Journal articles: '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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Ichikawa, Yuichi, Yoshifumi Nishimura, Hitoshi Kurumizaka, and Mitsuhiro Shimizu. "Nucleosome organization and chromatin dynamics in telomeres." Biomolecular Concepts 6, no. 1 (March 1, 2015): 67–75. http://dx.doi.org/10.1515/bmc-2014-0035.

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AbstractTelomeres are DNA-protein complexes located at the ends of linear eukaryotic chromosomes, and are essential for chromosome stability and maintenance. In most organisms, telomeres consist of tandemly repeated sequences of guanine-clusters. In higher eukaryotes, most of the telomeric repeat regions are tightly packaged into nucleosomes, even though telomeric repeats act as nucleosome-disfavoring sequences. Although telomeres were considered to be condensed heterochromatin structures, recent studies revealed that the chromatin structures in telomeres are actually dynamic. The dynamic properties of telomeric chromatin are considered to be important for the structural changes between the euchromatic and heterochromatic states during the cell cycle and in cellular differentiation. We propose that the nucleosome-disfavoring property of telomeric repeats is a crucial determinant for the lability of telomeric nucleosomes, and provides a platform for chromatin dynamics in telomeres. Furthermore, we discuss the influences of telomeric components on the nucleosome organization and chromatin dynamics in telomeres.

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Brandani, Giovanni B., Cheng Tan, and Shoji Takada. "The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study." PLOS Computational Biology 17, no. 7 (July 27, 2021): e1009253. http://dx.doi.org/10.1371/journal.pcbi.1009253.

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The organization of nucleosomes along the Eukaryotic genome is maintained over time despite disruptive events such as replication. During this complex process, histones and DNA can form a variety of non-canonical nucleosome conformations, but their precise molecular details and roles during nucleosome assembly remain unclear. In this study, employing coarse-grained molecular dynamics simulations and Markov state modeling, we characterized the complete kinetics of nucleosome assembly. On the nucleosome-positioning 601 DNA sequence, we observe a rich transition network among various canonical and non-canonical tetrasome, hexasome, and nucleosome conformations. A low salt environment makes nucleosomes stable, but the kinetic landscape becomes more rugged, so that the system is more likely to be trapped in off-pathway partially assembled intermediates. Finally, we find that the co-operativity between DNA bending and histone association enables positioning sequence motifs to direct the assembly process, with potential implications for the dynamic organization of nucleosomes on real genomic sequences.

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Filenko, Nina A., Dmytro B. Palets, and Yuri L. Lyubchenko. "Structure and Dynamics of Dinucleosomes Assessed by Atomic Force Microscopy." Journal of Amino Acids 2012 (October 23, 2012): 1–6. http://dx.doi.org/10.1155/2012/650840.

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Dynamics of nucleosomes and their interactions are important for understanding the mechanism of chromatin assembly. Internucleosomal interaction is required for the formation of higher-order chromatin structures. Although H1 histone is critically involved in the process of chromatin assembly, direct internucleosomal interactions contribute to this process as well. To characterize the interactions of nucleosomes within the nucleosome array, we designed a dinucleosome and performed direct AFM imaging. The analysis of the AFM data showed dinucleosomes are very dynamic systems, enabling the nucleosomes to move in a broad range along the DNA template. Di-nucleosomes in close proximity were observed, but their population was low. The use of the zwitterionic detergent, CHAPS, increased the dynamic range of the di-nucleosome, facilitating the formation of tight di-nucleosomes. The role of CHAPS and similar natural products in chromatin structure and dynamics is also discussed.

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Korber, Philipp, and Peter B. Becker. "Nucleosome dynamics and epigenetic stability." Essays in Biochemistry 48 (September 20, 2010): 63–74. http://dx.doi.org/10.1042/bse0480063.

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Nucleosome remodelling is an essential principle to assure that the packaging of eukaryotic genomes in chromatin remains flexible and adaptable to regulatory needs. Nucleosome remodelling enzymes spend the energy of ATP to alter histone–DNA interactions, to catalyse nucleosome displacement and reassembly, on histone exchange and on the relocation of histone octamers on DNA. Despite these dynamics, chromatin structures encode ‘epigenetic’ information that governs the expression of the underlying genes. These information-bearing structures must be maintained over extended periods of time in resting cells and may be sufficiently stable to resist the turmoil of the cell cycle to be passed on to the next cell generation. Intuitively, nucleosome remodelling should antagonize the maintenance of stable structures. However, upon closer inspection it becomes evident that nucleosome remodelling is intimately involved in the assembly of stable chromatin structures that correspond to functional states. Remodellers may even contribute structural information themselves. Their involvement can be seen at several structural levels: at the levels of positioning individual nucleosomes, homoeostasis of linker histones, histone variants and non-histone proteins, as well as the differential folding of the nucleosome fibre. All of them may contribute to the assembly of heritable epigenetic structures.

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Furukawa, Ayako, Masatoshi Wakamori, Yasuhiro Arimura, Hideaki Ohtomo, Yasuo Tsunaka, Hitoshi Kurumizaka, Takashi Umehara, and Yoshifumi Nishimura. "Acetylated histone H4 tail enhances histone H3 tail acetylation by altering their mutual dynamics in the nucleosome." Proceedings of the National Academy of Sciences 117, no. 33 (August 3, 2020): 19661–63. http://dx.doi.org/10.1073/pnas.2010506117.

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The structural unit of eukaryotic chromatin is a nucleosome, comprising two histone H2A-H2B heterodimers and one histone (H3-H4)2tetramer, wrapped around by ∼146 bp of DNA. The N-terminal flexible histone tails stick out from the histone core and have extensive posttranslational modifications, causing epigenetic changes of chromatin. Although crystal and cryogenic electron microscopy structures of nucleosomes are available, the flexible tail structures remain elusive. Using NMR, we have examined the dynamics of histone H3 tails in nucleosomes containing unmodified and tetra-acetylated H4 tails. In unmodified nucleosome, the H3 tail adopts a dynamic equilibrium structure between DNA-contact and reduced-contact states. In acetylated H4 nucleosome, however, the H3 tail equilibrium shifts to a mainly DNA-contact state with a minor reduced-contact state. The acetylated H4 tail is dynamically released from its own DNA-contact state to a reduced-contact state, while the H3 tail DNA-contact state becomes major. Notably, H3 K14 in the acetylated H4 nucleosome is much more accessible to acetyltransferase Gcn5 relative to unmodified nucleosome, possibly due to the formation of a favorable H3 tail conformation for Gcn5. In summary, each histone tail adopts a characteristic dynamic state but regulates one other, probably creating a histone tail network even on a nucleosome.

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Henikoff, Steven. "New Approaches for Mapping Epigenome Dynamics." Blood 126, no. 23 (December 3, 2015): SCI—21—SCI—21. http://dx.doi.org/10.1182/blood.v126.23.sci-21.sci-21.

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Abstract The protein complexes that package our genomes must be mobilized for active processes to occur, including replication and transcription, but until recently we have only had a static, low resolution view of the "epigenome". Genomes are packaged into nucleosomes, octamers of four core histones wrapped by 147 base pairs of DNA. Nucleosomes present obstacles to transcription, which over genes is the RNA Polymerase II (RNAPII) complex, and one current challenge is to understand what happens to a nucleosome when RNAPII transcribes through the DNA that it occupies. We study this process by developing methods for following nucleosomes as they are evicted and replaced. Among the factors that we have implicated in the process is torsional stress, which we can now measure genome-wide. RNAPII movement can unwrap nucleosomes and thus destabilize them, causing them to be occasionally evicted and replaced. Interestingly, we find that destabilization of nucleosomes during transcription is enhanced by anthracycline compounds, widely used chemotherapeutic drugs that intercalate between DNA base pairs, thus suggesting a new mechanism for cell killing during chemotherapy. We are also interested in what happens to RNAPII during its encounter with a nucleosomes. In vitro, RNAPII cannot transcribe completely through a nucleosome, but rather stalls as it tries to unwrap the DNA from around the core. We have been studying this process in vivo, and have developed a simple method for precisely mapping RNAPII genome-wide. We have used this method to show exactly where RNAPII stalls as it unwraps a nucleosome in vivo, surprisingly in a different place in vivo from where it stalls in vitro. We also have discovered that a variant histone, H2A.Z, which is found in essentially all eukaryotes, helps to reduce the nucleosome barrier to transcription, and in this way may modulate transcription. Other protein components of the epigenome involved in dynamic processes are nucleosome remodelers, which use the energy of ATP to slide or even evict nucleosomes from DNA. Some remodelers help RNAPII get started and others help it overcome the nucleosome barrier to transcription, and by mapping them at base-pair resolution, we can gain insight into how they act. We have also applied our high-resolution mapping tools to transcription factors, which bind DNA at specific sites to regulate transcription and other processes. Our ability to achieve high spatial and temporal resolution mapping of the binding and action of nucleosomes, transcription factors, remodelers and RNAPII provides us with a detailed picture of epigenome dynamics. By using these tools we are beginning to understand how DNA sequence and conformation are recognized for regulation of transcription and other epigenomic processes. Disclosures No relevant conflicts of interest to declare.

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Barbier, Jérémy, Cédric Vaillant, Jean-Nicolas Volff, Frédéric G. Brunet, and Benjamin Audit. "Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution." Genes 12, no. 6 (June 1, 2021): 851. http://dx.doi.org/10.3390/genes12060851.

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The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequence has an influence on the position of nucleosomes on genomes, although other factors are also implicated, such as ATP-dependent remodelers or competition of the nucleosome with DNA binding proteins. Different sequence motifs can promote or inhibit the nucleosome formation, thus influencing the accessibility to the DNA. Sequence-encoded nucleosome positioning having functional consequences on cell processes can then be selected or counter-selected during evolution. We review the interplay between sequence evolution and nucleosome positioning evolution. We first focus on the different ways to encode nucleosome positions in the DNA sequence, and to which extent these mechanisms are responsible of genome-wide nucleosome positioning in vivo. Then, we discuss the findings about selection of sequences for their nucleosomal properties. Finally, we illustrate how the nucleosome can directly influence sequence evolution through its interactions with DNA damage and repair mechanisms. This review aims to provide an overview of the mutual influence of sequence evolution and nucleosome positioning evolution, possibly leading to complex evolutionary dynamics.

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Ong, Michelle S., Dileep Vasudevan, and Curt A. Davey. "Divalent Metal- and High Mobility Group N Protein-Dependent Nucleosome Stability and Conformation." Journal of Nucleic Acids 2010 (2010): 1–10. http://dx.doi.org/10.4061/2010/143890.

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High mobility group N proteins (HMGNs) bind specifically to the nucleosome core and act as chromatin unfolding and activating factors. Using an all-Xenopussystem, we found that HMGN1 and HMGN2 binding to nucleosomes results in distinct ion-dependent conformation and stability. HMGN2 association with nucleosome core particle or nucleosomal array in the presence of divalent metal triggers a reversible transition to a species with much reduced electrophoretic mobility, consistent with a less compact state of the nucleosome. Residues outside of the nucleosome binding domain are required for the activity, which is also displayed by an HMGN1 truncation product lacking part of the regulatory domain. In addition, thermal denaturation assays show that the presence of 1 mM Mg2+> or Ca2+gives a reduction in nucleosome core terminus stability, which is further substantially diminished by the binding of HMGN2 or truncated HMGN1. Our findings emphasize the importance of divalent metals in nucleosome dynamics and suggest that the differential biological activities of HMGNs in chromatin activation may involve different conformational alterations and modulation of nucleosome core stability.

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Cole, Lauren, and Jonathan Dennis. "MNase Profiling of Promoter Chromatin in Salmonella typhimurium-Stimulated GM12878 Cells Reveals Dynamic and Response-Specific Nucleosome Architecture." G3: Genes|Genomes|Genetics 10, no. 7 (May 13, 2020): 2171–78. http://dx.doi.org/10.1534/g3.120.401266.

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The nucleosome is the primary unit of chromatin structure and commonly imputed as a regulator of nuclear events, although the exact mechanisms remain unclear. Recent studies have shown that certain nucleosomes can have different sensitivities to micrococcal nuclease (MNase) digestion, resulting in the release of populations of nucleosomes dependent on the concentration of MNase. Mapping MNase sensitivity of nucleosomes at transcription start sites genome-wide reveals an important functional nucleosome organization that correlates with gene expression levels and transcription factor binding. In order to understand nucleosome distribution and sensitivity dynamics during a robust genome response, we mapped nucleosome position and sensitivity using multiple concentrations of MNase. We used the innate immune response as a model system to understand chromatin-mediated regulation. Herein we demonstrate that stimulation of a human lymphoblastoid cell line (GM12878) with heat-killed Salmonella typhimurium (HKST) results in changes in nucleosome sensitivity to MNase. We show that the HKST response alters the sensitivity of -1 nucleosomes at highly expressed promoters. Finally, we correlate the increased sensitivity with response-specific transcription factor binding. These results indicate that nucleosome sensitivity dynamics reflect the cellular response to HKST and pave the way for further studies that will deepen our understanding of the specificity of genome response.

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Huertas, Jan, Hans Robert Schöler, and Vlad Cojocaru. "Histone tails cooperate to control the breathing of genomic nucleosomes." PLOS Computational Biology 17, no. 6 (June 3, 2021): e1009013. http://dx.doi.org/10.1371/journal.pcbi.1009013.

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Genomic DNA is packaged in chromatin, a dynamic fiber variable in size and compaction. In chromatin, repeating nucleosome units wrap 145–147 DNA basepairs around histone proteins. Genetic and epigenetic regulation of genes relies on structural transitions in chromatin which are driven by intra- and inter-nucleosome dynamics and modulated by chemical modifications of the unstructured terminal tails of histones. Here we demonstrate how the interplay between histone H3 and H2A tails control ample nucleosome breathing motions. We monitored large openings of two genomic nucleosomes, and only moderate breathing of an engineered nucleosome in atomistic molecular simulations amounting to 24 μs. Transitions between open and closed nucleosome conformations were mediated by the displacement and changes in compaction of the two histone tails. These motions involved changes in the DNA interaction profiles of clusters of epigenetic regulatory aminoacids in the tails. Removing the histone tails resulted in a large increase of the amplitude of nucleosome breathing but did not change the sequence dependent pattern of the motions. Histone tail modulated nucleosome breathing is a key mechanism of chromatin dynamics with important implications for epigenetic regulation.

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Sridhar, Akshay, Stephen E. Farr, Guillem Portella, Tamar Schlick, Modesto Orozco, and Rosana Collepardo-Guevara. "Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry." Proceedings of the National Academy of Sciences 117, no. 13 (March 12, 2020): 7216–24. http://dx.doi.org/10.1073/pnas.1910044117.

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Protein flexibility and disorder is emerging as a crucial modulator of chromatin structure. Histone tail disorder enables transient binding of different molecules to the nucleosomes, thereby promoting heterogeneous and dynamic internucleosome interactions and making possible recruitment of a wide-range of regulatory and remodeling proteins. On the basis of extensive multiscale modeling we reveal the importance of linker histone H1 protein disorder for chromatin hierarchical looping. Our multiscale approach bridges microsecond-long bias-exchange metadynamics molecular dynamics simulations of atomistic 211-bp nucleosomes with coarse-grained Monte Carlo simulations of 100-nucleosome systems. We show that the long C-terminal domain (CTD) of H1—a ubiquitous nucleosome-binding protein—remains disordered when bound to the nucleosome. Notably, such CTD disorder leads to an asymmetric and dynamical nucleosome conformation that promotes chromatin structural flexibility and establishes long-range hierarchical loops. Furthermore, the degree of condensation and flexibility of H1 can be fine-tuned, explaining chromosomal differences of interphase versus metaphase states that correspond to partial and hyperphosphorylated H1, respectively. This important role of H1 protein disorder in large-scale chromatin organization has a wide range of biological implications.

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Lequieu, Joshua, David C. Schwartz, and Juan J. de Pablo. "In silico evidence for sequence-dependent nucleosome sliding." Proceedings of the National Academy of Sciences 114, no. 44 (October 18, 2017): E9197—E9205. http://dx.doi.org/10.1073/pnas.1705685114.

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Nucleosomes represent the basic building block of chromatin and provide an important mechanism by which cellular processes are controlled. The locations of nucleosomes across the genome are not random but instead depend on both the underlying DNA sequence and the dynamic action of other proteins within the nucleus. These processes are central to cellular function, and the molecular details of the interplay between DNA sequence and nucleosome dynamics remain poorly understood. In this work, we investigate this interplay in detail by relying on a molecular model, which permits development of a comprehensive picture of the underlying free energy surfaces and the corresponding dynamics of nucleosome repositioning. The mechanism of nucleosome repositioning is shown to be strongly linked to DNA sequence and directly related to the binding energy of a given DNA sequence to the histone core. It is also demonstrated that chromatin remodelers can override DNA-sequence preferences by exerting torque, and the histone H4 tail is then identified as a key component by which DNA-sequence, histone modifications, and chromatin remodelers could in fact be coupled.

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Morse, Randall H. "Getting into chromatin: how do transcription factors get past the histones?" Biochemistry and Cell Biology 81, no. 3 (June 1, 2003): 101–12. http://dx.doi.org/10.1139/o03-039.

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Transcriptional activators and the general transcription machinery must gain access to DNA that in eukaryotes may be packaged into nucleosomes. In this review, I discuss this problem from the standpoint of the types of chromatin structures that these DNA-binding proteins may encounter, and the mechanisms by which they may contend with various chromatin structures. The discussion includes consideration of experiments in which chromatin structure is manipulated in vivo to confront activators with nucleosomal binding sites, and the roles of nucleosome dynamics and activation domains in facilitating access to such sites. Finally, the role of activators in facilitating access of the general transcriptional machinery to sites in chromatin is discussed. Key words: nucleosome, chromatin, transcriptional activation, Saccharomyces cerevisiae.

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Ferreira, Helder, Joanna Somers, Ryan Webster, Andrew Flaus, and Tom Owen-Hughes. "Histone Tails and the H3 αN Helix Regulate Nucleosome Mobility and Stability." Molecular and Cellular Biology 27, no. 11 (March 26, 2007): 4037–48. http://dx.doi.org/10.1128/mcb.02229-06.

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ABSTRACT Nucleosomes fulfill the apparently conflicting roles of compacting DNA within eukaryotic genomes while permitting access to regulatory factors. Central to this is their ability to stably associate with DNA while retaining the ability to undergo rearrangements that increase access to the underlying DNA. Here, we have studied different aspects of nucleosome dynamics including nucleosome sliding, histone dimer exchange, and DNA wrapping within nucleosomes. We find that alterations to histone proteins, especially the histone tails and vicinity of the histone H3 αN helix, can affect these processes differently, suggesting that they are mechanistically distinct. This raises the possibility that modifications to histone proteins may provide a means of fine-tuning specific aspects of the dynamic properties of nucleosomes to the context in which they are located.

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Catez, Frédéric, Jae-Hwan Lim, Robert Hock, Yuri V. Postnikov, and Michael Bustin. "HMGN dynamics and chromatin function." Biochemistry and Cell Biology 81, no. 3 (June 1, 2003): 113–22. http://dx.doi.org/10.1139/o03-040.

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Recent studies indicate that most nuclear proteins, including histone H1 and HMG are highly mobile and their interaction with chromatin is transient. These findings suggest that the structure of chromatin is dynamic and the protein composition at any particular chromatin site is not fixed. Here we discuss how the dynamic behavior of the nucleosome binding HMGN proteins affects the structure and function of chromatin. The high intranuclear mobility of HMGN insures adequate supply of protein throughout the nucleus and serves to target these proteins to their binding sites. Transient interactions of the proteins with nucleosomes destabilize the higher order chromatin, enhance the access to nucleosomal DNA, and impart flexibility to the chromatin fiber. While roaming the nucleus, the HMGN proteins encounter binding partners and form metastable multiprotein complexes, which modulate their chromatin interactions. Studies with HMGN proteins underscore the important role of protein dynamics in chromatin function.Key words: HMG, nuclear proteins, chromatin, HMGN.

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Willhoft, Oliver, Mohamed Ghoneim, Chia-Liang Lin, Eugene Y. D. Chua, Martin Wilkinson, Yuriy Chaban, Rafael Ayala, et al. "Structure and dynamics of the yeast SWR1-nucleosome complex." Science 362, no. 6411 (October 11, 2018): eaat7716. http://dx.doi.org/10.1126/science.aat7716.

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The yeast SWR1 complex exchanges histone H2A in nucleosomes with Htz1 (H2A.Z in humans). The cryo–electron microscopy structure of the SWR1 complex bound to a nucleosome at 3.6-angstrom resolution reveals details of the intricate interactions between components of the SWR1 complex and its nucleosome substrate. Interactions between the Swr1 motor domains and the DNA wrap at superhelical location 2 distort the DNA, causing a bulge with concomitant translocation of the DNA by one base pair, coupled to conformational changes of the histone core. Furthermore, partial unwrapping of the DNA from the histone core takes place upon binding of nucleosomes to SWR1 complex. The unwrapping, as monitored by single-molecule data, is stabilized and has its dynamics altered by adenosine triphosphate binding but does not require hydrolysis.

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Chen, Ping, Wei Li, and Guohong Li. "Structures and Functions of Chromatin Fibers." Annual Review of Biophysics 50, no. 1 (May 6, 2021): 95–116. http://dx.doi.org/10.1146/annurev-biophys-062920-063639.

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In eukaryotes, genomic DNA is packaged into chromatin in the nucleus. The accessibility of DNA is dependent on the chromatin structure and dynamics, which essentially control DNA-related processes, including transcription, DNA replication, and repair. All of the factors that affect the structure and dynamics of nucleosomes, the nucleosome–nucleosome interaction interfaces, and the binding of linker histones or other chromatin-binding proteins need to be considered to understand the organization and function of chromatin fibers. In this review, we provide a summary of recent progress on the structure of chromatin fibers in vitro and in the nucleus, highlight studies on the dynamic regulation of chromatin fibers, and discuss their related biological functions and abnormal organization in diseases.

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Jing, Yihang, Dongbo Ding, Gaofei Tian, Ka Chun Jonathan Kwan, Zheng Liu, Toyotaka Ishibashi, and Xiang David Li. "Semisynthesis of site-specifically succinylated histone reveals that succinylation regulates nucleosome unwrapping rate and DNA accessibility." Nucleic Acids Research 48, no. 17 (August 7, 2020): 9538–49. http://dx.doi.org/10.1093/nar/gkaa663.

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Abstract Posttranslational modifications (PTMs) of histones represent a crucial regulatory mechanism of nucleosome and chromatin dynamics in various of DNA-based cellular processes, such as replication, transcription and DNA damage repair. Lysine succinylation (Ksucc) is a newly identified histone PTM, but its regulation and function in chromatin remain poorly understood. Here, we utilized an expressed protein ligation (EPL) strategy to synthesize histone H4 with site-specific succinylation at K77 residue (H4K77succ), an evolutionarily conserved succinylation site at the nucleosomal DNA-histone interface. We then assembled mononucleosomes with the semisynthetic H4K77succ in vitro. We demonstrated that this succinylation impacts nucleosome dynamics and promotes DNA unwrapping from the histone surface, which allows proteins such as transcription factors to rapidly access buried regions of the nucleosomal DNA. In budding yeast, a lysine-to-glutamic acid mutation, which mimics Ksucc, at the H4K77 site reduced nucleosome stability and led to defects in DNA damage repair and telomere silencing in vivo. Our findings revealed this uncharacterized histone modification has important roles in nucleosome and chromatin dynamics.

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Gursoy-Yuzugullu, Ozge, Marina K. Ayrapetov, and Brendan D. Price. "Histone chaperone Anp32e removes H2A.Z from DNA double-strand breaks and promotes nucleosome reorganization and DNA repair." Proceedings of the National Academy of Sciences 112, no. 24 (June 1, 2015): 7507–12. http://dx.doi.org/10.1073/pnas.1504868112.

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The repair of DNA double-strand breaks (DSBs) requires open, flexible chromatin domains. The NuA4–Tip60 complex creates these flexible chromatin structures by exchanging histone H2A.Z onto nucleosomes and promoting acetylation of histone H4. Here, we demonstrate that the accumulation of H2A.Z on nucleosomes at DSBs is transient, and that rapid eviction of H2A.Z is required for DSB repair. Anp32e, an H2A.Z chaperone that interacts with the C-terminal docking domain of H2A.Z, is rapidly recruited to DSBs. Anp32e functions to remove H2A.Z from nucleosomes, so that H2A.Z levels return to basal within 10 min of DNA damage. Further, H2A.Z removal by Anp32e disrupts inhibitory interactions between the histone H4 tail and the nucleosome surface, facilitating increased acetylation of histone H4 following DNA damage. When H2A.Z removal by Anp32e is blocked, nucleosomes at DSBs retain elevated levels of H2A.Z, and assume a more stable, hypoacetylated conformation. Further, loss of Anp32e leads to increased CtIP-dependent end resection, accumulation of single-stranded DNA, and an increase in repair by the alternative nonhomologous end joining pathway. Exchange of H2A.Z onto the chromatin and subsequent rapid removal by Anp32e are therefore critical for creating open, acetylated nucleosome structures and for controlling end resection by CtIP. Dynamic modulation of H2A.Z exchange and removal by Anp32e reveals the importance of the nucleosome surface and nucleosome dynamics in processing the damaged chromatin template during DSB repair.

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Soman, Aghil, Chong Wai Liew, Hsiang Ling Teo, Nikolay V. Berezhnoy, Vincent Olieric, Nikolay Korolev, Daniela Rhodes, and Lars Nordenskiöld. "The human telomeric nucleosome displays distinct structural and dynamic properties." Nucleic Acids Research 48, no. 10 (May 6, 2020): 5383–96. http://dx.doi.org/10.1093/nar/gkaa289.

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Abstract Telomeres protect the ends of our chromosomes and are key to maintaining genomic integrity during cell division and differentiation. However, our knowledge of telomeric chromatin and nucleosome structure at the molecular level is limited. Here, we aimed to define the structure, dynamics as well as properties in solution of the human telomeric nucleosome. We first determined the 2.2 Å crystal structure of a human telomeric nucleosome core particle (NCP) containing 145 bp DNA, which revealed the same helical path for the DNA as well as symmetric stretching in both halves of the NCP as that of the 145 bp ‘601’ NCP. In solution, the telomeric nucleosome exhibited a less stable and a markedly more dynamic structure compared to NCPs containing DNA positioning sequences. These observations provide molecular insights into how telomeric DNA forms nucleosomes and chromatin and advance our understanding of the unique biological role of telomeres.

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le Paige, Ulric B., ShengQi Xiang, Marco M. R. M. Hendrix, Yi Zhang, Gert E. Folkers, Markus Weingarth, Alexandre M. J. J. Bonvin, et al. "Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy." Magnetic Resonance 2, no. 1 (April 21, 2021): 187–202. http://dx.doi.org/10.5194/mr-2-187-2021.

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Abstract. Regulation of DNA-templated processes such as gene transcription and DNA repair depend on the interaction of a wide range of proteins with the nucleosome, the fundamental building block of chromatin. Both solution and solid-state NMR spectroscopy have become an attractive approach to study the dynamics and interactions of nucleosomes, despite their high molecular weight of ∼200 kDa. For solid-state NMR (ssNMR) studies, dilute solutions of nucleosomes are converted to a dense phase by sedimentation or precipitation. Since nucleosomes are known to self-associate, these dense phases may induce extensive interactions between nucleosomes, which could interfere with protein-binding studies. Here, we characterized the packing of nucleosomes in the dense phase created by sedimentation using NMR and small-angle X-ray scattering (SAXS) experiments. We found that nucleosome sediments are gels with variable degrees of solidity, have nucleosome concentration close to that found in crystals, and are stable for weeks under high-speed magic angle spinning (MAS). Furthermore, SAXS data recorded on recovered sediments indicate that there is no pronounced long-range ordering of nucleosomes in the sediment. Finally, we show that the sedimentation approach can also be used to study low-affinity protein interactions with the nucleosome. Together, our results give new insights into the sample characteristics of nucleosome sediments for ssNMR studies and illustrate the broad applicability of sedimentation-based NMR studies.

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Tan, Cheng, and Shoji Takada. "Nucleosome allostery in pioneer transcription factor binding." Proceedings of the National Academy of Sciences 117, no. 34 (August 10, 2020): 20586–96. http://dx.doi.org/10.1073/pnas.2005500117.

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While recent experiments revealed that some pioneer transcription factors (TFs) can bind to their target DNA sequences inside a nucleosome, the binding dynamics of their target recognitions are poorly understood. Here we used the latest coarse-grained models and molecular dynamics simulations to study the nucleosome-binding procedure of the two pioneer TFs, Sox2 and Oct4. In the simulations for a strongly positioning nucleosome, Sox2 selected its target DNA sequence only when the target was exposed. Otherwise, Sox2 entropically bound to the dyad region nonspecifically. In contrast, Oct4 plastically bound on the nucleosome mainly in two ways. First, the two POU domains of Oct4 separately bound to the two parallel gyres of the nucleosomal DNA, supporting the previous experimental results of the partial motif recognition. Second, the POUSdomain of Oct4 favored binding on the acidic patch of histones. Then, simulating the TFs binding to a genomic nucleosome, theLIN28Bnucleosome, we found that the recognition of a pseudo motif by Sox2 induced the local DNA bending and shifted the population of the rotational position of the nucleosomal DNA. The redistributed DNA phase, in turn, changed the accessibility of a distant TF binding site, which consequently affected the binding probability of a second Sox2 or Oct4. These results revealed a nucleosomal DNA-mediated allosteric mechanism, through which one TF binding event can change the global conformation, and effectively regulate the binding of another TF at distant sites. Our simulations provide insights into the binding mechanism of single and multiple TFs on the nucleosome.

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Wen, Zengqi, Liwei Zhang, Haihe Ruan, and Guohong Li. "Histone variant H2A.Z regulates nucleosome unwrapping and CTCF binding in mouse ES cells." Nucleic Acids Research 48, no. 11 (May 11, 2020): 5939–52. http://dx.doi.org/10.1093/nar/gkaa360.

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Abstract Nucleosome is the basic structural unit of chromatin, and its dynamics plays critical roles in the regulation of genome functions. However, how the nucleosome structure is regulated by histone variants in vivo is still largely uncharacterized. Here, by employing Micrococcal nuclease (MNase) digestion of crosslinked chromatin followed by chromatin immunoprecipitation (ChIP) and paired-end sequencing (MNase-X-ChIP-seq), we mapped unwrapping states of nucleosomes containing histone variant H2A.Z in mouse embryonic stem (ES) cells. We found that H2A.Z nucleosomes are more enriched with unwrapping states compared with canonical nucleosomes. Interestingly, +1 H2A.Z nucleosomes with 30–80 bp DNA is correlated with less active genes compared with +1 H2A.Z nucleosomes with 120–140 bp DNA. We confirmed the unwrapping of H2A.Z nucleosomes under native condition by re-ChIP of H2A.Z and H2A after CTCF CUT&RUN in mouse ES cells. Importantly, we found that depletion of H2A.Z results in decreased unwrapping of H3.3 nucleosomes and increased CTCF binding. Taken together, through MNase-X-ChIP-seq, we showed that histone variant H2A.Z regulates nucleosome unwrapping in vivo and that its function in regulating transcription or CTCF binding is correlated with unwrapping states of H2A.Z nucleosomes.

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Reinberg, Danny, and Robert J. Sims. "de FACTo Nucleosome Dynamics." Journal of Biological Chemistry 281, no. 33 (June 9, 2006): 23297–301. http://dx.doi.org/10.1074/jbc.r600007200.

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Eslami-Mossallam, Behrouz, Helmut Schiessel, and John van Noort. "Nucleosome dynamics: Sequence matters." Advances in Colloid and Interface Science 232 (June 2016): 101–13. http://dx.doi.org/10.1016/j.cis.2016.01.007.

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Chatterjee, Nilanjana, Justin A. North, Mekonnen Lemma Dechassa, Mridula Manohar, Rashmi Prasad, Karolin Luger, Jennifer J. Ottesen, Michael G. Poirier, and Blaine Bartholomew. "Histone Acetylation near the Nucleosome Dyad Axis Enhances Nucleosome Disassembly by RSC and SWI/SNF." Molecular and Cellular Biology 35, no. 23 (September 28, 2015): 4083–92. http://dx.doi.org/10.1128/mcb.00441-15.

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Signaling associated with transcription activation occurs through posttranslational modification of histones and is best exemplified by lysine acetylation. Lysines are acetylated in histone tails and the core domain/lateral surface of histone octamers. While acetylated lysines in histone tails are frequently recognized by other factors referred to as “readers,” which promote transcription, the mechanistic role of the modifications in the lateral surface of the histone octamer remains unclear. By using X-ray crystallography, we found that acetylated lysines 115 and 122 in histone H3 are solvent accessible, but in biochemical assays they appear not to interact with the bromodomains of SWI/SNF and RSC to enhance recruitment or nucleosome mobilization, as previously shown for acetylated lysines in H3 histone tails. Instead, we found that acetylation of lysines 115 and 122 increases the predisposition of nucleosomes for disassembly by SWI/SNF and RSC up to 7-fold, independent of bromodomains, and only in conjunction with contiguous nucleosomes. Thus, in combination with SWI/SNF and RSC, acetylation of lateral surface lysines in the histone octamer serves as a crucial regulator of nucleosomal dynamics distinct from the histone code readers and writers.

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Lehmann, Kathrin, Suren Felekyan, Ralf Kühnemuth, Mykola Dimura, Katalin Tóth, Claus A. M. Seidel, and Jörg Langowski. "Dynamics of the nucleosomal histone H3 N-terminal tail revealed by high precision single-molecule FRET." Nucleic Acids Research 48, no. 3 (January 20, 2020): 1551–71. http://dx.doi.org/10.1093/nar/gkz1186.

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Abstract Chromatin compaction and gene accessibility are orchestrated by assembly and disassembly of nucleosomes. Although the disassembly process was widely studied, little is known about the structure and dynamics of the disordered histone tails, which play a pivotal role for nucleosome integrity. This is a gap filling experimental FRET study from the perspective of the histone H3 N-terminal tail (H3NtT) of reconstituted mononucleosomes. By systematic variation of the labeling positions we monitored the motions of the H3NtT relative to the dyad axis and linker DNA. Single-molecule FRET unveiled that H3NtTs do not diffuse freely but follow the DNA motions with multiple interaction modes with certain permitted dynamic transitions in the μs to ms time range. We also demonstrate that the H3NtT can allosterically sense charge-modifying mutations within the histone core (helix α3 of histone H2A (R81E/R88E)) resulting in increased dynamic transitions and lower rate constants. Those results complement our earlier model on the NaCl induced nucleosome disassembly as changes in H3NtT configurations coincide with two major steps: unwrapping of one linker DNA and weakening of the internal DNA - histone interactions on the other side. This emphasizes the contribution of the H3NtT to the fine-tuned equilibrium between overall nucleosome stability and DNA accessibility.

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Luo, Yi, Justin A. North, Sean D. Rose, and Michael G. Poirier. "Nucleosomes accelerate transcription factor dissociation." Nucleic Acids Research 42, no. 5 (December 17, 2013): 3017–27. http://dx.doi.org/10.1093/nar/gkt1319.

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AbstractTranscription factors (TF) bind DNA-target sites within promoters to activate gene expression. TFs target their DNA-recognition sequences with high specificity by binding with resident times of up to hours in vitro. However, in vivo TFs can exchange on the order of seconds. The factors that regulate TF dynamics in vivo and increase dissociation rates by orders of magnitude are not known. We investigated TF binding and dissociation dynamics at their recognition sequence within duplex DNA, single nucleosomes and short nucleosome arrays with single molecule total internal reflection fluorescence (smTIRF) microscopy. We find that the rate of TF dissociation from its site within either nucleosomes or nucleosome arrays is increased by 1000-fold relative to duplex DNA. Our results suggest that TF binding within chromatin could be responsible for the dramatic increase in TF exchange in vivo. Furthermore, these studies demonstrate that nucleosomes regulate DNA–protein interactions not only by preventing DNA–protein binding but by dramatically increasing the dissociation rate of protein complexes from their DNA-binding sites.

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Sharma, Shantanu, Feng Ding, and Nikolay V. Dokholyan. "Multiscale Modeling of Nucleosome Dynamics." Biophysical Journal 92, no. 5 (March 2007): 1457–70. http://dx.doi.org/10.1529/biophysj.106.094805.

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Huynh, Mai T., Satya P. Yadav, Joseph C. Reese, and Tae-Hee Lee. "Nucleosome Dynamics during Transcription Elongation." ACS Chemical Biology 15, no. 12 (December 2, 2020): 3133–42. http://dx.doi.org/10.1021/acschembio.0c00617.

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Ahmad, Kami, and Steven Henikoff. "Epigenetic Consequences of Nucleosome Dynamics." Cell 111, no. 3 (November 2002): 281–84. http://dx.doi.org/10.1016/s0092-8674(02)01081-4.

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Ray-Gallet, Dominique, and Geneviève Almouzni. "Nucleosome dynamics and histone variants." Essays in Biochemistry 48 (September 20, 2010): 75–87. http://dx.doi.org/10.1042/bse0480075.

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In eukaryotes, DNA is organized into chromatin, a dynamic structure that enables DNA to be accessed for processes such as transcription, replication and repair. To form, maintain or alter this organization according to cellular needs, histones, the main protein component of chromatin, are deposited, replaced, exchanged and post-translationally modified. Histone variants, which exhibit specialized deposition modes in relation to the cell cycle and possibly particular chromatin regions, add an additional level of complexity in the regulation of histone flow. During their metabolism, from their synthesis to their delivery for nucleosome formation, the histones are escorted by proteins called histone chaperones. In the present chapter we summarize our current knowledge concerning histone chaperones and their interaction with particular histones based on key structural properties. From a compilation of selected histone chaperones identified to date, we discuss how they may be placed in a network to regulate histone dynamics. Finally, we provide working models to explain how H3 variants, deposited on to DNA using different histone chaperone machineries, can be transmitted or lost through cell divisions.

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Luger, Karolin, and Jeffrey C. Hansen. "Nucleosome and chromatin fiber dynamics." Current Opinion in Structural Biology 15, no. 2 (April 2005): 188–96. http://dx.doi.org/10.1016/j.sbi.2005.03.006.

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Adkins, Nicholas L., Hengyao Niu, Patrick Sung, and Craig L. Peterson. "Nucleosome dynamics regulates DNA processing." Nature Structural & Molecular Biology 20, no. 7 (June 2, 2013): 836–42. http://dx.doi.org/10.1038/nsmb.2585.

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He, Housheng Hansen, Clifford A. Meyer, Hyunjin Shin, Shannon T. Bailey, Gang Wei, Qianben Wang, Yong Zhang, et al. "Nucleosome dynamics define transcriptional enhancers." Nature Genetics 42, no. 4 (March 7, 2010): 343–47. http://dx.doi.org/10.1038/ng.545.

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Huang, Rongsheng, and Jinzhi Lei. "Dynamics of gene expression with positive feedback to histone modifications at bivalent domains." International Journal of Modern Physics B 32, no. 07 (March 5, 2018): 1850075. http://dx.doi.org/10.1142/s0217979218500753.

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Experiments have shown that in embryonic stem cells, the promoters of many lineage-control genes contain “bivalent domains”, within which the nucleosomes possess both active (H3K4me3) and repressive (H3K27me3) marks. Such bivalent modifications play important roles in maintaining pluripotency in embryonic stem cells. Here, to investigate gene expression dynamics when there are regulations in bivalent histone modifications and random partition in cell divisions, we study how positive feedback to histone methylation/demethylation controls the transition dynamics of the histone modification patterns along with cell cycles. We constructed a computational model that includes dynamics of histone marks, three-stage chromatin state transitions, transcription and translation, feedbacks from protein product to enzymes to regulate the addition and removal of histone marks, and the inheritance of nucleosome state between cell cycles. The model reveals how dynamics of both nucleosome state transition and gene expression are dependent on the enzyme activities and feedback regulations. Results show that the combination of stochastic histone modification at each cell division and the deterministic feedback regulation work together to adjust the dynamics of chromatin state transition in stem cell regenerations.

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Wan, Yakun, Ramsey A. Saleem, Alexander V. Ratushny, Oriol Roda, Jennifer J. Smith, Chan-Hsien Lin, Jung-Hsien Chiang, and John D. Aitchison. "Role of the Histone Variant H2A.Z/Htz1p in TBP Recruitment, Chromatin Dynamics, and Regulated Expression of Oleate-Responsive Genes." Molecular and Cellular Biology 29, no. 9 (March 9, 2009): 2346–58. http://dx.doi.org/10.1128/mcb.01233-08.

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ABSTRACT The histone variant H2A.Z (Htz1p) has been implicated in transcriptional regulation in numerous organisms, including Saccharomyces cerevisiae. Genome-wide transcriptome profiling and chromatin immunoprecipitation studies identified a role for Htz1p in the rapid and robust activation of many oleate-responsive genes encoding peroxisomal proteins, in particular POT1, POX1, FOX2, and CTA1. The Swr1p-, Gcn5p-, and Chz1p-dependent association of Htz1p with these promoters in their repressed states appears to establish an epigenetic marker for the rapid and strong expression of these highly inducible promoters. Isw2p also plays a role in establishing the nucleosome state of these promoters and associates stably in the absence of Htz1p. An analysis of the nucleosome dynamics and Htz1p association with these promoters suggests a complex mechanism in which Htz1p-containing nucleosomes at fatty acid-responsive promoters are disassembled upon initial exposure to oleic acid leading to the loss of Htz1p from the promoter. These nucleosomes reassemble at later stages of gene expression. While these new nucleosomes do not incorporate Htz1p, the initial presence of Htz1p appears to mark the promoter for sustained gene expression and the recruitment of TATA-binding protein.

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Öztürk, Mehmet Ali, Madhura De, Vlad Cojocaru, and Rebecca C. Wade. "Chromatosome Structure and Dynamics from Molecular Simulations." Annual Review of Physical Chemistry 71, no. 1 (April 20, 2020): 101–19. http://dx.doi.org/10.1146/annurev-physchem-071119-040043.

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Chromatosomes are fundamental units of chromatin structure that are formed when a linker histone protein binds to a nucleosome. The positioning of the linker histone on the nucleosome influences the packing of chromatin. Recent simulations and experiments have shown that chromatosomes adopt an ensemble of structures that differ in the geometry of the linker histone–nucleosome interaction. In this article we review the application of Brownian, Monte Carlo, and molecular dynamics simulations to predict the structure of linker histone–nucleosome complexes, to study the binding mechanisms involved, and to predict how this binding affects chromatin fiber structure. These simulations have revealed the sensitivityof the chromatosome structure to variations in DNA and linker histone sequence, as well as to posttranslational modifications, thereby explaining the structural variability observed in experiments. We propose that a concerted application of experimental and computational approaches will reveal the determinants of chromatosome structural variability and how it impacts chromatin packing.

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Selth, Luke A., Yahli Lorch, Maria T. Ocampo-Hafalla, Richard Mitter, Michael Shales, Nevan J. Krogan, Roger D. Kornberg, and Jesper Q. Svejstrup. "An Rtt109-Independent Role for Vps75 in Transcription-Associated Nucleosome Dynamics." Molecular and Cellular Biology 29, no. 15 (May 26, 2009): 4220–34. http://dx.doi.org/10.1128/mcb.01882-08.

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ABSTRACT The histone chaperone Vps75 forms a complex with, and stimulates the activity of, the histone acetyltransferase Rtt109. However, Vps75 can also be isolated on its own and might therefore possess Rtt109-independent functions. Analysis of epistatic miniarray profiles showed that VPS75 genetically interacts with factors involved in transcription regulation whereas RTT109 clusters with genes linked to DNA replication/repair. Additional genetic and biochemical experiments revealed a close relationship between Vps75 and RNA polymerase II. Furthermore, Vps75 is recruited to activated genes in an Rtt109-independent manner, and its genome-wide association with genes correlates with transcription rate. Expression microarray analysis identified a number of genes whose normal expression depends on VPS75. Interestingly, histone H2B dynamics at some of these genes are consistent with a role for Vps75 in histone H2A/H2B eviction/deposition during transcription. Indeed, reconstitution of nucleosome disassembly using the ATP-dependent chromatin remodeler Rsc and Vps75 revealed that these proteins can cooperate to remove H2A/H2B dimers from nucleosomes. These results indicate a role for Vps75 in nucleosome dynamics during transcription, and importantly, this function appears to be largely independent of Rtt109.

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Ramaswamy, Amutha, Ivet Bahar, and Ilya Ioshikhes. "Structural dynamics of nucleosome core particle: Comparison with nucleosomes containing histone variants." Proteins: Structure, Function, and Bioinformatics 58, no. 3 (December 28, 2004): 683–96. http://dx.doi.org/10.1002/prot.20357.

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Journal articles on the topic 'Nucleosome Dynamics'

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