Relevant bibliographies by topics / Nucleosome Dynamics

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Nucleosome Dynamics'

Author: Grafiati
Published: 4 June 2021
Last updated: 17 February 2022

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Journal articles on the topic "Nucleosome Dynamics"

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Ashwin, S. S., Tadasu Nozaki, Kazuhiro Maeshima, and Masaki Sasai. "Organization of fast and slow chromatin revealed by single-nucleosome dynamics." Proceedings of the National Academy of Sciences 116, no. 40 (September 16, 2019): 19939–44. http://dx.doi.org/10.1073/pnas.1907342116.

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Understanding chromatin organization and dynamics is important, since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bimodal nature of the mean square displacement distribution of nucleosomes allows for a natural categorization of the nucleosomes as fast and slow. Analyses of the nucleosome–nucleosome correlation functions within these categories along with the density of vibrational modes show that the nucleosomes form dynamically correlated fluid regions (i.e., dynamic domains of fast and slow nucleosomes). Perturbed nucleosome dynamics by global histone acetylation or cohesin inactivation indicate that nucleosome–nucleosome interactions along with tethering of chromatin chains organize nucleosomes into fast and slow dynamic domains. A simple polymer model is introduced, which shows the consistency of this dynamic domain picture. Statistical analyses of single-nucleosome movement provide rich information on how chromatin is dynamically organized in a fluid manner in living cells.
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Stockdale, Chris, Michael Bruno, Helder Ferreira, Elisa Garcia-Wilson, Nicola Wiechens, Maik Engeholm, Andrew Flaus, and Tom Owen-Hughes. "Nucleosome dynamics." Biochemical Society Symposia 73 (January 1, 2006): 109–19. http://dx.doi.org/10.1042/bss0730109.

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In the 30 years since the discovery of the nucleosome, our picture of it has come into sharp focus. The recent high-resolution structures have provided a wealth of insight into the function of the nucleosome, but they are inherently static. Our current knowledge of how nucleosomes can be reconfigured dynamically is at a much earlier stage. Here, recent advances in the understanding of chromatin structure and dynamics are highlighted. The ways in which different modes of nucleosome reconfiguration are likely to influence each other are discussed, and some of the factors likely to regulate the dynamic properties of nucleosomes are considered.
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Fitz, Veronika, Jaeoh Shin, Christoph Ehrlich, Lucas Farnung, Patrick Cramer, Vasily Zaburdaev, and Stephan W. Grill. "Nucleosomal arrangement affects single-molecule transcription dynamics." Proceedings of the National Academy of Sciences 113, no. 45 (October 24, 2016): 12733–38. http://dx.doi.org/10.1073/pnas.1602764113.

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In eukaryotes, gene expression depends on chromatin organization. However, how chromatin affects the transcription dynamics of individual RNA polymerases has remained elusive. Here, we use dual trap optical tweezers to study single yeast RNA polymerase II (Pol II) molecules transcribing along a DNA template with two nucleosomes. The slowdown and the changes in pausing behavior within the nucleosomal region allow us to determine a drift coefficient, χ, which characterizes the ability of the enzyme to recover from a nucleosomal backtrack. Notably, χ can be used to predict the probability to pass the first nucleosome. Importantly, the presence of a second nucleosome changes χ in a manner that depends on the spacing between the two nucleosomes, as well as on their rotational arrangement on the helical DNA molecule. Our results indicate that the ability of Pol II to pass the first nucleosome is increased when the next nucleosome is turned away from the first one to face the opposite side of the DNA template. These findings help to rationalize how chromatin arrangement affects Pol II transcription dynamics.
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Kelbauskas, L., N. Woodbury, and D. Lohr. "DNA sequence-dependent variation in nucleosome structure, stability, and dynamics detected by a FRET-based analysisThis paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process." Biochemistry and Cell Biology 87, no. 1 (February 2009): 323–35. http://dx.doi.org/10.1139/o08-126.

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Förster resonance energy transfer (FRET) techniques provide powerful and sensitive methods for the study of conformational features in biomolecules. Here, we review FRET-based studies of nucleosomes, focusing particularly on our work comparing the widely used nucleosome standard, 5S rDNA, and 2 promoter-derived regulatory element-containing nucleosomes, mouse mammary tumor virus (MMTV)-B and GAL10. Using several FRET approaches, we detected significant DNA sequence-dependent structure, stability, and dynamics differences among the three. In particular, 5S nucleosomes and 5S H2A/H2B-depleted nucleosomal particles have enhanced stability and diminished DNA dynamics, compared with MMTV-B and GAL10 nucleosomes and particles. H2A/H2B-depleted nucleosomes are of interest because they are produced by the activities of many transcription-associated complexes. Significant location-dependent (intranucleosomal) stability and dynamics variations were also observed. These also vary among nucleosome types. Nucleosomes restrict regulatory factor access to DNA, thereby impeding genetic processes. Eukaryotic cells possess mechanisms to alter nucleosome structure, to generate DNA access, but alterations often must be targeted to specific nucleosomes on critical regulatory DNA elements. By endowing specific nucleosomes with intrinsically higher DNA accessibility and (or) enhanced facility for conformational transitions, DNA sequence-dependent nucleosome dynamics and stability variations have the potential to facilitate nucleosome recognition and, thus, aid in the crucial targeting process. This and other nucleosome structure and function conclusions from FRET analyses are discussed.
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Anderson, J. D., A. Thåström, and J. Widom. "Spontaneous Access of Proteins to Buried Nucleosomal DNA Target Sites Occurs via a Mechanism That Is Distinct from Nucleosome Translocation." Molecular and Cellular Biology 22, no. 20 (October 15, 2002): 7147–57. http://dx.doi.org/10.1128/mcb.22.20.7147-7157.2002.

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ABSTRACT Intrinsic nucleosome dynamics termed “site exposure” provides spontaneous and cooperative access to buried regions of nucleosomal DNA in vitro. Two different mechanisms for site exposure have been proposed, one based on nucleosome translocation, the other on dynamic nucleosome conformational changes in which a stretch of the nucleosomal DNA is transiently released off the histone surface. Here we report on three experiments that distinguish between these mechanisms. One experiment investigates the effects on the accessibilities of restriction enzyme target sites inside nucleosomes when extra DNA (onto which the nucleosome may move at low energetic cost) is appended onto one end. The other two experiments test directly for nucleosome mobility under the conditions used to probe accessibility to restriction enzymes: one on a selected nonnatural nucleosome positioning sequence, the other on the well-studied 5S rRNA gene nucleosome positioning sequence. We find from all three assays that restriction enzymes gain access to sites throughout the entire length of the nucleosomal DNA without contribution from nucleosome translocation. We conclude that site exposure in nucleosomes in vitro occurs via a nucleosome conformational change that leads to transient release of a stretch of DNA from the histone surface, most likely involving progressive uncoiling from an end. Recapture at a distal site along DNA that has partially uncoiled would result in looped structures which are believed to contribute to RNA polymerase elongation and may contribute to spontaneous or ATP-driven nucleosome mobility. Transient open states may facilitate the initial entry of transcription factors and enzymes in vivo.
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Hodges, Courtney, Lacramioara Bintu, Lucyna Lubkowska, Mikhail Kashlev, and Carlos Bustamante. "Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II." Science 325, no. 5940 (July 30, 2009): 626–28. http://dx.doi.org/10.1126/science.1172926.

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RNA polymerase II (Pol II) must overcome the barriers imposed by nucleosomes during transcription elongation. We have developed an optical tweezers assay to follow individual Pol II complexes as they transcribe nucleosomal DNA. Our results indicate that the nucleosome behaves as a fluctuating barrier that locally increases pause density, slows pause recovery, and reduces the apparent pause-free velocity of Pol II. The polymerase, rather than actively separating DNA from histones, functions instead as a ratchet that rectifies nucleosomal fluctuations. We also obtained direct evidence that transcription through a nucleosome involves transfer of the core histones behind the transcribing polymerase via a transient DNA loop. The interplay between polymerase dynamics and nucleosome fluctuations provides a physical basis for the regulation of eukaryotic transcription.
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Widom, J. "Role of DNA sequence in nucleosome stability and dynamics." Quarterly Reviews of Biophysics 34, no. 3 (August 2001): 269–324. http://dx.doi.org/10.1017/s0033583501003699.

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1. Introduction 2701.1 Overview of nucleosome structure 2712. Relative equilibrium stability (affinity) of histone–DNA interactions in nucleosomes 2722.1 Relative affinity equals relative equilibrium stability 2722.2 Competition assays for relative free-energy measurements 2732.3 Technical issues in relative free-energy measurements 2752.4 Range of affinities 2783. Relation of nucleosome stability to nucleosome positioning 2793.1 Translational nucleosome positioning 2793.2 Rotational positioning 2803.3 Unfavorable positioning 2813.4 Experiments 2814. Physical basis of DNA sequence preferences 2824.1 Free-energy cost of DNA bending 2834.2 Molecular mechanics of DNA bending and bendability 2844.3 Bent and bendable DNA sequences 2864.4 Parameter sets for prediction of DNA bending and bendability 2884.5 DNA twisting 2904.6 Energetics of nucleosomal DNA packaging 2915. DNA sequence motifs for nucleosome packaging 2925.1 Natural and designed nucleosomal DNAs 2935.2 New rules and reagents from physical selection studies 2945.3 Molecular basis of DNA sequence preferences 2995.4 Special properties of the TA step 3005.5 Unfavorable sequences 3025.6 Natural genomes 3035.7 Evolutionary approach toward an optimal sequence 3055.8 Optimization by design 3056. Dynamic nucleosome instability 3086.1 Site-exposure equilibria 3086.2 DNA sequence-dependence to site-exposure equilibria 3126.3 Nucleosome translocation 3156.4 Action of processive enzymes 3197. Conclusions 3198. Acknowledgements 3209. References 320The nucleosome core particle is the fundamental repeating subunit of chromatin. It consists of two molecules each of the four ‘core histone’ proteins, H2A, H2B, H3 and H4, and a 147 bp stretch of DNA. The lowest level of chromatin organization consists of a repeated array of nucleosome core particles separated by variable lengths of ‘linker DNA’. In many, but not all, cases, each core particle plus its linker DNA is associated with one molecule of a fifth ‘linker’ histone protein, H1. The complex of the core particle plus its linker DNA and H1 (when present) is called a ‘nucleosome’.
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Fierz, Beat, and Michael G. Poirier. "Biophysics of Chromatin Dynamics." Annual Review of Biophysics 48, no. 1 (May 6, 2019): 321–45. http://dx.doi.org/10.1146/annurev-biophys-070317-032847.

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Nucleosomes and chromatin control eukaryotic genome accessibility and thereby regulate DNA processes, including transcription, replication, and repair. Conformational dynamics within the nucleosome and chromatin structure play a key role in this regulatory function. Structural fluctuations continuously expose internal DNA sequences and nucleosome surfaces, thereby providing transient access for the nuclear machinery. Progress in structural studies of nucleosomes and chromatin has provided detailed insight into local chromatin organization and has set the stage for recent in-depth investigations of the structural dynamics of nucleosomes and chromatin fibers. Here, we discuss the dynamic processes observed in chromatin over different length scales and timescales and review current knowledge about the biophysics of distinct structural transitions.
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Neumann, Heinz, and Bryan J. Wilkins. "Spanning the gap: unraveling RSC dynamics in vivo." Current Genetics 67, no. 3 (January 23, 2021): 399–406. http://dx.doi.org/10.1007/s00294-020-01144-1.

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AbstractMultiple reports over the past 2 years have provided the first complete structural analyses for the essential yeast chromatin remodeler, RSC, providing elaborate molecular details for its engagement with the nucleosome. However, there still remain gaps in resolution, particularly within the many RSC subunits that harbor histone binding domains.Solving contacts at these interfaces is crucial because they are regulated by posttranslational modifications that control remodeler binding modes and function. Modifications are dynamic in nature often corresponding to transcriptional activation states and cell cycle stage, highlighting not only a need for enriched spatial resolution but also temporal understanding of remodeler engagement with the nucleosome. Our recent work sheds light on some of those gaps by exploring the binding interface between the RSC catalytic motor protein, Sth1, and the nucleosome, in the living nucleus. Using genetically encoded photo-activatable amino acids incorporated into histones of living yeast we are able to monitor the nucleosomal binding of RSC, emphasizing the regulatory roles of histone modifications in a spatiotemporal manner. We observe that RSC prefers to bind H2B SUMOylated nucleosomes in vivo and interacts with neighboring nucleosomes via H3K14ac. Additionally, we establish that RSC is constitutively bound to the nucleosome and is not ejected during mitotic chromatin compaction but alters its binding mode as it progresses through the cell cycle. Our data offer a renewed perspective on RSC mechanics under true physiological conditions.
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Buitrago, Diana, Laia Codó, Ricard Illa, Pau de Jorge, Federica Battistini, Oscar Flores, Genis Bayarri, et al. "Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning." Nucleic Acids Research 47, no. 18 (August 31, 2019): 9511–23. http://dx.doi.org/10.1093/nar/gkz759.

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Abstract We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucleosomal organization due to changes in cellular conditions. Results are displayed in the context of genomic information thanks to different visualizers and browsers, allowing the user a holistic, multidimensional view of the genome/transcriptome. The package shows good performance for both locating equilibrium nucleosome architecture and nucleosome dynamics and provides abundant useful information in several test cases, where experimental data on nucleosome position (and for some cases expression level) have been collected for cells under different external conditions (cell cycle phase, yeast metabolic cycle progression, changes in nutrients or difference in MNase digestion level). Nucleosome Dynamics is a free software and is provided under several distribution models.
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Dissertations / Theses on the topic "Nucleosome Dynamics"

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Venkataraman, Shanmugasundaram. "Histone acetylation and nucleosome dynamics." Thesis, University of Edinburgh, 2001. http://hdl.handle.net/1842/23234.

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In this report, I will describe purification of core histone octamers from chicken blood, HeLa nuclei and yeast cells, along with preparation of DNA fragments containing the 208 bp 5S rDNA gene and the adult beta (bA)-globin gene promoter. In vitro experiments studying the effect of histone acetylation on the positioning and mobility of nucleosomes on the sea urchin 5S rDNA gene and the chicken bA-globin gene promoter will be described. The former provides a well studied nucleosome positioning and mobility model system, while the latter is a developmentally regulated gene, with globin gene switching through the early stages of the lifetime of the chicken, and a proposed involvement of positioned nucleosomes in its regulation. The aim was to determine the difference between hypoacetylated and hyperacetylated core histones in terms of their influence upon nucleosome positioning and mobility. In earlier studies, it was noted that there was a difference in relative positioning intensities between the two forms (ie. hypoacetylated core histones preferentially positioned at certain sites, while hyperacetylated core histones positioned at the same sites but with different relative affinities). Therefore, acetylation affects where a nucleosomes is able to position. I have carried on this work to further characterize nucleosome positioning and to study the implications of histone acetylation on nucleosome mobility. I have found subtle differences in the thermodynamics and kinetics of hyperacetylated nucleosomes compared to hypeoacetylated nucleosomes: hyperacetylated nucleosomes appear to have a lower threshold in both these parameters when studied using the 208 pb rDNA fragment. Experiments involving two other types of core histones, trypsinized chicken core histone octamers and chicken core histone tetramers will also be described, which will be placed into the context of the results found with the other types of core histones. Finally, I will describe the effect of reconstituting hyperacetylated core histones with methylated DNA, long known to be a mediator of transcriptional repression, in the form of the chicken bA-globin gene promoter.
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Dorigo, Benedetta. "Studies of nucleosome array structure and dynamics /." Zürich, 2004. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=15710.

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Hu, Zhenhua. "Nucleosome positioning dynamics in evolution and disease." Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/25399.

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Nucleosome positioning is involved in a variety of cellular processes, and it provides a likely substrate for species evolution and may play roles in human disease. However, many fundamental aspects of nucleosome positioning remain controversial, such as the relative importance of underlying sequence features, genomic neighbourhood and trans-acting factors. In this thesis, I have focused on analyses of the divergence and conservation of nucleosome positioning, associated substitution spectra, and the interplay between them. I have investigated the extent to which nucleosome positioning patterns change following the duplication of a DNA sequence and its insertion into a new genomic region within the same species, by assessing the relative nucleosome positioning between paralogous regions in both the human (using in vitro and in vivo datasets) and yeast (in vivo) genomes. I observed that the positioning of paralogous nucleosomes is generally well conserved and detected a strong rotational preference where nucleosome positioning has diverged. I have also found, in all datasets, that DNA sequence features appear to be more important than local chromosomal environments in nucleosome positioning evolution, while controlling for trans-acting factors that can potentially confound inter-species comparisons. I have also examined the relationships between chromatin structure and DNA sequence variation, with a particular focus on the spectra of (germline and somatic) substitutions seen in human diseases. Both somatic and germline substitutions are found to be enriched at sequences coinciding with nucleosome cores. In addition, transitions appear to be enriched in germline relative to somatic substitutions at nucleosome core regions. This difference in transition to transversion ratio is also seen at transcription start sites (TSSs) genome wide. However, the contrasts seen between somatic and germline mutational spectra do not appear to be attributable to alterations in nucleosome positioning between cell types. Examination of multiple human nucleosome positioning datasets shows conserved positioning across TSSs and strongly conserved global phasing between 4 cancer cell lines and 7 non-cancer cell lines. This suggests that the particular mutational profiles seen for somatic and germline cells occur upon a common landscape of conserved chromatin structure. I extended my studies of mutational spectra by analysing genome sequencing data from various tissues in a cohort of individuals to identify human somatic mutations. This allowed an assessment of the relationship between age and mutation accumulation and a search for inherited genetic variants linked to high somatic mutation rates. A list of candidate germline variants that potentially predispose to increased somatic mutation rates was the outcome. Together these analyses contribute to an integrated view of genome evolution, encompassing the divergence of DNA sequence and chromatin structure, and explorations of how they may interact in human disease.
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Pohl, Andy 1979. "Nucleosome dynamics and analysis in breast cancer cells." Doctoral thesis, Universitat Pompeu Fabra, 2014. http://hdl.handle.net/10803/328416.

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Genome-wide analysis of the nucleosome positioning and histone H1 isoform content of the T47D breast cancer cell line has found a number of observations, namely that with a gentle digestion of microccocal nuclease (MNase), a nucleosome is visible just upstream of the transcription start site, in the region known as the “nucleosome-free region” (NFR). H1 isoforms bind to chromatin mainly in a redundant manner, but H1.2 and H1.3 show some specificity while H1.5 increases its binding dramatically after a progesterone stimulus. In the course of these studies, a general-purpose software package was developed for the manipulation and analysis of bigWig files, a data format for storing continuous signal data assigned to genome coordinates
En el meu estudi genòmic sobre el posicionament de nucleosomes i sobre elcontingut de les isoformes de la histona H1 en cèl•lules de càncer de mama T47D he dut a terme una sèrie d'observacions. Específicament he trobat que amb una digestió suau amb nucleasa micrococcal, es pot identificar un nucleosoma just abans del lloc d'inici de transcripció, en la regió coneguda com a "regió lliure de nucleosomes". També he vist que les diferents isoformes somàtiques de la histona H1 (H1.0-H1.5, H1x) s'uneixen a la cromatina de manera redundant, però que la H1.2 i la H1.3 presenten certa especificitat, mentre que la H1.5 mostra un augment de la unió generalitzat després d'estimular les cèl•lules amb progesterona. En el decurs de la meva recerca, he desenvolupat un programari general per la manipulació i l'anàlisi d'arxius amb format bigWig, un format per a l'emmagetzematge de dades de senyals continus al llarg de les coordenades del genoma.
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Hada, Arjan. "DYNAMICS OF NUCLEOSOME REMODELING BY ATP-DEPENDENT CHROMATIN REMODELERS." OpenSIUC, 2017. https://opensiuc.lib.siu.edu/dissertations/1431.

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Chromatin is highly regulated nucleoprotein complex facilitating the dynamic balance between genome packaging and accessibility. The central workhorses regulating the dynamic nature of chromatin are ATP-dependent chromatin remodelers- ISWI, SWI/SNF, INO80, and CHD/Mi2. All chromatin remodelers transduce the energy from ATP hydrolysis to translocate on DNA, break histone-DNA contacts, and mobilize nucleosomes. However, the final outcomes of nucleosome remodeling are diverse - nucleosome sliding, dimer exchange, nucleosome disassembly, and nucleosome conformation alteration. This study sheds light on how different chromatin remodelers catalyze various structural transformations. We provide novel insights into the nucleosome dynamics, the role of histone octamer dynamics on nucleosome remodeling by ISW2, mechanism of dimer exchange by INO80 and mechanism of nucleosome disassembly by the coordinated action of RSC and histone chaperone Nap1. We also provide insights on how aberrant SWI/SNF complexes affect fundamental enzymatic properties such as ATPase and processive nucleosome remodeling. ISW2 remodelers sense and respond to the length of linker DNA separating the nucleosome and centers nucleosome. Histone octamers are perceived as a mostly static structure whereas DNA deforms itself to fit nucleosome. We have found change in histone octamer conformation as a novel step in ISW2 mobilizing DNA through the nucleosome. We provide evidence for an induced fit mechanism where histone-histone and histone-DNA interactions change in respond to remodeler, and these changes promote DNA entry into the nucleosome. Our data supports a model in which DNA translocation causes the change in histone octamer conformation, followed by DNA entry into nucleosome and resetting of the histone octamer core. We also move a step ahead and show that SANT domain promotes the entry of DNA into nucleosome and resets the histone octamer core allowing processive nucleosome mobilization. INO80 nucleosome remodeling provides two outcomes- nucleosome centering and dimer exchange. INO80 exchanges H2A.Z-H2B dimer for H2A-H2B. We show that INO80 is incredibly slow at centering nucleosome compared to ISW2. We also provide evidence for a mechanism where INO80 persistently displaces DNA from the dimer interface, unlike ISW2, facilitating dimer exchange. In another instance, we show that kinetic step sizes are modulated by a combination of enzyme and DNA sequence properties, and are not hardwired into the enzyme. ISW2 has been previously shown to translocate DNA with a kinetic step sizes of ~7bp and ~3bp. We show that kinetic step sizes may vary depending on nucleosomal location where we monitor DNA movement. Next, we studied the mechanism of nucleosome disassembly by RSC in the presence of Nap1. We found that Nap1 promotes the disassembly of the distal nucleosome that RSC collides with rather than the proximal nucleosomes it mobilizes. SWI/SNF tops the list of the frequently mutated epigenetic factor in cancer with its subunits mutated in more than 20% of all cancers. Loss of hSnf5 is a driver mutation in pediatric rhabdoid tumors. Our lab has previously identified that the deletion of Snf5 causes yeast SWI/SNF to lose an entire module comprised of Snf5, Swp82, and Taf14. In this study, we establish the properties of aberrant SWI/SNF complex formed in the absence of Snf5 module. The deletion resulted in lower ATP hydrolysis and nucleosome mobilization activities of the mutant SWI/SNF. We found that Snf5 module is necessary to couple ATP hydrolysis with DNA translocation. We studied the role of accessory domain AT-hooks in the ATPase subunit of SWI/SNF and found similar results. Interestingly, AT hook and SnAC domains, and Snf5 subunit were found to communicate with the same region in ATPase domain physically. These studies provide valuable mechanistic insights into chromatin structure and function and highlight how different chromatin remodelers catalyze different chromatin remodeling outcomes. We also provide new insights on how the activity of the core ATPase motor is regulated either by accessory domains on the same subunit or by accessory subunits as a part of the larger complex.
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North, Justin A. "Regulation of Nucleosome Dynamics: Mechanisms for Chromatin Accessibility and Metabolism." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1354737862.

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Luo, Yi. "Nucleosome Regulation of Transcription Factor Binding Dynamics: a Single-molecule Study." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1449093157.

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Jessen, Walter Joseph. "Chromatin dynamics at the Saccharomyces cerevisiae PHO5 promoter." Diss., Texas A&M University, 2004. http://hdl.handle.net/1969.1/3306.

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In eukaryotes, the organization of DNA into chromatin is a primary determinant of gene expression. Positioned nucleosomes in promoter regions are frequently found to regulate gene expression by obstructing the accessibility of cis-regulatory elements in DNA to trans-factors. This dissertation focuses on the chromatin structure and remodeling program at the S. cerevisiae PHO5 promoter, extending the use of DNA methyltransferases as in vivo probes of chromatin structure. Our studies address the diversity of histone-DNA interactions in vivo by examining nucleosome conformational stabilities at the PHO5 promoter. We present high-resolution chromatin structural mapping of the promoter, required to relate in vivo site accessibility to nucleosome stability and show that the PHO5 promoter nucleosomes have different accessibilities. We show a correlation between DNA curvature and nucleosome positioning, which is consistent with the observed differences in accessibility/stability. Kinetic analyses of the chromatin remodeling program at PHO5 show that nucleosomes proximal to the enhancer are disrupted preferentially and prior to those more distal, demonstrating bidirectional and finite propagation of chromatin remodeling from bound activators and providing a novel mechanism by which transactivation at a distance occurs.
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Topal, Salih. "Chromatin Dynamics Regulate Transcriptional Homeostasis." eScholarship@UMMS, 2019. https://escholarship.umassmed.edu/gsbs_diss/1062.

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Eukaryotic promoters are inherently bidirectional and allow RNA Polymerase II to transcribe both coding and noncoding RNAs. Dynamic disassembly and reassembly is a prominent feature of nucleosomes around eukaryotic promoters. While H3K56 acetylation (H3K56Ac) enhances turnover events of these promoter-proximal nucleosomes, the chromatin remodeler INO80C ensures their proper positioning. In my dissertation, I explore how chromatin dynamics regulate transcriptional homeostasis. In the first part, I investigate the role of H3K56Ac on the nascent transcriptome throughout the eukaryotic cell cycle. I find that H3K56Ac is a global, positive regulator for coding and noncoding transcription by promoting both initiation and elongation/termination. On the contrary, I find that H3K56Ac represses promiscuous transcription following replication fork passage by ensuring efficient nucleosome assembly during S-phase. In addition, I show that there is a stepwise increase in transcription in the S-G2 transition, and this response to gene dosage imbalance does not require H3K56Ac. This study clearly shows that a single histone modification, H3K56Ac can exert both positive and negative effects on transcription at different cell cycle stages. In the second part, I investigate the role of the chromatin remodeler INO80C on the nascent transcription around replication origins. I show that INO80C, together with the transcription factor Mot1, prevents cryptic transcription around yeast replication origins, and the loss of these proteins lead to an increase in DNA double strand breaks. I hypothesize that recruitment of INO80C ensures proper positioning of nucleosomes around origins and the exclusion of RNA Pol II to prevent cryptic initiation. Together these findings indicate that H3K56Ac regulates transcription globally by enhancing nucleosome turnover, and it prevents cryptic transcription and reinforces transcriptional fidelity by promoting efficient nucleosome assembly in the S-phase. In addition, INO80C maintains genome stability by preventing cryptic transcription around the origins.
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Le, Jenny Vi Le. "Tunable Nanocalipers to Probe Structure and Dynamics in Chromatin." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1543163132011865.

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Books on the topic "Nucleosome Dynamics"

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Li, Min, Cizhong Jiang, and Jiannan Lin. Nucleosome Dynamics in Epigenetic Regulation. Taylor & Francis Group, 2018.

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Book chapters on the topic "Nucleosome Dynamics"

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Gansen, Alexander, and Jörg Langowski. "Nucleosome Dynamics Studied by Förster Resonance Energy Transfer." In The Functional Nucleus, 329–56. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-38882-3_15.

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Paro, Renato, Ueli Grossniklaus, Raffaella Santoro, and Anton Wutz. "Chromatin Dynamics." In Introduction to Epigenetics, 29–47. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-68670-3_2.

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AbstractThe nucleus of a eukaryotic cell is a very busy place. Not only during replication of the DNA, but at any time in the cell cycle specific enzymes need access to genetic information to process reactions such as transcription and DNA repair. Yet, the nucleosomal structure of chromatin is primarily inhibitory to these processes and needs to be resolved in a highly orchestrated manner to allow developmental, organismal, and cell type-specific nuclear activities. This chapter explains how nucleosomes organize and structure the genome by interacting with specific DNA sequences. Variants of canonical histones can change the stability of the nucleosomal structure and also provide additional epigenetic layers of information. Chromatin remodeling complexes work locally to alter the regular beads-on-a-string organization and provide access to transcription and other DNA processing factors. Conversely, factors like histone chaperones and highly precise templating and copying mechanisms are required for the reassembly of nucleosomes and reestablishment of the epigenetic landscape after passage of activities processing DNA sequence information. A very intricate molecular machinery ensures a highly dynamic yet heritable chromatin template.
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Paul, Amit, and Shubho Chaudhuri. "Change in Nucleosome Dynamics During Stress Responses in Plants." In Methods in Molecular Biology, 91–100. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9458-8_10.

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Mirzabekov, A., V. Karpov, O. Preobrazhenskaya, S. Bavykin, K. Ebralidse, A. Belyavsky, and V. Studitsky. "Structural Dynamics of Nucleosomes and Chromatin upon Transcription." In Organization and Function of the Eucaryotic Genome, 16–17. Berlin, Heidelberg: Springer Berlin Heidelberg, 1987. http://dx.doi.org/10.1007/978-3-642-46611-3_20.

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Paro, Renato, Ueli Grossniklaus, Raffaella Santoro, and Anton Wutz. "Biology of Chromatin." In Introduction to Epigenetics, 1–28. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-68670-3_1.

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Abstract:
AbstractThis chapter provides an introduction to chromatin. We will examine the organization of the genome into a nucleosomal structure. DNA is wrapped around a globular complex of 8 core histone proteins, two of each histone H2A, H2B, H3, and H4. This nucleosomal arrangement is the context in which information can be established along the sequence of the DNA for regulating different aspects of the chromosome, including transcription, DNA replication and repair processes, recombination, kinetochore function, and telomere function. Posttranslational modifications of histone proteins and modifications of DNA bases underlie chromatin-based epigenetic regulation. Enzymes that catalyze histone modifications are considered writers. Conceptually, erasers remove these modifications, and readers are proteins binding these modifications and can target specific functions. On a larger scale, the 3-dimensional (3D) organization of chromatin in the nucleus also contributes to gene regulation. Whereas chromosomes are condensed during mitosis and segregated during cell division, they occupy discrete volumes called chromosome territories during interphase. Looping or folding of DNA can bring regulatory elements including enhancers close to gene promoters. Recent techniques facilitate understanding of 3D contacts at high resolution. Lastly, chromatin is dynamic and changes in histone occupancy, histone modifications, and accessibility of DNA contribute to epigenetic regulation.
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Govind, Chhabi K., Daniel Ginsburg, and Alan G. Hinnebusch. "Measuring Dynamic Changes in Histone Modifications and Nucleosome Density during Activated Transcription in Budding Yeast." In Methods in Molecular Biology, 15–27. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-477-3_2.

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Travers, Andrew A., and Tom Owen-Hughes. "Nucleosome remodeling." In Chromatin Structure and Dynamics: State-of-the-Art, 421–65. Elsevier, 2004. http://dx.doi.org/10.1016/s0167-7306(03)39016-7.

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Harp, Joel M., B. Leif Hanson, and Gerard J. Bunick. "The core particle of the nucleosome." In Chromatin Structure and Dynamics: State-of-the-Art, 13–44. Elsevier, 2004. http://dx.doi.org/10.1016/s0167-7306(03)39002-7.

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Arneodo, Alain, Guénola Drillon, Françoise Argoul, and Benjamin Audit. "The Role of Nucleosome Positioning in Genome Function and Evolution." In Nuclear Architecture and Dynamics, 41–79. Elsevier, 2018. http://dx.doi.org/10.1016/b978-0-12-803480-4.00002-8.

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"Nucleosome as an Example of a Nanosystem Formation: Structural Dynamics of Nucleosomal DNA." In Nanobiophysics, 111–44. Jenny Stanford Publishing, 2016. http://dx.doi.org/10.1201/b20480-6.

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Conference papers on the topic "Nucleosome Dynamics"

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Li, Zhaoyu. "Abstract A34: Nucleosome dynamics of cell differentiation." In Abstracts: AACR Special Conference on Chromatin and Epigenetics in Cancer - June 19-22, 2013; Atlanta, GA. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.cec13-a34.

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Wang, Debby D., and Hong Yan. "Analysis of nucleosome structures based on molecular dynamics." In 2011 IEEE International Conference on Systems, Man and Cybernetics - SMC. IEEE, 2011. http://dx.doi.org/10.1109/icsmc.2011.6084132.

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He, Housheng H., Clifford A. Meyer, Shirley X. Liu, and Myles Brown. "Abstract 2960: Factor dependent chromatin structure and nucleosome dynamics." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-2960.

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Takami, Tomohide, Jun-ichi Uewaki, Hiroshi Ochiai, Masato Koyama, Yoshihide Ogawa, Mikako Saito, Hideaki Matsuoka, and Shin-ichi Tate. "Live Dynamics on Femtoinjection of GFP-Tagged Nucleosome Chaperones into HeLa Cell." In JSAP-OSA Joint Symposia. Washington, D.C.: OSA, 2014. http://dx.doi.org/10.1364/jsap.2014.18p_c4_12.

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"BAYESIAN NETWORK ANALYSIS OF RELATIONSHIPS BETWEEN NUCLEOSOME DYNAMICS AND TRANSCRIPTIONAL REGULATORY FACTORS." In International Conference on Bioinformatics Models, Methods and Algorithms. SciTePress - Science and and Technology Publications, 2012. http://dx.doi.org/10.5220/0003773502990302.

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Fujimori, R., Y. Komatsu, M. Fukuda, T. Miyakawa, R. Morikawa, and M. Takasu. "Analysis of the histone protein tail and DNA in nucleosome using molecular dynamics simulation." In 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: Keep Going Tohoku. American Institute of Physics, 2013. http://dx.doi.org/10.1063/1.4794641.

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Ho, Bich Hai, Ngoc Tu Le, and Tu Bao Ho. "Quantitatively Assessing the Effects of Regulatory Factors on Nucleosome Dynamics by Multiple Kernel Learning." In Communication Technologies, Research, Innovation, and Vision for the Future (RIVF). IEEE, 2010. http://dx.doi.org/10.1109/rivf.2010.5632497.

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Rao, Satyanarayan, Amy Han, Alexis Zukowski, Etana Kopin, Peter Kabos, and Srinivas Ramachandran. "Abstract 2611: Transcription factor-nucleosome dynamics inferred from plasma cfDNA delineates tumor and tumor-microenvironment phenotype." In Proceedings: AACR Annual Meeting 2021; April 10-15, 2021 and May 17-21, 2021; Philadelphia, PA. American Association for Cancer Research, 2021. http://dx.doi.org/10.1158/1538-7445.am2021-2611.

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Zhang, Yiru, Changchang Cao, Hongde Liu, and Xiao Sun. "A dynamic programming algorithm for nucleosome positions alignment." In 2014 8th International Conference on Systems Biology (ISB). IEEE, 2014. http://dx.doi.org/10.1109/isb.2014.6990422.

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Conlon, T. M., J. Dorer, R. S. J. Sarker, G. Burgstaller, L. Merthan, V. Gailus-Durner, H. Fuchs, et al. "Chromatin Dynamics Regulates Chronic Obstructive Pulmonary Disease Susceptibility via the Nucleosomal Binding Protein HMGN5." In American Thoracic Society 2020 International Conference, May 15-20, 2020 - Philadelphia, PA. American Thoracic Society, 2020. http://dx.doi.org/10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a1215.

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Reports on the topic "Nucleosome Dynamics"

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Zlatanova, Jordanka. BRCA 1-Mediated Histone Monoubiquitylation: Effect on Nucleosome Dynamics. Fort Belvoir, VA: Defense Technical Information Center, February 2008. http://dx.doi.org/10.21236/ada482568.

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Howell, Steven C. Dynamic Conformations of Nucleosome Arrays in Solution from Small-Angle X-ray Scattering. Office of Scientific and Technical Information (OSTI), January 2016. http://dx.doi.org/10.2172/1338475.

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