Neutron scattering on nuclei

Baudy, Pierre; Bram, Stanley

doi:10.1093/nar/6.4.1721

Cited by 20 publications

(8 citation statements)

References 20 publications

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“…How nucleosomes are positioned, spaced, remodelled, and whether and how nucleosome chains fold into fibres at physiological salt concentrations have been matters of continuing debate (e.g. [20]): Finch and Klug [21] proposed a relatively regular solenoid and in vivo neutron scattering experiments revealed a compacted fibre with a diameter of 30 ± 5 nm as a dominant nuclear feature [22][23][24][25]. In contrast other and especially more recent suggestions range from basically no compaction at all (rev.…”

Section: Open Accessmentioning

confidence: 99%

The Detailed 3D Multi-Loop Aggregate/Rosette Chromatin Architecture and Functional Dynamic Organization of the Human and Mouse Genomes

Knoch

Wachsmuth

Kepper

et al. 2016

Preprint

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Background:The dynamic three-dimensional chromatin architecture of genomes and its co-evolutionary connection to its function-the storage, expression, and replication of genetic information-is still one of the central issues in biology. Here, we describe the much debated 3D architecture of the human and mouse genomes from the nucleosomal to the megabase pair level by a novel approach combining selective high-throughput high-resolution chromosomal interaction capture (T2C), polymer simulations, and scaling analysis of the 3D architecture and the DNA sequence. Results:The genome is compacted into a chromatin quasi-fibre with ~5 ± 1 nucleosomes/11 nm, folded into stable ~30-100 kbp loops forming stable loop aggregates/rosettes connected by similar sized linkers. Minor but significant variations in the architecture are seen between cell types and functional states. The architecture and the DNA sequence show very similar fine-structured multi-scaling behaviour confirming their co-evolution and the above. Conclusions:This architecture, its dynamics, and accessibility, balance stability and flexibility ensuring genome integrity and variation enabling gene expression/regulation by self-organization of (in)active units already in proximity. Our results agree with the heuristics of the field and allow "architectural sequencing" at a genome mechanics level to understand the inseparable systems genomic properties.

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Section: Open Accessmentioning

confidence: 99%

The Detailed 3D Multi-Loop Aggregate/Rosette Chromatin Architecture and Functional Dynamic Organization of the Human and Mouse Genomes

Knoch

Wachsmuth

Kepper

et al. 2016

Preprint

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“…As pointed out by Luzzati and Nicolaieff (36,37) and Olins et al (47,48), reproducible shoulders at ~11.0 and 5.5 nm are found in the diffraction patterns from chicken erythrocyte nuclei, although the 11.0 was not visible in calf thymus nuclei. However, Subirana et al (65) and Baudy and Brain (4) were unable to detect the 11.0rim reflection and questioned the validity of the earlier reports. In addition, Notbohm and Harbers (46) were unable to detect any maxima at 11.0, 6.0, or 3.8 nm from nuclei.…”

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confidence: 91%

Low angle x-ray diffraction studies of chromatin structure in vivo and in isolated nuclei and metaphase chromosomes

Langmore¹,

Paulson²

1983

The Journal of Cell Biology

123

109

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Diffraction of x-rays from living cells, isolated nuclei, and metaphase chromosomes gives rise to several major low angle reflections characteristic of a highly conserved pattern of nucleosome packing within the chromatin fibers. We answer three questions about the x-ray data: Which reflections are characteristic of chromosomes in vivo? How can these reflections be preserved in vitro? What chromosome structures give rise to the reflections?Our consistent observation of diffraction peaks at 11.0, 6.0, 3.8, 2.7 and 2.1 nm from a variety of living cells, isolated nuclei, and metaphase chromosomes establishes these periodicities as characteristic of eucaryotic chromosomes in vivo. In addition, a 30-40-nm peak is observed from all somatic cells that have substantial amounts of condensed chromatin, and a weak 18-nm reflection is observed from nucleated erythrocytes. These observations provide a standard for judging the structural integrity of isolated nuclei, chromosomes, and chromatin, and thus resolve long standing controversy about the "true" nature of chromosome diffraction. All of the reflections seen in vivo can be preserved in vitro provided that the proper ionic conditions are maintained.Our results show clearly that the 30-40-nm maximum is a packing reflection. The packing we observe in vivo is directly correlated to the side-by-side arrangement of 20-30-nm fibers observed in thin sections of fixed and dehydrated cells and isolated chromosomes. This confirms that such packing is present in living cells and is not merely an artifact of electron microscopy. As expected, the packing reflection is shifted to longer spacings when the fibers are spread apart by reducing the concentration of divalent cations in vitro. Because the 18-, 11.0-, 6.0-, 3.8-, 2.7-, and 2.1-nm reflections are not affected by the decondensation caused by removal of divalent cations, these periodicities must reflect the internal structure of the chromatin fibers.Packaging of DNA in chromosomes can be best understood in terms of three distinct levels of structure. The lowest level of structure is the nucleosome, a repeating subunit consisting of a highly conserved nucleosome core particle with ~ 146 base pairs (bp) of DNA wrapped around an octamer of the "core histones" (H32 H42 H2A2 H2B2), and a variable amount (20-100 bp) of "linker DNA" probably associated with histone H 1 (34, 40). The primary structure of chromosomes is a linear arrangement of nucleosomes along the DNA, the so-called "string of beads." Nucleosome cores have been shown by 1120 electron microscopy, neutron scattering, and crystallography to be flattened disks 11.0 nm in diameter and 5.7 nm high with two parallel turns of DNA ~2.8 nm apart (21,32,58). At the second level, the "string of beads" is further folded to form the basic chromatin fiber (20,67,68). At the third level, the chromatin fibers are further folded into loops anchored together at the axis of the chromatid or on the nuclear matrix (5, 11,16,29). Here we describe our x-ray diffraction studies of the...

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“…The mass per unit length of chromatin has been measured by small-angle scattering (10)(11)(12)(13)(14). The parameter has also been measured by hydrodynamic methods (7,15) and light scattering (16).…”

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confidence: 99%

Chromatin higher-order structure studied by neutron scattering and scanning transmission electron microscopy.

Gerchman

Ramakrishnan

1987

Proc. Natl. Acad. Sci. U.S.A.

132

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Neutron scattering in solution and scanning transmission electron microscopy were simultaneously done on chicken erythrocyte chromatin at various salt and magnesium concentrations. We show that chromatin is organized into a higher-order structure even at low ionic strength and that the mass per unit length increases continuously as a function of salt concentration, reaching a limiting value of between six and seven nucleosomes per 11 nm. There is no evidence of a transition from a 10-nm to a 30-nm fiber. Fiber diameter is correlated with mass per unit length, showing that both increase during condensation. We also find that there is no essential difference between the mass per unit length measured by scanning transmission electron microscopy and neutron scattering in solution, showing that the ordered regions seen in micrographs are representative of chromatin in solution.Nucleosomes in chromatin interact to form a higher-order structure, referred to as the 30-nm filament. Despite a large number of structural studies on chromatin, there is no unanimity on its higher-order structure. The nature and sources ofconflicting views ofthe structure ofthe 30-nm fiber have been summarized (1).Several models of the 30-nm fiber propose a helical structure for chromatin. These include the solenoidal model (2), the helical-ribbon model (3,4), the crossed-linker doublehelical model (5), and the nonsequential single-helix model (6). All of these models share certain similarities; for example, they all satisfy constraints imposed by electric dichroism measurements on the angle of the nucleosomal disk with respect to the fiber axis (7,8). Most ofthe models have similar repeat dimensions that would show up as peaks in a diffraction pattern. The helical-ribbon model predicts certain additional peaks due to the width of the ribbon. These additional peaks have not been observed in an experiment on oriented chromatin (9), but it is possible that an adjustment in the parameters of the helical-ribbon model would eliminate the additional reflections that are predicted.Despite such similarities, the models differ considerably in detail. Even at a coarse level, the various models predict different values for the mass per unit length of condensed chromatin. Thus a measurement of the physical characteristics of chromatin condensation could help to substantiate or rule out some of the existing models for chromatin structure.The mass per unit length of chromatin has been measured by small-angle scattering (10-14). The parameter has also been measured by hydrodynamic methods (7, 15) and light scattering (16). These experiments generally yield a value of 6-7 nucleosomes per 11 nm for the mass per unit length of the condensed 30-nm fiber. However, scanning transmission electron microscopy (STEM) studies on chromatin (4, 5) have yielded much higher values, of up to 11.6 nucleosomes per nm. Felsenfeld and McGhee (1) have pointed out that the discrepancy may be due to the fact that in STEM studies one selects ordered regions of chromatin, wh...

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Neutron scattering on nuclei

Cited by 20 publications

References 20 publications

The Detailed 3D Multi-Loop Aggregate/Rosette Chromatin Architecture and Functional Dynamic Organization of the Human and Mouse Genomes

The Detailed 3D Multi-Loop Aggregate/Rosette Chromatin Architecture and Functional Dynamic Organization of the Human and Mouse Genomes

Low angle x-ray diffraction studies of chromatin structure in vivo and in isolated nuclei and metaphase chromosomes

Chromatin higher-order structure studied by neutron scattering and scanning transmission electron microscopy.

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