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 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 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 Assembling a Single molecule View on Nucleosome Dynamics written by Rifka Vlijm and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Schrankenlose Werbung oder Baukultur written by Patriotische Gesellschaft von 1765 and published by . This book was released on 1995 with total page 12 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Single Molecule Biology written by Alexander E. Knight and published by Academic Press. This book was released on 2009-02-26 with total page 369 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single molecule techniques, including single molecule fluorescence, optical tweezers, and scanning probe microscopy, allow for the manipulation and measurement of single biological molecules within a live cell or in culture. These approaches, amongst the most exciting tools available in biology today, offer powerful new ways to elucidate biological function, both in terms of revealing mechanisms of action on a molecular level as well as tracking the behaviour of molecules in living cells. This book provides the first complete and authoritative treatment of this rapidly emerging field, explicitly from a biological perspective.The contents are organized by biological system or molecule. Each chapter discusses insights that have been revealed about their mechanism, structure or function by single molecule techniques. Among the topics covered are enzymes, motor proteins, membrane channels, DNA, ribozymes, cytoskeletal proteins, and other key molecules of current interest. An introduction by the editor provides a concise review of key principles and an historical overview. The last section discusses applications in molecular diagnostics and drug discovery. - Organized by biological system or molecule - Each chapter discusses insights into mechanism of action, structure, and function - Covers enzymes, motor proteins, membrane channels, DNA, ribozymes, etc - Includes an introduction to key principles and an historical overview - Discusses applications in molecular diagnostics and drug discovery - Provides an expert's perspective on future development

Download or read book DNA Interactions with Polymers and Surfactants written by Rita Dias and published by John Wiley & Sons. This book was released on 2008-07-14 with total page 550 pages. Available in PDF, EPUB and Kindle. Book excerpt: A broad overview of the interaction of DNA with surfactants and polymers Due to the potential benefits of biotechnology, interest in the interaction between DNA and surfactants and polymers has become increasingly significant. Now, DNA Interactions with Polymers and Surfactants provides an extensive, up-to-date overview of the subject, giving readers a basis for understanding the factors leading to complexation between DNA and different cosolutes, including metal ions, polyelectrolytes, spermine, spermidine, surfactants and lipids, and proteins. Topical coverage includes: Polyelectrolytes, physico-chemical aspects and biological significance Solution behavior of nucleic acids Single DNA molecules: compaction and decompaction Interaction of DNA with surfactants and cationic polymers Interactions of histones with DNA DNA-DNA interactions The hydration of DNA-amphiphile complexes DNA-surfactant/lipid complexes at liquid interfaces DNA and DNA-surfactant complexes at solid surfaces The role of correlation forces for DNA-cosolute interactions Simulations of polyions Cross-linked DNA gels and gel particles DNA as an amphiphilic polymer Lipid-DNA interactions Covering both theoretical and practical aspects of the subject, DNA Interactions with Polymers and Surfactants is an ideal resource for chemists and biochemists working in gene and DNA delivery research in industry and academia, as well as for cell biologists, chemical engineers, molecular biologists, and development biologists in the pharmaceutical industry.

Download or read book Molecular Biology written by Jordanka Zlatanova and published by Taylor & Francis. This book was released on 2023-03-21 with total page 732 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Biology: Structure and Dynamics of Genomes and Proteomes second edition illustrates the essential principles behind the transmission and expression of genetic information at the level of DNA, RNA, and proteins. Emphasis is on the experimental basis of discovery and the most recent advances in the field while presenting a rigorous, yet still concise, summary of the structural mechanisms of molecular biology. Topics new to this edition include the CRISPR-Cas gene editing system, Coronaviruses – structure, genome, vaccine and drug development, and newly recognized mechanisms for transcription termination. The text is written for advanced undergraduate or graduate-level courses in molecular biology. Key Features · Highlights the experimental basis of important discoveries in molecular biology. · Thoroughly updated with new information on gene editing tools, viruses, and transcription mechanisms, termination and antisense. · Provides learning objectives for each chapter. · Includes a list of relevant videos from the Internet about the topics covered in the chapter.

Download or read book Nucleosomes Histones and Chromatin Part B written by and published by Academic Press. This book was released on 2012-12-31 with total page 429 pages. Available in PDF, EPUB and Kindle. Book excerpt: This new volume of Methods in Enzymology continues the legacy of this premier serial by containing quality chapters authored by leaders in the field. The volume covers nucleosomes, histones and chromatin and has chapters on dynamic mapping of histone-DNA interactions in nucleosomes by unzipping single molecules of DNA, digital DNase technology, and genome-wide analysis of chromatin transition. - Contains quality chapters authored by leaders in the field - The volume covers nucleosomes, histones and chromatin - Has chapters on dynamic mapping of histone-DNA interactions in nucleosomes by unzipping single molecules of DNA, digital DNase technology, and genome-wide analysis of chromatin transition

Download or read book Photochemistry written by Angelo Albini and published by Royal Society of Chemistry. This book was released on 2017-10-10 with total page 237 pages. Available in PDF, EPUB and Kindle. Book excerpt: Drawing on the continued wealth of photochemical research, this volume combines reviews in the latest advances in the field with specific topical highlights. Starting with periodical reports of the literature from 2015-2016 on physical and inorganic aspects, light induced reactions in cryogenic matrices, triplet states on polymers and related materials, properties of transition-metal compounds and the exploitation of solar energy. Coverage continues with highlighted topics in the second part from photoredox systems for building C-C bonds from carbon dioxide, photochemistry in art, photoresponsive devices targeting nucleic acid structures, developments in photodynamic therapy devices and photocatalysis with donor-acceptor polymers. Providing critical analysis of the topics, this book is essential reading for anyone wanting to keep up to date with the literature on photochemistry and its applications.

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 Nucleosomes Histones Chromatin written by Carl Wu and published by Academic Press. This book was released on 2012 with total page 430 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covers nucleosomes, histones and chromatin, with chapters on dynamic mapping of histone-DNA interactions in nucleosomes by unzipping single molecules of DNA, Digital DNase technology, and Genome-wide Analysis of Chromatin Transition.

Download or read book Fluorescence Correlation Spectroscopy written by R. Rigler and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 503 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first book-length treatment of both the theoretical background to fluorescence correlation spectroscopy (FCS) and a variety of applications in various fields of science. The high spatial and temporal resolution of FCS has made it a powerful tool for the analysis of molecular interactions and kinetics, transport properties due to thermal motion, and flow. It contains an essential contribution from Nobel Prize winner M. Eigen, who is credited with inventing FCS.

Download or read book Chromatin Dynamics and Transcription Through Nucleosomes written by Pooja Gupta and published by . This book was released on 2009 with total page 162 pages. Available in PDF, EPUB and Kindle. Book excerpt: In living cells, DNA is wrapped around proteins called histones in the form of chromatin fibers which limit its accessibility to proteins and protein complexes involved in DNA transcription, replication, recombination and repair. These processes occur throughout the life of a cell, and therefore chromatin structure must change to allow the genetic information of the DNA to be processed. The classical biochemical and biophysical methods used in chromatin research are population-averaged methods, which assess properties of the whole population of macromolecules. They are neither capable of detecting possible heterogeneities among individual molecules nor of observing transitional structural changes in real-time. On the other hand, recently developed single-molecule methods allow observation of individual molecules in real-time, thus providing molecular parameters important for understanding structural dynamics. Single molecule techniques can be sorted into several groups: (i) imaging methods (AFM), (ii) fluorescence methods, used to study structural changes, either spontaneous or occurring during biochemical processes like enzymatic action, and (iii) methods that allow application and measurements of force. The latter probe the mechanical response of biomacromolecules to applied stretching force or torque. Applying single-molecule techniques to the study of chromatin is especially advantageous in view of the complexity of its structure and the enormous heterogeneity in terms of post-synthetic modifications. Nucleosome assembly and transcription are related because they address the broader issue of how cellular machineries deal with the organization of DNA into chromatin structure. The answer to these questions will lead to a better understanding of whether the enzymatic machineries, by themselves being molecular motors, can deal with chromatin structure, or whether they need the help of external factors to do so. Specifically, we aim at understanding the behaviour of the chromatin fiber upon external application of tension and/or torsion to mimic similar conditions created by physiological processes in vivo . My work is aimed at studying the dynamics of chromatin fibers and transcription through nucleosomes with the use of home-built magnetic tweezers (MT). In this instrumental set-up, a single DNA molecule is attached at one of its termini to the surface of the observation chamber and at the other terminus to a magnetic bead. Manipulation of the magnetic bead with the help of external magnets allows the introduction of positive or negative supercoiling in the DNA molecule, as well as stretching it with a defined force. This set-up was used to approach the following issues: (1) Nucleosome assembly in real-time on topologically-constrained DNA molecules using Magnetic Tweezers Assembly was achieved using chicken erythrocyte core histones and histone chaperone protein Nap1 under constant low force. We observed partial assembly when the DNA was topologically-constrained and complete assembly on unconstrained (nicked) DNA tethers. To verify that the lack of full nucleosome assembly on topologically-constrained tethers was due to compensatory accumulation of positive supercoiling in the rest of the template, we performed experiments in which we mechanically relieved the positive supercoiling by rotating the external magnetic field at certain time points of the assembly process. Such rotation did lead to complete saturation of the template with nucleosomes. (2) Effect of histone H2A.Z on transcription depending on the DNA sequence Recent observations have shown that some histone variants that are deposited in nonreplicating chromatin are found in genes that are actively transcribed. Although the phenomenology of the deposition process is more or less understood, the structural consequences of the presence of these variants are unclear. My work addresses the issue of whether the 'active' variants H3.3 and H2A.Z directly affect the ability of reconstituted nucleosomes to be transcribed. We used nucleosomal particles reconstituted with human recombinant core histones and naturally occurring nucleosome positioning sequences. T7 RNA polymerase was used as a model enzyme to transcribe reconstituted nucleosomes containing either canonical human recombinant histones, or two histone variants, H2A.Z or H3.3, whose presence has been associated with active transcription. H2A.Z-containing nucleosomes were refractive to transcription, with the actual level of transcription determined by the sequence of the underlying DNA template. These results underscore the interplay between the presence of H2A.Z and the DNA sequence in determining transcription through nucleosomes. (3) Fate of nucleosome during transcription elongation using magnetic tweezers We used an array of nucleosomes reconstituted on 18 tandem repeats of nucleosomal positioning DNA containing 208 bp. For transcription through nucleosomes we used a nucleosomal array construct and T7 RNA polymerase molecules freely moving along the DNA tether. Bulk transcription experiments were carried out to confirm that transcription occurred under our experimental conditions. In the MT experiments, transcription on the freely moving polymerase construct was achieved using transcription buffer, T7 RNA polymerase, RNase A and all four NTPs. We observed a net extension in the DNA length during transcription due to nucleosome disassembly. When analyzing the step size of both upward steps and downward steps, a dominant peak at ~50 nm was observed which may be due to the release of entire octamer.

Download or read book Structure and Dynamics of Nucleic Acids Proteins and Membranes written by E. Clementi and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 454 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume collects a number of the invited lectures and a few selected contrib utions presented at the International Symposium on Structure and Dynamics of Nucleic Acids, Proteins and Membranes held August 31st through September 5th, 1986, in Riva del Garda, Italy. The title of the conference as well as a number of the topics covered represent a continuation of two previous conferences, the first held in 1982 at the University of California in San Diego, and the second in 1984 in Rome at the Accademia dei Lincei. These two earlier conferences have been documented in Structure and Dynamics: Nucleic Acids and Proteins, edited by E. Clementi and R. H. Sarma, Adenine Press, New York, 1983, and Structure and Motion: Membranes, Nucleic Acids and Proteins, edited by E. Clementi, G. Corongiu, M. H. Sarma and R. H. Sarma, Adenine Press, New York, 1985. At this conference in Riva del Garda we were very hesitant to keep the name of the conference the same as the two previous ones. Indeed, a number of topics discussed in this conference were not included in the previous ones and even the emphasis of this gathering is only partly reflected in the conference title. An alternative title would have been Structure and Dynamics of Nucleic Acids, Proteins, and Higher Functions, or, possibly, "higher components" rather than "higher functions.

Download or read book Physical Biology of the Cell written by Rob Phillips and published by Garland Science. This book was released on 2012-10-29 with total page 1089 pages. Available in PDF, EPUB and Kindle. Book excerpt: Physical Biology of the Cell is a textbook for a first course in physical biology or biophysics for undergraduate or graduate students. It maps the huge and complex landscape of cell and molecular biology from the distinct perspective of physical biology. As a key organizing principle, the proximity of topics is based on the physical concepts that

Download or read book Investigating the Relationship Between Nucleosome Structure and Dynamics written by Joanna Karen Somers and published by . This book was released on 2008 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: