Nucleosome Arcs and Helices

Dubochet, Jacques; Noll, Markus

doi:10.1126/science.694532

Cited by 94 publications

(57 citation statements)

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“…An equivalent interdigitation between the successive helical turns of 30 nm chromatin fibres was proposed previously [2,53,54], and electron microscopy [55,56], X-ray crystallography [1,4,57,58] and modelling studies [5,[25][26][27]59] indicated that nucleosomes have a high tendency to interact through their faces. Furthermore, the intense scattering peak corresponding to a spacing of approximately 6 nm found in a recent synchrotron X-ray scattering study of human mitotic chromosomes [60] also suggests a lateral association between nucleosomes in condensed chromatids.…”

Section: Surface Energy Differences Of Stacked Chromatin Layers Can Ementioning

confidence: 99%

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%

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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“…341 This NCP-NCP stacking governs the formation of NCP columns also in NCP crystals, 342 semicrystalline NCP phases, 343 as well as in NCP arcs and multilayered helices. 344 The side-to-side contacts, with the wrapped DNA duplexes being often in close contact, on the contrary are likely ES in nature, see Fig. 22.…”

Section: B Dense Phases Of Ncpsmentioning

confidence: 99%

“…Predictive power of such theory should however not be over-estimated. The geometrical wedge-shape of NCPs 344,363 and interaction-mediated 364 constraints anticipated for isolated NCPs will interfere with constraints of continuous DNA ''wrapping'' through the fiber structure. Looping and bending of linker DNAs 365 influenced by binding of linker H1/H5 histones is another stabilization mechanisms of a particular forms of ''30 nm'' chromatin fibers.…”

Section: Implications For the Fiber Structurementioning

confidence: 99%

Electrostatic interactions in biological DNA-related systems

Cherstvy

2011

Phys. Chem. Chem. Phys.

163

148

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In this perspective article, we focus on recent developments in the theory of charge effects in biological DNA-related systems. The electrostatic effects on different levels of DNA organization are considered, including the DNA-DNA interactions, DNA complexation with cationic lipid membranes, DNA condensates and DNA-dense cholesteric phases, protein-DNA recognition, DNA wrapping in nucleosomes, and inter-nucleosomal interactions. For these systems, we develop a theoretical framework to describe the physical-chemical mechanisms of structure formation and anticipate some biological consequences. General biophysical principles of DNA compaction in chromatin fibers and DNA spooling inside viral capsids are discussed in the end, with emphasis on electrostatic aspects.

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“…These are the only surfaces of the nucleosome that could participate in stereospecific, symmetrical internucleosome contacts (4,30). The arrangement of the nucleosome cores in Fig.…”

mentioning

confidence: 99%

“…Under those conditions, nonhistone proteins and histone H1 are removed from chromatin and the spacer DNA is supercoiled (39). The extra coils in the spacer DNA, which are probably responsible for stacking neighboring nucleosomes onto each other (11), could be the result of overwinding of the duplex DNA by the high salt concentration (30,40,41). Under isotonic conditions, the spacer DNA is not supercoiled (16) and neighboring nucleosomes do not stack onto each other (Fig.…”

mentioning

confidence: 99%

Structure of chromatin and the linking number of DNA.

Worcel¹,

Strogatz²,

Riley³

1981

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

200

118

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Recent observations suggest that the basic supranucleosomal structure of chromatin is a zigzag helical ribbon with a repeat unit made of two nucleosomes connected by a relaxed spacer DNA. A remarkable feature of one particular ribbon is that it solves the apparent paradox between the number of DNA turns per nucleosome and the total linking number of a nucleosome-containing closed circular DNA molecule. We show here that the repeat unit of the proposed structure, which contains two nucleosomes with -13/4 DNA turns per nucleosome and one spacer crossover per repeat, contributes -2 to the linking number of closed circular DNA. Space-filling models show that the cylindrical 250-A chromatin fiber can be generated by twisting the ribbon.It is now well-established that the unit structure of chromatin, the nucleosome (1-3), is a flat cylindrical particle (110 X 110 x 57 A) with DNA wrapped around a histone octamer in a lefthanded toroidal supercoil of approximately 80 base pairs (bp) per turn (4). There are 146 bp of DNA in the nucleosome core describing -13/4 superhelical turns (5) and 20-95 bp of spacer DNA between neighboring nucleosome cores (6).The nature of the supranucleosomal structure of chromatin is less clear. Electron microscopic studies of eukaryotic nuclei have revealed a "thin" 100-A chromatin fiber and a "thick" 250-A fiber (7-9). Many past models have assumed that neighboring nucleosomes are stacked side by side to generate a 100-A nucleofilament, which is further coiled into a 250-A "solenoid" (10, 11). The unstacked 100-A fiber ("beads on a string") can be readily observed in nuclei and chromatin preparations spread under isotonic conditions (1, 2, 12). A stacked 100-A nucleofilament also has been detected, but only at high salt concentrations (11). Although the 100-A fiber is present in histone Hi-depleted chromatin, the 250-A fiber is never observed under these conditions (11, 12). Thus, histone HI must play a role in the further compaction of the linear chain of beads (12, 13). Reconstitution studies with the four intranucleosomal histones and small circular DNAs in the presence of nicking-closing enzyme have revealed that the DNA coiling around a nucleosome changes the DNA linking number by -1 (14). The histone Hl-induced compaction of the "beads on a string" into a 250-A-diameter supranucleosomal structure (15) does not cause further changes in the linking number (16). Because the nicking-closing enzyme relaxes the spacer DNA (16), the observed change in the linking number must be due to the particular DNA structure in the nucleosome.The linking number L of a closed circular DNA (ccDNA) molecule is the number of topological revolutions made by one strand about the other [counted after the molecule is constrained to lie in a plane (17)]. L is a topological invariant (i.e., an integer which is unchanged by all deformations that leave the strands intact). Moreover, it is related to the writhing number W and the twist number T by the equation (18-21)W is a real number that measures the shape...

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Nucleosome Arcs and Helices

Cited by 94 publications

References 50 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

Electrostatic interactions in biological DNA-related systems

Structure of chromatin and the linking number of DNA.

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