chromatin regulation and dynamics with a cross-disciplinary perspective Promotes crosstalk between basic sciences and their applications in medicine Provides a framework for future studies on complex diseases by integrating various aspects of chromatin biology with cellular metabolic states, with an emphasis on the dynamic nature of chromatin and stochastic principles Integrates knowledge on the dynamic regulation of primary chromatin fiber with 3D nuclear architecture, then connects related processes to circadian regulation of cellular metabolic states, representing a paradigm of adaptation to environmental changes
Download or read book Towards a Mechanism of Epigenetic Regulation by Chemically Modified Nucleosomes written by Samuel Bowerman and published by . This book was released on 2018 with total page 316 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Nucleosome Structure and Dynamics Studied with Single molecule Methods written by Sijie Wei and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Nucleosomes, the basic building blocks of chromatin, condense linear DNA eventually into a chromosome, and serve as the platform of epigenetic information. DNA and histone modifications, histone variants, and nucleosome positioning form an epigenetic signal network, regulate various genome transactions such as transcription, replication, and DNA repair. It is crucial to learn how these epigenetic marks affect the structure and dynamic of nucleosomes and chromatin in order to understand their biophysical roles in epigenetic mechanisms for gene regulation.Single molecule fluorescence methods provide efficient means to study unsynchronized dynamics in a complex system. Fluorescence resonance energy transfer (FRET), serving as a molecular ruler, has helped solving many important biological problems. Variations of single molecule FRET (smFRET) are good methods to study the structure and dynamics of nucleosome, while there are still some technical barriers to overcome. I have developed two smFRET methods to study two problems in nucleosome biophysics. One method I developed was to study fast and unsynchronized nucleosomal DNA termini opening motion and how it is affected by salt conditions, DNA sequence, and histone H3 variation. My results indicate that nucleosome termini repeatedly open and close at 0.3~1 ms-1. The kinetics depends on salt and DNA-histone interactions but not much on DNA sequence, suggesting that this dynamics is universal, imposing the ultimate kinetic limit to gene access that can be modulated by histone variation or modification.The other method was to study transient interactions between nucleosomes and how they are affected by two histone acetylation marks and one SUMOylation mark. I found that internucleosomal interactions are inhibited by H4K16 acetylation (H4K16ac), H4K12 acetylation (H4K12ac), and H4K12 sumoylation (suH4). However, my single molecule observation suggests that the extents of inhibition in the long- and short-range internucleosomal interactions are different in each case. suH4 and H4K16ac inhibit long-range internucleosomal interactions more than the H4K12ac case. H4K16ac and H4K12ac inhibit short-range internucleosomal interactions more than the suH4 case. These observations led us to a conclusion that H4K16 acetylation inhibits nucleosome array folding by weakening both long- and short-range internucleosomal interactions, making this acetylation the most efficient way to inhibit nucleosome array folding, while H4K12ac and suH4 weaken mainly short-range and long-range interactions, respectively, making them less efficient in array folding inhibition than H4K16ac.My research demonstrates that single molecule methods can provide efficient means to study fast and unsynchronized dynamics of complex systems that are difficult to probe with conventional structural biology tools.
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
Download or read book Chromatin and Disease written by Tapas K. Kundu and published by Springer Science & Business Media. This book was released on 2007-05-04 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book includes a collection of articles with the broad theme of disease connection to chromatin structure and function. It elaborates on the molecular pharmacology of the drugs targeting chromatin structure and its components. The book contains up-to-date information about the chromatin structure and chromatin related diseases and drug functions. This work is the first endeavor to present different aspects encompassing the above theme.
Download or read book Nucleosome Dynamics in Epigenetic Regulation written by Cizhong Jiang and published by . This book was released on 2015-10-06 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Fundamentals of Chromatin written by Jerry L. Workman and published by Springer Science & Business Media. This book was released on 2013-12-04 with total page 594 pages. Available in PDF, EPUB and Kindle. Book excerpt: While there has been an increasing number of books on various aspects of epigenetics, there has been a gap over the years in books that provide a comprehensive understanding of the fundamentals of chromatin. Chromatin is the combination of DNA and proteins that make up the genetic material of chromosomes. Its primary function is to package DNA to fit into the cell, to strengthen the DNA to prevent damage, to allow mitosis and meiosis, and to control the expression of genes and DNA replication. The audience for this book is mainly newly established scientists and graduate students. Rather than going into the more specific areas of recent research on chromatin the chapters in this book give a strong, updated groundwork about the topic. Some the fundamentals that this book will cover include the structure of chromatin and biochemistry and the enzyme complexes that manage it.
Download or read book Chromatin written by Ralf Blossey and published by CRC Press. This book was released on 2017-08-04 with total page 204 pages. Available in PDF, EPUB and Kindle. Book excerpt: An invaluable resource for computational biologists and researchers from other fields seeking an introduction to the topic, Chromatin: Structure, Dynamics, Regulation offers comprehensive coverage of this dynamic interdisciplinary field, from the basics to the latest research. Computational methods from statistical physics and bioinformatics are detailed whenever possible without lengthy recourse to specialized techniques.
Download or read book Epigenetic Contributions in Autoimmune Disease written by Esteban Ballestar and published by Springer. This book was released on 2011-08-23 with total page 182 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume focuses on the relevance of epigenetic mechanisms in autoimmune disease. It provides new directions for future research in autoimmune disease.
Download or read book Nucleosome Structure and Dynamics Investigated with Single Molecule Methods written by JaeHyoun Lee and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Nucleosomes are the repeating units that comprise chromatin, the DNA-histone complex that holds the genetic information in eukaryotic cell nuclei. Eukaryotic DNA wraps around a histone octamer protein core forming a superhelical structure, thereby being packaged into the nucleosome. The nucleosome imposes a physical barrier to nuclear transactions that require access to DNA including transcription, DNA replication, and DNA repair. Therefore, nucleosomes must at least in part disassemble during these transactions. It is widely accepted that nucleosomes undergo dynamic changes in order to allow for regulated access to genes. These changes include structural changes that lead to regulated nucleosome disassembly or exchanges of histones with histone variants that trigger cascading biochemical events on the nucleosome. These changes are often strongly coupled to post- translational modifications of histones and DNA methylation. Histone chaperones and nucleosome remodelers can facilitate these nucleosome dynamics by depositing or evicting histones in and out of the nucleosome. Understanding the nature of these dynamical changes in the nucleosome and how they are coupled to chemical modifications to the nucleosome are crucial to understanding eukaryotic gene regulation mechanisms.In this dissertation, I present my PhD research on the structure and the dynamics of nucleosomes based on single-molecule fluorescence resonance energy transfer (FRET) measurements. In Chapter 1, following the introduction of the nucleosome and chromatin structure, the processes that alter the structure and dynamics of nucleosomes and the theory of FRET are reviewed. In Chapter 2, experimental methods and materials used for the research is reviewed. In Chapter 3, the mechanism of the nucleosome structure transition upon the incorporation of a histone variant CENP-A is presented. In Chapter 4, the dynamics of nucleosome disassembly mediated by the histone chaperone Nap1 and the effects of histone acetylation on the dynamics are detailed. In Chapter 5, nucleosome disassembly during transcription elongation and the effects of Nap1 on elongation kinetics are discussed. Finally in Chapter 6, brief concluding remarks and future directions of the transcription elongation research are discussed.
Download or read book Chemical Epigenetics written by Antonello Mai and published by Springer Nature. This book was released on 2020-03-31 with total page 569 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an authoritative review of the most significant findings about all the epigenetic targets (writers, readers, and erasers) and their implication in physiology and pathology. The book also covers the design, synthesis and biological validation of epigenetic chemical modulators, which can be useful as novel chemotherapeutic agents. Particular attention is given to the chemical mechanisms of action of these molecules and to the drug discovery prose which allows their identification. This book will appeal to students who want to know the extensive progresses made by epigenetics (targets and modulators) in the last years from the beginning, and to specialized scientists who need an instrument to quickly search and check historical and/or updated notices about epigenetics.
Download or read book Differential Ion Mobility Spectrometry written by Alexandre A. Shvartsburg and published by CRC Press. This book was released on 2008-12-24 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the last decade, scientific and engineering interests have been shifting from conventional ion mobility spectrometry (IMS) to field asymmetric waveform ion mobility spectrometry (FAIMS). Differential Ion Mobility Spectrometry: Nonlinear Ion Transport and Fundamentals of FAIMS explores this new analytical technology that separates and characterizes ions by the difference between their mobility in gases at high and low electric fields. It also covers the novel topics of higher-order differential IMS and IMS with alignment of dipole direction. The book relates the fundamentals of FAIMS and other nonlinear IMS methods to the physics of gas-phase ion transport. It begins with the basics of ion diffusion and mobility in gases, covering the main attributes of conventional IMS that are relevant to all IMS approaches. Building on this foundation, the author reviews diverse high-field transport phenomena that underlie differential IMS. He discusses the conceptual implementation and first-principles optimization of FAIMS as a filtering technique, emphasizing the dependence of FAIMS performance metrics on instrumental parameters and properties of ion species. He also explores ion reactions in FAIMS caused by field heating and the effects of inhomogeneous electric field in curved FAIMS gaps. Written by an accomplished scientist in the field, this state-of-the-art book supplies the foundation to understand the new technology of nonlinear IMS methods.
Download or read book The Structure and Dynamics of the Nucleosome at a Single Molecule Level written by Mai Huynh and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The basic unit of packaging for a eukaryotic genome is the nucleosome. The kinetics of numerous DNA-templated processes, including transcription elongation by RNA Polymerase II (Pol II), are controlled by dynamic interactions between DNA and histones in the nucleosome. The global and local stability of the nucleosome can be regulated by a number of elements, such as histone modifications and histone chaperones. By utilizing single-molecule FRET measurements with chemically modified histones, we investigated the effects of histone H2B ubiquitylations at K34 (H2BK34ub) and K120 (H2BK120ub) on the structure of the nucleosome and the interactions between two nucleosomes as well as the potential effects of histone H3 acetylation at K56 (H3K56ac), histone H2B ubiquitylations at K34 (H2BK34ub) and K120 (H2BK120ub) and H3K79 trimethylation (H3K79me3) on the kinetics of transcription elongation by Pol II. We found that whereas H2BK120 ubiquitylation has no effect on the nucleosome structure or internucleosomal contacts, H2BK34 ubiquitylation expands the DNA gyre gap in the nucleosome and stabilizes long- and short-range interactions. We also observed that H3K56 acetylation and H2B ubiquitylation suppress pauses and decrease pause durations close to the nucleosome entry, while H3K79me3 shortens pause durations and speeds up RNA elongation close to the nucleosome center. Additionally, we discovered that H2BK34ub promotes partial nucleosome rewrapping upon Pol II passage. All these results imply that H3K56ac and H3K79me3 promote Pol II progression perhaps by disrupting the local nucleosome structure, while H2B ubiquitylations promote transcription elongation and aid in maintaining the chromatin structure by inducing and stabilizing nucleosome intermediates. Overall, our findings outline the processes by which these changes, when joined by a network of regulatory proteins, enable transcription in various nucleosome areas and assist in maintaining the structure of the chromatin during active transcription.
Download or read book Epigenetics Development and Disease written by Tapas Kumar Kundu and published by Springer Science & Business Media. This book was released on 2012-11-13 with total page 698 pages. Available in PDF, EPUB and Kindle. Book excerpt: Epigenetics fine-tunes the life processes dictated by DNA sequences, but also kick-starts pathophysiological processes including diabetes, AIDS and cancer. This volume tracks the latest research on epigenetics, including work on new-generation therapeutics.
Download or read book Epigenetics of Aging written by Trygve O. Tollefsbol and published by Springer Science & Business Media. This book was released on 2009-11-11 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent studies have indicated that epigenetic processes may play a major role in both cellular and organismal aging. These epigenetic processes include not only DNA methylation and histone modifications, but also extend to many other epigenetic mediators such as the polycomb group proteins, chromosomal position effects, and noncoding RNA. The topics of this book range from fundamental changes in DNA methylation in aging to the most recent research on intervention into epigenetic modifications to modulate the aging process. The major topics of epigenetics and aging covered in this book are: 1) DNA methylation and histone modifications in aging; 2) Other epigenetic processes and aging; 3) Impact of epigenetics on aging; 4) Epigenetics of age-related diseases; 5) Epigenetic interventions and aging: and 6) Future directions in epigenetic aging research. The most studied of epigenetic processes, DNA methylation, has been associated with cellular aging and aging of organisms for many years. It is now apparent that both global and gene-specific alterations occur not only in DNA methylation during aging, but also in several histone alterations. Many epigenetic alterations can have an impact on aging processes such as stem cell aging, control of telomerase, modifications of telomeres, and epigenetic drift can impact the aging process as evident in the recent studies of aging monozygotic twins. Numerous age-related diseases are affected by epigenetic mechanisms. For example, recent studies have shown that DNA methylation is altered in Alzheimer’s disease and autoimmunity. Other prevalent diseases that have been associated with age-related epigenetic changes include cancer and diabetes. Paternal age and epigenetic changes appear to have an effect on schizophrenia and epigenetic silencing has been associated with several of the progeroid syndromes of premature aging. Moreover, the impact of dietary or drug intervention into epigenetic processes as they affect normal aging or age-related diseases is becoming increasingly feasible.
Download or read book Regulation of Alternative Splicing written by Philippe Jeanteur and published by . This book was released on 2014-01-15 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt:
