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Journal articles on the topic 'Fibre de chromatine'

Author: Grafiati

Published: 4 June 2021

Last updated: 19 February 2022

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1

Daban, Joan-Ramon. "The energy components of stacked chromatin layers explain the morphology, dimensions and mechanical properties of metaphase chromosomes." Journal of The Royal Society Interface 11, no. 92 (March 6, 2014): 20131043. http://dx.doi.org/10.1098/rsif.2013.1043.

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The measurement of the dimensions of metaphase chromosomes in different animal and plant karyotypes prepared in different laboratories indicates that chromatids have a great variety of sizes which are dependent on the amount of DNA that they contain. However, all chromatids are elongated cylinders that have relatively similar shape proportions (length to diameter ratio approx. 13). To explain this geometry, it is considered that chromosomes are self-organizing structures formed by stacked layers of planar chromatin and that the energy of nucleosome–nucleosome interactions between chromatin layers inside the chromatid is approximately 3.6 × 10 −20 J per nucleosome, which is the value reported by other authors for internucleosome interactions in chromatin fibres. Nucleosomes in the periphery of the chromatid are in contact with the medium; they cannot fully interact with bulk chromatin within layers and this generates a surface potential that destabilizes the structure. Chromatids are smooth cylinders because this morphology has a lower surface energy than structures having irregular surfaces. The elongated shape of chromatids can be explained if the destabilizing surface potential is higher in the telomeres (approx. 0.16 mJ m −2 ) than in the lateral surface (approx. 0.012 mJ m −2 ). The results obtained by other authors in experimental studies of chromosome mechanics have been used to test the proposed supramolecular structure. It is demonstrated quantitatively that internucleosome interactions between chromatin layers can justify the work required for elastic chromosome stretching (approx. 0.1 pJ for large chromosomes). The high amount of work (up to approx. 10 pJ) required for large chromosome extensions is probably absorbed by chromatin layers through a mechanism involving nucleosome unwrapping.

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2

Jack, E. M., C. J. Harrison, G. R. White, C. H. Ockey, and T. D. Allen. "Fine-structural aspects of bromodeoxyuridine incorporation in sister chromatid differentiation and replication banding." Journal of Cell Science 94, no. 2 (October 1, 1989): 287–97. http://dx.doi.org/10.1242/jcs.94.2.287.

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The structure of harlequin-stained chromosomes following substitution with low levels of 5-bromodeoxyuridine (BrdUrd) over two cell cycles and high levels over the last part of one cycle (replication banding) was studied in Chinese hamster ovary (CHO) cells. By using correlative light (LM) and scanning electron microscopy (SEM), it was shown that the effects of both the ultraviolet light (u.v.) and hot SSC treatment steps of the harlequin staining procedure were necessary to obtain sister-chromatid differentiation (SCD) or replication banding. u.v. treatment alone resulted in dark Giemsa staining of both chromatids with SEM morphology of short compact protuberances and an overall flattened smooth appearance in both the unsubstituted and BrdUrd-substituted chromatids, a morphology essentially similar to that of untreated chromosomes. SSC alone on the other hand resulted in dark-staining chromatids with an SEM morphology of raised, loosely packed loops of fibres in both types of chromatids. u.v. and SSC treatment together resulted in differentiation, with dark-staining unifilarly (TB) chromatids in the LM corresponding to raised loosely packed loops in the SEM and pale bifilarly (BB) chromatids corresponding to the smooth compact flattened SEM appearance. Where the BrdUrd-substituted strand became the template (BT), or when the nascent strand TB contained high levels of BrdUrd substitution in replication banding, the chromatid stained pale and showed the compact smooth appearance in the SEM. The Giemsa staining ability and ultrastructural morphology of harlequin staining is discussed with respect to putative DNA loss and also in terms of preferential protein-protein, protein-DNA cross-linkage in BrdUrd-containing DNA. These changes are also compared with the ultrastructural morphology observed after other banding methods, where deterioration of protein and DNA-protein interaction resulting in aggregation of chromatin fibres appears to be the major mechanism.

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3

Gilbert, Nick, and Wendy A. Bickmore. "The relationship between higher-order chromatin structure and transcription." Biochemical Society Symposia 73 (January 1, 2006): 59–66. http://dx.doi.org/10.1042/bss0730059.

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It has generally been assumed that transcriptionally active genes are in an ‘open’ chromatin structure and that silent genes have a ‘closed’ chromatin structure. Here we re-assess this axiom in the light of genome-wide studies of chromatin fibre structure. Using a combination of sucrose gradient sedimentation and genomic microarrays of the human genome, we argue that open chromatin fibres originate from regions of high gene density, whether or not those genes are transcriptionally active.

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4

Barbi, Maria, Julien Mozziconacci, Jean-Marc Victor, Hua Wong, and Christophe Lavelle. "On the topology of chromatin fibres." Interface Focus 2, no. 5 (February 2012): 546–54. http://dx.doi.org/10.1098/rsfs.2011.0101.

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The ability of cells to pack, use and duplicate DNA remains one of the most fascinating questions in biology. To understand DNA organization and dynamics, it is important to consider the physical and topological constraints acting on it. In the eukaryotic cell nucleus, DNA is organized by proteins acting as spools on which DNA can be wrapped. These proteins can subsequently interact and form a structure called the chromatin fibre. Using a simple geometric model, we propose a general method for computing topological properties ( twist , writhe and linking number ) of the DNA embedded in those fibres. The relevance of the method is reviewed through the analysis of magnetic tweezers single molecule experiments that revealed unexpected properties of the chromatin fibre. Possible biological implications of these results are discussed.

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5

Mullinger, A. M., and R. T. Johnson. "Disassembly of the mammalian metaphase chromosome into its subunits: studies with ultraviolet light and repair synthesis inhibitors." Journal of Cell Science 87, no. 1 (February 1, 1987): 55–69. http://dx.doi.org/10.1242/jcs.87.1.55.

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Metaphase chromosomes of a simian virus-transformed Indian muntjac cell line have been examined by scanning electron microscopy of material in which the fully packed metaphase structure is progressively relaxed. Such chromosomes are seen in standard, spread preparations of ultraviolet light-irradiated, metaphase-arrested cells, which have been incubated in the presence of inhibitors of DNA synthesis; they are processed for electron microscopy by trypsinization, further fixation and osmium impregnation. Decondensation is initially associated with a gradual elongation and loosening of the chromosome axis and, as loosening proceeds, the appearance of unexpected higher order structures—clusters of 20–40 nm diameter fibres. The arrangement of the clusters shows much variation between spreads. In the most fully extended chromosomes clusters are arranged in two longitudinal series with pairing between sister chromatids; the diameter of the majority of clusters in such chromosomes is in the range 0.4-0.6 micron. In the final stages of decondensation, clusters separate and individual chromosomes are no longer recognizable. Similar fibre clusters are found in interphase nuclei prepared by the same method. We suggest that the clusters of chromatin fibres may assemble as intermediates in the construction of an axial structure, which is further compacted in the fully condensed metaphase chromosome.

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6

Hashemipour, S. H. "Chromatic Dispersion in Traditional Fiber and Silicon Nanocrystal and Er Doped Fiber Optical Amplifier." International Journal of Engineering and Technology 4, no. 5 (2012): 518–21. http://dx.doi.org/10.7763/ijet.2012.v4.423.

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7

Wu, Chenyi, and Andrew Travers. "Modelling and DNA topology of compact 2-start and 1-start chromatin fibres." Nucleic Acids Research 47, no. 18 (June 20, 2019): 9902–24. http://dx.doi.org/10.1093/nar/gkz495.

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Abstract We have investigated the structure of the most compact 30-nm chromatin fibres by modelling those with 2-start or 1-start crossed-linker organisations. Using an iterative procedure we obtained possible structural solutions for fibres of the highest possible compaction permitted by physical constraints, including the helical repeat of linker DNA. We find that this procedure predicts a quantized nucleosome repeat length (NRL) and that only fibres with longer NRLs (≥197 bp) can more likely adopt the 1-start organisation. The transition from 2-start to 1-start fibres is consistent with reported differing binding modes of the linker histone. We also calculate that in 1-start fibres the DNA constrains more torsion (as writhe) than 2-start fibres with the same NRL and that the maximum constraint obtained is in accord with previous experimental results. We posit that the coiling of the fibre is driven by overtwisting of linker DNA which, in the most compact forms - for example, in echinoderm sperm and avian erythrocytes - could adopt a helical repeat of ∼10 bp/turn. We argue that in vivo the total twist of linker DNA could be modulated by interaction with other abundant chromatin-associated proteins and by epigenetic modifications of the C-terminal tail of linker histones.

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8

Racko, Dusan, Fabrizio Benedetti, Dimos Goundaroulis, and Andrzej Stasiak. "Chromatin Loop Extrusion and Chromatin Unknotting." Polymers 10, no. 10 (October 11, 2018): 1126. http://dx.doi.org/10.3390/polym10101126.

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It has been a puzzle how decondensed interphase chromosomes remain essentially unknotted. The natural expectation is that in the presence of type II DNA topoisomerases that permit passages of double-stranded DNA regions through each other, all chromosomes should reach the state of topological equilibrium. The topological equilibrium in highly crowded interphase chromosomes forming chromosome territories would result in formation of highly knotted chromatin fibres. However, Chromosome Conformation Capture (3C) methods revealed that the decay of contact probabilities with the genomic distance in interphase chromosomes is practically the same as in the crumpled globule state that is formed when long polymers condense without formation of any knots. To remove knots from highly crowded chromatin, one would need an active process that should not only provide the energy to move the system from the state of topological equilibrium but also guide topoisomerase-mediated passages in such a way that knots would be efficiently unknotted instead of making the knots even more complex. We perform coarse-grained molecular dynamics simulations of the process of chromatin loop extrusion involving knotted and catenated chromatin fibres to check whether chromatin loop extrusion may be involved in active unknotting of chromatin fibres. Our simulations show that the process of chromatin loop extrusion is ideally suited to actively unknot, decatenate and demix chromatin fibres in interphase chromosomes.

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9

Heliot, Laurent, Hervé Kaplan, Laurent Lucas, Christophe Klein, Adrien Beorchia, Martine Doco-Fenzy, Monique Menager, Marc Thiry, Marie-Françoise O’Donohue, and Dominique Ploton. "Electron Tomography of Metaphase Nucleolar Organizer Regions: Evidence for a Twisted-Loop Organization." Molecular Biology of the Cell 8, no. 11 (November 1997): 2199–216. http://dx.doi.org/10.1091/mbc.8.11.2199.

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Metaphase nucleolar organizer regions (NORs), one of four types of chromosome bands, are located on human acrocentric chromosomes. They contain r-chromatin, i.e., ribosomal genes complexed with proteins such as upstream binding factor and RNA polymerase I, which are argyrophilic NOR proteins. Immunocytochemical and cytochemical labelings of these proteins were used to reveal r-chromatin in situ and to investigate its spatial organization within NORs by confocal microscopy and by electron tomography. For each labeling, confocal microscopy revealed small and large double-spotted NORs and crescent-shaped NORs. Their internal three-dimensional (3D) organization was studied by using electron tomography on specifically silver-stained NORs. The 3D reconstructions allow us to conclude that the argyrophilic NOR proteins are grouped as a fiber of 60–80 nm in diameter that constitutes either one part of a turn or two or three turns of a helix within small and large double-spotted NORs, respectively. Within crescent-shaped NORs, virtual slices reveal that the fiber constitutes several longitudinally twisted loops, grouped as two helical 250- to 300-nm coils, each centered on a nonargyrophilic axis of condensed chromatin. We propose a model of the 3D organization of r-chromatin within elongated NORs, in which loops are twisted and bent to constitute one basic chromatid coil.

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10

Sinclair, Paul, Qian Bian, Matt Plutz, Edith Heard, and Andrew S. Belmont. "Dynamic plasticity of large-scale chromatin structure revealed by self-assembly of engineered chromosome regions." Journal of Cell Biology 190, no. 5 (September 6, 2010): 761–76. http://dx.doi.org/10.1083/jcb.200912167.

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Interphase chromatin compaction well above the 30-nm fiber is well documented, but the structural motifs underlying this level of chromatin folding remain unknown. Taking a reductionist approach, we analyzed in mouse embryonic stem (ES) cells and ES-derived fibroblasts and erythroblasts the folding of 10–160-megabase pair engineered chromosome regions consisting of tandem repeats of bacterial artificial chromosomes (BACs) containing ∼200 kilobases of mammalian genomic DNA tagged with lac operator (LacO) arrays. Unexpectedly, linear mitotic and interphase chromatid regions formed from noncontiguously folded DNA topologies. Particularly, in ES cells, these model chromosome regions self-organized with distant sequences segregating into functionally distinct, compact domains. Transcriptionally active and histone H3K27me3-modified regions positioned toward the engineered chromosome subterritory exterior, with LacO repeats and the BAC vector backbone localizing within an H3K9me3, HP1-enriched core. Differential compaction of Dhfr and α- and β-globin transgenes was superimposed on dramatic, lineage-specific reorganization of large-scale chromatin folding, demonstrating a surprising plasticity of large-scale chromatin organization.

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11

Li, Gang, Gail Sudlow, and Andrew S. Belmont. "Interphase Cell Cycle Dynamics of a Late-Replicating, Heterochromatic Homogeneously Staining Region: Precise Choreography of Condensation/Decondensation and Nuclear Positioning." Journal of Cell Biology 140, no. 5 (March 9, 1998): 975–89. http://dx.doi.org/10.1083/jcb.140.5.975.

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Recently we described a new method for in situ localization of specific DNA sequences, based on lac operator/repressor recognition (Robinett, C.C., A. Straight, G. Li, C. Willhelm, G. Sudlow, A. Murray, and A.S. Belmont. 1996. J. Cell Biol. 135:1685–1700). We have applied this methodology to visualize the cell cycle dynamics of an ∼90 Mbp, late-replicating, heterochromatic homogeneously staining region (HSR) in CHO cells, combining immunostaining with direct in vivo observations. Between anaphase and early G1, the HSR extends approximately twofold to a linear, ∼0.3-μm-diam chromatid, and then recondenses to a compact mass adjacent to the nuclear envelope. No further changes in HSR conformation or position are seen through mid-S phase. However, HSR DNA replication is preceded by a decondensation and movement of the HSR into the nuclear interior 4–6 h into S phase. During DNA replication the HSR resolves into linear chromatids and then recondenses into a compact mass; this is followed by a third extension of the HSR during G2/ prophase. Surprisingly, compaction of the HSR is extremely high at all stages of interphase. Preliminary ultrastructural analysis of the HSR suggests at least three levels of large-scale chromatin organization above the 30-nm fiber.

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12

Min Zhang, Min Zhang, Shanfeng Li Shanfeng Li, Nuannuan Shi Nuannuan Shi, Yiying Gu Yiying Gu, Pengsheng Wu Pengsheng Wu, and Xiuyou Han and Mingshan Zhao Xiuyou Han and Mingshan Zhao. "Novel method for fiber chromatic dispersion measurement based on microwave photonic technique." Chinese Optics Letters 10, no. 7 (2012): 070602–70604. http://dx.doi.org/10.3788/col201210.070602.

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13

Staynov, Dontcho Z. "The controversial 30 nm chromatin fibre." BioEssays 30, no. 10 (October 2008): 1003–9. http://dx.doi.org/10.1002/bies.20816.

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14

Rakhmania, Amalia Eka, Sholeh Hadi Pramono, and Dwi Fadila Kurniawan. "KINERJA ORTHOGONAL FREQUENCY DIVISION MULTIPLE ACCESS (OFDMA) PADA TEKNOLOGI RADIO OVER FIBER (ROF)." Gema Teknologi 20, no. 3 (October 31, 2019): 68. http://dx.doi.org/10.14710/gt.v20i3.25779.

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Amalia Eka Rakhmania, Sholeh Hadi Pramono, Dwi Fadila Kurniawan, in this paper explain that radio over Fiber (RoF) is a technology that integrates wireless and wireline transmission system to transmit radio signal through optical fibre cable. This paper evaluates the performance of Orthogonal Frequency Division Multiple Access (OFDMA) implemented in RoF system for mobile WiMAX network. RoF channel model includes both optical fiber with Relative Intensity Noise, shot noise, thermal noise, and chromatic dispersion, and also wireless channel with Additive White Gaussian Noise (AWGN). Through simulation, signal to noise ratio (SNR), channel capacity, bit rate, and bit error rate (BER) with the influence of optical fiber length and wavelength. Result shows that optical fiber length is proportional to SNR, channel capacity, and bit rate but inversely proportional to BER. 1550 nm wavelength has better channel capacity but lesser bit rate than 1310 nm.

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15

Tate, Shin-ichi. "Establishing a model to demonstrate physical and mathematical properties of chromatin fibres in fission yeast cells - Research in the Molecular Biophysics Lab at Hiroshima University." Impact 2018, no. 3 (June 15, 2018): 89–91. http://dx.doi.org/10.21820/23987073.2018.3.89.

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The field of molecular biology has provided great insights into the structure and function of key molecules. Thanks to this area of research, we can now grasp the biological details of DNA and have characterised an enormous number of molecules in massive data bases. These 'biological periodic tables' have allowed scientists to connect molecules to particular cellular events, furthering scientific understanding of biological processes. However, molecular biology has yet to answer questions regarding 'higher-order' molecular architecture, such as that of chromatin. Chromatin is the molecular material that serves as the building block for chromosomes, the structures that carry an organism's genetic information inside of the cell's nucleus. Understanding the physical properties of chromatin is crucial in developing a more thorough picture of how chromatin's structure relate to its key cellular functions. Moreover, by establishing a physical model of chromatin, scientists will be able to open the doors into the true inner workings of the cell nucleus. Professor Shin-ichi Tate and his team of researchers at Hiroshima University's Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), are attempting to do just that. Through a five-year grant funded by the Platform for Dynamic Approaches to Living Systems from the Ministry of Education, Culture, Sports, Science and Technology, Tate is aiming to gain a clearer understanding of the structure and dynamics of chromatin.

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Collepardo-Guevara, Rosana, and Tamar Schlick. "Insights into chromatin fibre structure by in vitro and in silico single-molecule stretching experiments." Biochemical Society Transactions 41, no. 2 (March 21, 2013): 494–500. http://dx.doi.org/10.1042/bst20120349.

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The detailed structure and dynamics of the chromatin fibre and their relation to gene regulation represent important open biological questions. Recent advances in single-molecule force spectroscopy experiments have addressed these questions by directly measuring the forces that stabilize and alter the folded states of chromatin, and by investigating the mechanisms of fibre unfolding. We present examples that demonstrate how complementary modelling approaches have helped not only to interpret the experimental findings, but also to advance our knowledge of force-induced events such as unfolding of chromatin with dynamically bound linker histones and nucleosome unwrapping.

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17

Daban, Joan-Ramon. "High concentration of DNA in condensed chromatin." Biochemistry and Cell Biology 81, no. 3 (June 1, 2003): 91–99. http://dx.doi.org/10.1139/o03-037.

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The lengths of the DNA molecules of eukaryotic genomes are much greater than the dimensions of the metaphase chromosomes in which they are contained during mitosis. From this observation it has been generally assumed that the linear packing ratio of DNA is an adequate measure of the degree of DNA compaction. This review summarizes the evidence suggesting that the local concentration of DNA is more appropriate than the linear packing ratio for the study of chromatin condensation. The DNA concentrations corresponding to most of the models proposed for the 3040 nm chromatin fiber are not high enough for the construction of metaphase chromosomes. The interdigitated solenoid model has a higher density because of the stacking of nucleosomes in secondary helices and, after further folding into chromatids, it yields a final concentration of DNA that approaches the experimental value found for condensed chromosomes. Since recent results have shown that metaphase chromosomes contain high concentrations of the chromatin packing ions Mg2+ and Ca2+, it is discussed that dynamic rather than rigid models are required to explain the condensation of the extended fibers observed in the absence of these cations. Finally, considering the different lines of evidence demonstrating the stacking of nucleosomes in different chromatin complexes, it is suggested that the face-to-face interactions between nucleosomes may be the driving force for the formation of higher order structures with a high local concentration of DNA.Key words: chromosomes, metaphase chromosomes, chromatin, chromatin higher order structure, DNA.

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18

Bennink, M. L., L. H. Pope, S. H. Leuba, B. G. de Grooth, and J. Greve. "Single Chromatin Fibre Assembly Using Optical Tweezers." Single Molecules 2, no. 2 (July 2001): 91–97. http://dx.doi.org/10.1002/1438-5171(200107)2:2<91::aid-simo91>3.0.co;2-s.

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19

Grigoryev, Sergei A., and Christopher L. Woodcock. "Chromatin organization — The 30nm fiber." Experimental Cell Research 318, no. 12 (July 2012): 1448–55. http://dx.doi.org/10.1016/j.yexcr.2012.02.014.

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20

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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21

Hayes, Jeffrey J., and Jeffrey C. Hansen. "Nucleosomes and the chromatin fiber." Current Opinion in Genetics & Development 11, no. 2 (April 2001): 124–29. http://dx.doi.org/10.1016/s0959-437x(00)00168-4.

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22

Kalashnikova, Anna A., Mary E. Porter-Goff, Uma M. Muthurajan, Karolin Luger, and Jeffrey C. Hansen. "The role of the nucleosome acidic patch in modulating higher order chromatin structure." Journal of The Royal Society Interface 10, no. 82 (May 6, 2013): 20121022. http://dx.doi.org/10.1098/rsif.2012.1022.

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Higher order folding of chromatin fibre is mediated by interactions of the histone H4 N-terminal tail domains with neighbouring nucleosomes. Mechanistically, the H4 tails of one nucleosome bind to the acidic patch region on the surface of adjacent nucleosomes, causing fibre compaction. The functionality of the chromatin fibre can be modified by proteins that interact with the nucleosome. The co-structures of five different proteins with the nucleosome (LANA, IL-33, RCC1, Sir3 and HMGN2) recently have been examined by experimental and computational studies. Interestingly, each of these proteins displays steric, ionic and hydrogen bond complementarity with the acidic patch, and therefore will compete with each other for binding to the nucleosome. We first review the molecular details of each interface, focusing on the key non-covalent interactions that stabilize the protein–acidic patch interactions. We then propose a model in which binding of proteins to the nucleosome disrupts interaction of the H4 tail domains with the acidic patch, preventing the intrinsic chromatin folding pathway and leading to assembly of alternative higher order chromatin structures with unique biological functions.

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23

Moronta-Gines, Macarena, Thomas R. H. van Staveren, and Kerstin S. Wendt. "One ring to bind them – Cohesin’s interaction with chromatin fibers." Essays in Biochemistry 63, no. 1 (March 22, 2019): 167–76. http://dx.doi.org/10.1042/ebc20180064.

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Abstract In the nuclei of eukaryotic cells, the genetic information is organized at several levels. First, the DNA is wound around the histone proteins, to form a structure termed as chromatin fiber. This fiber is then arranged into chromatin loops that can cluster together and form higher order structures. This packaging of chromatin provides on one side compaction but also functional compartmentalization. The cohesin complex is a multifunctional ring-shaped multiprotein complex that organizes the chromatin fiber to establish functional domains important for transcriptional regulation, help with DNA damage repair, and ascertain stable inheritance of the genome during cell division. Our current model for cohesin function suggests that cohesin tethers chromatin strands by topologically entrapping them within its ring. To achieve this, cohesin’s association with chromatin needs to be very precisely regulated in timing and position on the chromatin strand. Here we will review the current insight in when and where cohesin associates with chromatin and which factors regulate this. Further, we will discuss the latest insights into where and how the cohesin ring opens to embrace chromatin and also the current knowledge about the ‘exit gates’ when cohesin is released from chromatin.

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Asp, Patrik, Margareta Wihlborg, Mattias Karlén, and Ann-Kristin Östlund Farrants. "Expression of BRG1, a human SWI/SNF component, affects the organisation of actin filaments through the RhoA signalling pathway." Journal of Cell Science 115, no. 13 (July 1, 2002): 2735–46. http://dx.doi.org/10.1242/jcs.115.13.2735.

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The human BRG1 (brahma-related gene 1) protein is a component of the SWI/SNF family of the ATP-dependent chromatin remodelling complexes. We show here that expression of the BRG1 protein, but not of an ATPase-deficient BRG1 protein, in BRG1-deficient SW13 cells alters the organisation of actin filaments. BRG1 expression induces the formation of thick actin filament bundles resembling stress-fibres, structures that are rarely seen in native SW13 cells. BRG1 expression does not influence the activity state of the RhoA-GTPase, which is involved in stress-fibre formation. We find that RhoA is equally activated by stimuli, such as serum, in BRG1-expressing cells,ATPase-deficient BRG1-expressing cells and native SW13 cells. However, the activation of RhoA by lysophosphatidic acid and serum does not trigger the formation of stress-fibre-like structures in SW13 cells. Activation of the RhoA-GTPase in BRG1-expressing cells induces stress-fibre-like structures,indicating that the BRG1 can couple RhoA activation to stress-fibre formation. At least two downstream effectors are involved in stress-fibre formation,Rho-kinase/ROCK and Dia. BRG1 expression, but not the expression of the ATP-deficient BRG1, increases the protein level of ROCK1, one form of the Rho-kinase/ROCK. That this is of importance is supported by the findings that an increased Rho-kinase/ROCK activity in SW13 cells, obtained by overexpressing wild-type ROCK1 and ROCK2, induces stress-fibre formation. No specificity between the two Rho-kinase/ROCK forms exists. Our results suggest that the BRG1 protein affects the RhoA pathway by increasing the protein level of ROCK1, which allows stress-fibre-like structures to form.

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25

Catez, Frédéric, Huan Yang, Kevin J. Tracey, Raymond Reeves, Tom Misteli, and Michael Bustin. "Network of Dynamic Interactions between Histone H1 and High-Mobility-Group Proteins in Chromatin." Molecular and Cellular Biology 24, no. 10 (May 15, 2004): 4321–28. http://dx.doi.org/10.1128/mcb.24.10.4321-4328.2004.

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ABSTRACT Histone H1 and the high-mobility group (HMG) proteins are chromatin binding proteins that regulate gene expression by modulating the compactness of the chromatin fiber and affecting the ability of regulatory factors to access their nucleosomal targets. Histone H1 stabilizes the higher-order chromatin structure and decreases nucleosomal access, while the HMG proteins decrease the compactness of the chromatin fiber and enhance the accessibility of chromatin targets to regulatory factors. Here we show that in living cells, each of the three families of HMG proteins weakens the binding of H1 to nucleosomes by dynamically competing for chromatin binding sites. The HMG families weaken H1 binding synergistically and do not compete among each other, suggesting that they affect distinct H1 binding sites. We suggest that a network of dynamic and competitive interactions involving HMG proteins and H1, and perhaps other structural proteins, constantly modulates nucleosome accessibility and the local structure of the chromatin fiber.

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26

Prieto, Eloise I., and Kazuhiro Maeshima. "Dynamic chromatin organization in the cell." Essays in Biochemistry 63, no. 1 (April 2019): 133–45. http://dx.doi.org/10.1042/ebc20180054.

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Abstract The organization and regulation of genomic DNA as nuclear chromatin is necessary for proper DNA function inside living eukaryotic cells. While this has been extensively explored, no true consensus is currently reached regarding the exact mechanism of chromatin organization. The traditional view has assumed that the DNA is packaged into a hierarchy of structures inside the nucleus based on the regular 30-nm chromatin fiber. This is currently being challenged by the fluid-like model of the chromatin which views the chromatin as a dynamic structure based on the irregular 10-nm fiber. In this review, we focus on the recent progress in chromatin structure elucidation highlighting the paradigm shift in chromatin folding mechanism from the classical textbook perspective of the regularly folded chromatin to the more dynamic fluid-like perspective.

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Razin, Sergey V., and Alexey A. Gavrilov. "Chromatin without the 30-nm fiber." Epigenetics 9, no. 5 (February 21, 2014): 653–57. http://dx.doi.org/10.4161/epi.28297.

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28

Krietenstein, Nils, and Oliver J. Rando. "Mesoscale organization of the chromatin fiber." Current Opinion in Genetics & Development 61 (April 2020): 32–36. http://dx.doi.org/10.1016/j.gde.2020.02.022.

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29

Langowski, Jörg, and Dieter W. Heermann. "Computational modeling of the chromatin fiber." Seminars in Cell & Developmental Biology 18, no. 5 (October 2007): 659–67. http://dx.doi.org/10.1016/j.semcdb.2007.08.011.

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30

Ben-Haı̈m, Eli, Annick Lesne, and Jean-Marc Victor. "Adaptive elastic properties of chromatin fiber." Physica A: Statistical Mechanics and its Applications 314, no. 1-4 (November 2002): 592–99. http://dx.doi.org/10.1016/s0378-4371(02)01073-7.

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31

Korolev, Nikolay, Alexander P. Lyubartsev, and Aatto Laaksonen. "Electrostatic Background of Chromatin Fiber Stretching." Journal of Biomolecular Structure and Dynamics 22, no. 2 (October 2004): 215–26. http://dx.doi.org/10.1080/07391102.2004.10506997.

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32

Boulé, Jean-Baptiste, Julien Mozziconacci, and Christophe Lavelle. "The polymorphisms of the chromatin fiber." Journal of Physics: Condensed Matter 27, no. 3 (December 1, 2014): 033101. http://dx.doi.org/10.1088/0953-8984/27/3/033101.

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33

Depken, Martin, and Helmut Schiessel. "Nucleosome Shape Dictates Chromatin Fiber Structure." Biophysical Journal 96, no. 3 (February 2009): 777–84. http://dx.doi.org/10.1016/j.bpj.2008.09.055.

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34

Smith, M. F., B. D. Athey, S. P. Williams, and J. P. Langmore. "Radial density distribution of chromatin: evidence that chromatin fibers have solid centers." Journal of Cell Biology 110, no. 2 (February 1, 1990): 245–54. http://dx.doi.org/10.1083/jcb.110.2.245.

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Fiber diameter, radial distribution of density, and radius of gyration were determined from scanning transmission electron microscopy (STEM) of unstained, frozen-dried chromatin fibers. Chromatin fibers isolated under physiological conditions (ionic strength, 124 mM) from Thyone briareus sperm (DNA linker length, n = 87 bp) and Necturus maculosus erythrocytes (n = 48 bp) were analyzed by objective image-processing techniques. The mean outer diameters were determined to be 38.0 nm (SD = 3.7 nm; SEM = 0.36 nm) and 31.2 nm (SD = 3.6 nm; SEM = 0.32 nm) for Thyone and Necturus, respectively. These data are inconsistent with the twisted-ribbon and solenoid models, which predict constant diameters of approximately 30 nm, independent of DNA linker length. Calculated radial density distributions of chromatin exhibited relatively uniform density with no central hole, although the 4-nm hole in tobacco mosaic virus (TMV) from the same micrographs was visualized clearly. The existence of density at the center of chromatin fibers is in strong disagreement with the hollow-solenoid and hollow-twisted-ribbon models, which predict central holes of 16 and 9 nm for chromatin of 38 and 31 nm diameter, respectively. The cross-sectional radii of gyration were calculated from the radial density distributions and found to be 13.6 nm for Thyone and 11.1 nm for Necturus, in good agreement with x-ray and neutron scattering. The STEM data do not support the solenoid or twisted-ribbon models for chromatin fiber structure. They do, however, support the double-helical crossed-linker models, which exhibit a strong dependence of fiber diameter upon DNA linker length and have linker DNA at the center.

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35

Jones, G. R., S. Kwan, C. Beavan, P. Henderson, and E. Lewis. "Optical fibre based sensing using chromatic modulation." Optics & Laser Technology 19, no. 6 (December 1987): 297–303. http://dx.doi.org/10.1016/0030-3992(87)90036-3.

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36

Calvo, Soledad, Pratap Venepally, Jun Cheng, and Andres Buonanno. "Fiber-Type-Specific Transcription of the Troponin I Slow Gene Is Regulated by Multiple Elements." Molecular and Cellular Biology 19, no. 1 (January 1, 1999): 515–25. http://dx.doi.org/10.1128/mcb.19.1.515.

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ABSTRACT The regulatory elements that restrict transcription of genes encoding contractile proteins specifically to either slow- or fast-twitch skeletal muscles are unknown. As an initial step towards understanding the mechanisms that generate muscle diversity during development, we have identified a 128-bp troponin I slow upstream element (SURE) and a 144-bp troponin I fast intronic element (FIRE) that confer fiber type specificity in transgenic mice (M. Nakayama et al., Mol. Cell. Biol. 16:2408–2417, 1996). SURE and FIRE have maintained the spatial organization of four conserved motifs (3′ to 5′): an E box, an AT-rich site (A/T2) that binds MEF-2, a CACC site, and a novel CAGG motif. Troponin I slow (TnIs) constructs harboring mutations in these motifs were analyzed in transiently and stably transfected Sol8 myocytes and in transgenic mice to assess their function. Mutations of the E-box, A/T2, and CAGG motifs completely abolish transcription from the TnI SURE. In contrast, mutation of the CACC motif had no significant effect in transfected myocytes or on the slow-specific transcription of the TnI SURE in transgenic mice. To assess the role of E boxes in fiber type specificity, a chimeric enhancer was constructed in which the E box of SURE was replaced with the E box from FIRE. This TnI E box chimera, which lacks the SURE NFAT site, confers essentially the same levels of transcription in transgenic mice as those conferred by wild-type SURE and is specifically expressed in slow-twitch muscles, indicating that the E box on its own cannot determine the fiber-type-specific expression of the TnI promoter. The importance of the 5′ half of SURE, which bears little homology to the TnI FIRE, in muscle-specific expression was analyzed by deletion and linker scanning analyses. Removal of the 5′ half of SURE (−846 to −811) results in the loss of expression in stably transfected but not in transiently expressing myocytes. Linker scanning mutations identified sequences in this region that are necessary for the function of SURE when integrated into chromatin. One of these sites (GTTAATCCG), which is highly homologous to a bicoid consensus site, binds to nuclear proteins from several mesodermal cells. These results show that multiple elements are involved in the muscle-specific activity of the TnIs promoter and that interactions between upstream and downstream regions of SURE are important for transcription in the context of native chromatin.

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37

Bermudez, A., S. Bartolome, and J. R. Daban. "Partial denaturation of small chromatin fragments: direct evidence for the radial distribution of nucleosomes in folded chromatin fibers." Journal of Cell Science 111, no. 12 (June 15, 1998): 1707–15. http://dx.doi.org/10.1242/jcs.111.12.1707.

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To examine the internal structure of chromatin fibers, we have developed procedures for partial denaturation of small chromatin fragments (8–30 nucleosomes) from chicken erythrocytes. Electron micrographs of samples prepared under conditions that cause nucleosome dissociation show rods and loops projecting from short compact fibers fixed by glutaraldehyde in 1.7 mM Mg2+. According to previous studies in our laboratory, these images correspond to the top view of partially denatured fibers. Our results indicate that rods and loops consist of extended duplex DNA of different lengths. DNA in loops is nicked, as demonstrated by experiments performed in the presence of high concentrations of ethidium bromide. Length measurements indicate that the radial projections of DNA are produced by unfolding of nucleosomal units. Loops are formed by DNA from denatured nucleosomes in internal positions of the fiber; DNA from denatured nucleosomes in terminal positions form rods. Our micrographs show clearly a radial distribution of DNA loops and rods projecting from fibers. Rods are orthogonal to the surface of the chromatin fragments. Considering that the high ionic strength used in this study (0.8-2.0 M NaCl) neutralizes the electrostatic repulsions between rods and fiber, this observation suggests that rods are extensions of nucleosomes radially organized inside the fiber. The position of the entry points of DNA loops into the fiber could be influenced by constraint on loops, but our results showing that the arc that separates these points in dinucleosome loops is relatively short suggest that consecutive nucleosomes are relatively close to each other in the folded fiber.

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Wu, Chenyi, Andrew Bassett, and Andrew Travers. "A variable topology for the 30‐nm chromatin fibre." EMBO reports 8, no. 12 (December 2007): 1129–34. http://dx.doi.org/10.1038/sj.embor.7401115.

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39

Yang, Guoliang, Sanford H. Leuba, Carlos Bustamante, Jordanka Zlatanove, and Kensal van Holde. "Role of linker histones in extended chromatin fibre structure." Nature Structural Biology 1, no. 11 (November 1994): 761–63. http://dx.doi.org/10.1038/nsb1194-761.

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40

Hamilton, Charlotte, Richard L. Hayward, and Nick Gilbert. "Global chromatin fibre compaction in response to DNA damage." Biochemical and Biophysical Research Communications 414, no. 4 (November 2011): 820–25. http://dx.doi.org/10.1016/j.bbrc.2011.10.021.

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41

Stergachis, Andrew B., Brian M. Debo, Eric Haugen, L. Stirling Churchman, and John A. Stamatoyannopoulos. "Single-molecule regulatory architectures captured by chromatin fiber sequencing." Science 368, no. 6498 (June 25, 2020): 1449–54. http://dx.doi.org/10.1126/science.aaz1646.

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Gene regulation is chiefly determined at the level of individual linear chromatin molecules, yet our current understanding of cis-regulatory architectures derives from fragmented sampling of large numbers of disparate molecules. We developed an approach for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using nonspecific DNA N6-adenine methyltransferases. Single-molecule long-read sequencing of chromatin stencils enabled nucleotide-resolution readout of the primary architecture of multikilobase chromatin fibers (Fiber-seq). Fiber-seq exposed widespread plasticity in the linear organization of individual chromatin fibers and illuminated principles guiding regulatory DNA actuation, the coordinated actuation of neighboring regulatory elements, single-molecule nucleosome positioning, and single-molecule transcription factor occupancy. Our approach and results open new vistas on the primary architecture of gene regulation.

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42

Bartolome, S., A. Bermudez, and J. R. Daban. "Internal structure of the 30 nm chromatin fiber." Journal of Cell Science 107, no. 11 (November 1, 1994): 2983–92. http://dx.doi.org/10.1242/jcs.107.11.2983.

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In the presence of 1.7 mM Mg2+, the diameter of the circular structures produced by small chromatin fragments isolated from chicken erythrocytes remains essentially unchanged when the number of nucleosomes in these fragments increases from 10 to 36. In contrast, the results obtained in unidirectional shadowing experiments show that under the same conditions the height of the chromatin fragments increases with the number of nucleosomes. These observations indicate that the electron microscope images studied in this work correspond to a top view of small chromatin fragments. Rotary-shadowed chromatin fragments show three parts: (a) a contour with a heavy deposition of platinum; (b) an annular zone between the central region and the periphery; and (c) a central hole. The heterogeneous ring generated by the deposition of platinum in the periphery suggests that nucleosomes form a one-start helix (5-7 nucleosomes per turn) that apparently can be left- or right-handed. The annular region (thickness of about 11 nm) shows spokes probably due to flat faces and core DNA of radially oriented nucleosomes. The central hole (8-12 nm) is clearly seen in many images but it is not empty because some deformed fragments show coated material (probably linker DNA) that protrudes from this central depression. We have observed that these structural elements directly detected in short chromatin fragments are also present in long chromatin fibers. This allows us to conclude that these elements are basic structural components of the 30 nm chromatin fiber.

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43

Woodcock, C. L., H. Woodcock, and R. A. Horowitz. "Ultrastructure of chromatin. I. Negative staining of isolated fibers." Journal of Cell Science 99, no. 1 (May 1, 1991): 99–106. http://dx.doi.org/10.1242/jcs.99.1.99.

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The ultrastructure of chromatin fibers isolated from erythrocyte nuclei of Necturus maculosus and contrasted with a number of negative stains is described. Long (greater than 1000 nm) fibers are prepared under ionic conditions that promote fiber integrity, fixed with glutaraldehyde and negatively stained with aurothioglucose, ammonium molybdate, methylamine tungstate, sodium phosphotungstate, uranyl acetate and a uranyl acetate-sodium phosphotungstate sequence. All stains yield images of ‘30 nm’ chromatin fibers, but aurothioglucose gives the most consistent diameter measurements (33 nm, S.D. 3.5 nm), and provides the clearest images of individual nucleosomes. Regions of fiber showing structural order are seen with all stains. The most commonly observed is a regular pattern of oblique cross-striations consistent with the visualization of the ‘top’ or ‘bottom’ of a helical structure. There is a significant relationship between fiber diameter and the cross-striation angle, consistent with an extensible chromatin fiber. Examination of power spectra prepared from selected ordered regions confirms the visual impressions, and indicates a striation spacing ranging from 11 nm to 18 nm, and dependent on the stain type. Fibers allowed to unfold slightly in a buffer containing 50 mM monovalent ions show evidence of a two-stranded helix-like organization. These results are discussed in terms of current models for the structure of the chromatin fiber.

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44

McBryant, Steven J., Christine Krause, Christopher L. Woodcock, and Jeffrey C. Hansen. "The Silent Information Regulator 3 Protein, SIR3p, Binds to Chromatin Fibers and Assembles a Hypercondensed Chromatin Architecture in the Presence of Salt." Molecular and Cellular Biology 28, no. 11 (March 24, 2008): 3563–72. http://dx.doi.org/10.1128/mcb.01389-07.

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ABSTRACT The telomeres and mating-type loci of budding yeast adopt a condensed, heterochromatin-like state through recruitment of the silent information regulator (SIR) proteins SIR2p, SIR3p, and SIR4p. In this study we characterize the chromatin binding determinants of recombinant SIR3p and identify how SIR3p mediates chromatin fiber condensation in vitro. Purified full-length SIR3p was incubated with naked DNA, nucleosome core particles, or defined nucleosomal arrays, and the resulting complexes were analyzed by electrophoretic shift assays, sedimentation velocity, and electron microscopy. SIR3p bound avidly to all three types of templates. SIR3p loading onto its nucleosomal sites in chromatin produced thickened condensed fibers that retained a beaded morphology. At higher SIR3p concentrations, individual nucleosomal arrays formed oligomeric suprastructures bridged by SIR3p oligomers. When condensed SIR3p-bound chromatin fibers were incubated in Mg2+, they folded and oligomerized even further to produce hypercondensed higher-order chromatin structures. Collectively, these results define how SIR3p may function as a chromatin architectural protein and provide new insight into the interplay between endogenous and protein-mediated chromatin fiber condensation pathways.

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45

Horowitz, R. A., D. A. Agard, J. W. Sedat, and C. L. Woodcock. "The three-dimensional architecture of chromatin in situ: electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon." Journal of Cell Biology 125, no. 1 (April 1, 1994): 1–10. http://dx.doi.org/10.1083/jcb.125.1.1.

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The three dimensional (3D) structure of chromatin fibers in sections of nuclei has been determined using electron tomography. Low temperature embedding and nucleic acid-specific staining allowed individual nucleosomes to be clearly seen, and the tomographic data collection parameters provided a reconstruction resolution of 2.5 nm. Chromatin fibers have complex 3D trajectories, with smoothly bending regions interspersed with abrupt changes in direction, and U turns. Nucleosomes are located predominantly at the fiber periphery, and linker DNA tends to project toward the fiber interior. Within the fibers, a unifying structural motif is a two nucleosome-wide ribbon that is variably bent and twisted, and in which there is little face-to-face contact between nucleosomes. It is suggested that this asymmetric 3D zig-zag of nucleosomes and linker DNA represents a basic principle of chromatin folding that is determined by the properties of the nucleosome-linker unit. This concept of chromatin fiber architecture is contrasted with helical models in which specific nucleosome-nucleosome contacts play a major role in generating a symmetrical higher order structure. The transcriptional control implications of a more open and irregular chromatin structure are discussed.

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46

Joti, Yasumasa, Takaaki Hikima, Yoshinori Nishino, Fukumi Kamada, Saera Hihara, Hideaki Takata, Tetsuya Ishikawa, and Kazuhiro Maeshima. "Chromosomes without a 30-nm chromatin fiber." Nucleus 3, no. 5 (September 2012): 404–10. http://dx.doi.org/10.4161/nucl.21222.

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47

Lavelle, Christophe, Jean-Marc Victor, and Jordanka Zlatanova. "Chromatin Fiber Dynamics under Tension and Torsion." International Journal of Molecular Sciences 11, no. 4 (April 12, 2010): 1557–79. http://dx.doi.org/10.3390/ijms11041557.

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48

Ozer, Gungor, Antoni Luque, and Tamar Schlick. "The chromatin fiber: multiscale problems and approaches." Current Opinion in Structural Biology 31 (April 2015): 124–39. http://dx.doi.org/10.1016/j.sbi.2015.04.002.

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49

Boopathi, Ramachandran, Stefan Dimitrov, Ali Hamiche, Carlo Petosa, and Jan Bednar. "Cryo-electron microscopy of the chromatin fiber." Current Opinion in Structural Biology 64 (October 2020): 97–103. http://dx.doi.org/10.1016/j.sbi.2020.06.016.

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50

Lesne, A., and J. M. Victor. "Chromatin fiber functional organization: Some plausible models." European Physical Journal E 19, no. 3 (February 23, 2006): 279–90. http://dx.doi.org/10.1140/epje/i2005-10050-6.

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