The Folding of the Nucleosome Chain

Rippe, Karsten

doi:10.1002/9783527639991.ch6

Cited by 8 publications

(14 citation statements)

References 204 publications

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“…The DNA density in metaphase chromosomes is high [7,51] and edge-to-edge contacts between nucleosome cores must also be considered. However, the attractive energy of edge-to-edge interactions is only approximately 10 times lower than that corresponding to face-to-face interactions [5,25]. Thus, it is very likely that the energy 1 nn that stabilizes the stacking of the successive layers in chromosomes is essentially due to face-to-face interactions between nucleosomes.…”

Section: Surface Energy Differences Of Stacked Chromatin Layers Can Ementioning

confidence: 99%

“…The nucleosome core is a short cylinder (11 nm diameter and 5.7 nm height) formed by 147 bp of DNA wrapped in 1.7 superhelical turns around an octamer of core histones [1]. Nucleosome cores connected with linker DNA and complemented with histone H1 constitute long chromatin filaments that are folded within the nucleus [2][3][4][5][6]. During mitosis, in order to avoid entanglements of different filaments and to preserve DNA integrity, each chromatid contains only one chromatin filament that is densely packaged [7] before being transferred to the daughter cells.…”

Section: Introductionmentioning

confidence: 99%

“…Single-molecule techniques (optical and magnetic tweezers) and computer modelling have provided a wealth of information about the mechanochemical properties of chromatin [5,20]. It was found that stretching forces of 4-6 pN cause the unfolding of individual chromatin fibres [21,22] and that higher forces (20-40 pN) produce nucleosome unwrapping and eventually dissociation of core histones [21,23,24].…”

Section: Introductionmentioning

confidence: 99%

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The energy components of stacked chromatin layers explain the morphology, dimensions and mechanical properties of metaphase chromosomes

Daban

2014

J. R. Soc. Interface.

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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 Â 10 220 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 22 ) than in the lateral surface (approx. 0.012 mJ m 22 ). 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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Section: Surface Energy Differences Of Stacked Chromatin Layers Can Ementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The energy components of stacked chromatin layers explain the morphology, dimensions and mechanical properties of metaphase chromosomes

Daban

2014

J. R. Soc. Interface.

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“…Nucleosomes are the basic building blocks of chromatin and constitute the first level of DNA compaction in the cell nucleus. In vitro experiments showed that the compaction degree of the chromatin filament is extremely dependent on ionic conditions (Daban, 2011;Collepardo-Guevara & Schlick, 2012;Grigoryev & Woodcock, 2012;Luger et al, 2012;Rippe, 2012;Boulé et al, 2015). In the chromatin filament, nucleosome cores are connected by variable lengths of linker DNA associated with histone H1.…”

Section: Introductionmentioning

confidence: 99%

Frozen‐hydrated chromatin from metaphase chromosomes has an interdigitated multilayer structure

et al. 2019

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Cryo‐electron tomography and small‐angle X‐ray scattering were used to investigate the chromatin folding in metaphase chromosomes. The tomographic 3D reconstructions show that frozen‐hydrated chromatin emanated from chromosomes is planar and forms multilayered plates. The layer thickness was measured accounting for the contrast transfer function fringes at the plate edges, yielding a width of ~ 7.5 nm, which is compatible with the dimensions of a monolayer of nucleosomes slightly tilted with respect to the layer surface. Individual nucleosomes are visible decorating distorted plates, but typical plates are very dense and nucleosomes are not identifiable as individual units, indicating that they are tightly packed. Two layers in contact are ~ 13 nm thick, which is thinner than the sum of two independent layers, suggesting that nucleosomes in the layers interdigitate. X‐ray scattering of whole chromosomes shows a main scattering peak at ~ 6 nm, which can be correlated with the distance between layers and between interdigitating nucleosomes interacting through their faces. These observations support a model where compact chromosomes are composed of many chromatin layers stacked along the chromosome axis.

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“…In living cells, binding of proteins to DNA controls gene expression and packaging of the genome [1–3], requiring DNA-binding proteins to communicate and cooperate over a wide range of length scales. Many DNA-binding proteins distort the double helix, which has led to development of micromechanical methods for analyis of protein-DNA interactions [4–7].…”

mentioning

confidence: 99%

Range of Interaction between DNA-Bending Proteins is Controlled by the Second-Longest Correlation Length for Bending Fluctuations

Zhang

Marko

2012

Phys. Rev. Lett.

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When a DNA molecule is stretched, the zero-force correlation length for its bending fluctuations – the persistence length A – bifurcates into two different correlation lengths - the shorter “longitudinal” correlation length ξ‖(f) and the longer “transverse” correlation length ξ⊥(f). In the high-force limit, ξ‖false(ffalse)=ξ⊥false(ffalse)/2=kBTA/f/2. When DNA-bending proteins bind to the DNA molecule, there is an effective interaction between the protein-generated bends mediated by DNA elasticity and bending fluctuations. Surprisingly, the range of this interaction is not the longest correlation length associated with transverse fluctuations of the tangent vector along the polymer, but instead is the second longest longitudinal correlation length ξ‖ (f, μ). The effect arises from the protein-bend contribution to the Hamiltonian having an axial rotational symmetry which eliminates its coupling to the transverse fluctuations.

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The Folding of the Nucleosome Chain

Cited by 8 publications

References 204 publications

The energy components of stacked chromatin layers explain the morphology, dimensions and mechanical properties of metaphase chromosomes

The energy components of stacked chromatin layers explain the morphology, dimensions and mechanical properties of metaphase chromosomes

Frozen‐hydrated chromatin from metaphase chromosomes has an interdigitated multilayer structure

Range of Interaction between DNA-Bending Proteins is Controlled by the Second-Longest Correlation Length for Bending Fluctuations

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