Experimental evidence for asymmetrical shielding of nucleosomal DNA by histones

Girardet, Jean‐Luc; Lawrence, Jean‐Jacques

doi:10.1093/nar/7.8.2419

Cited by 9 publications

(4 citation statements)

References 30 publications

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“…It has been reported that about 40-60% of the total phosphate groups of DNA are covered with histones in chromatin (Leake et al, 1972;Schmidt et al, 1972;Clark & Felsenfeld, 1974;Jacobs et al, 1976) and about 40% in the nucleosome core (Girardet & Lawrence, 1979). The Mg2+ binding results obtained here for both chromatin and the nucleosome core are in this range.…”

Section: Discussionsupporting

confidence: 60%

“…The structure of DNA in chromatin has been studied by circular dichroism (Cowman & Fasman, 1980; McCtearly & Fasman, 1980; Watanabe & Iso, 1981), thermal denaturation experiments (Fulmer & Fasman, 1979), and binding experiments of ethidium bromide (Lawrence et al, 1976;Paoletti et al, 1977;Erard et al, 1979;Wu et al, 1980) or manganese (Clark & Felsenfeld, 1974; Girardet & Lawrence, 1979). In a previous paper, we analyzed the CD spectrum of nucleoproteins and showed that the spectrum of HI-depleted chromatin is representable by the linear combination of protein-free DNA and the nucleosome core above 260 nm (Watanabe & Iso, 1981).…”

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confidence: 99%

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Magnesium binding and conformational change of DNA in chromatin

Watanabe¹,

Iso²

1984

Biochemistry

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The structure of chromatin in the presence of Mg2+ ions was examined by circular dichroism and equilibrium dialysis. Circular dichroism (CD) shows that above 260 nm the intensity of the spectrum of DNA in nucleoproteins decreases as the Mg2+ concentration increases. This change is an intrinsic characteristic of DNA since it is also observed in protein-free DNA and has been attributed to a change in the winding angle of base pairs around the DNA axis. Some structural elements of the DNA in the nucleosome core, therefore, are as movable as those of protein-free DNA. The basic organization of H1-depleted chromatin, 146 base pairs (bp) of DNA wound around core histones and a residual 49 bp in the linker region in the repeating unit, is maintained both in the presence and in the absence of Mg2+ ions, as shown by the fact that the CD spectrum of H1-depleted chromatin has the same type of linear combination between the spectrum of protein-free DNA and that of the nucleosome core in 0.2 mM MgCl2-10 mM triethanolamine (pH 7.8) as it has in 1 mM ethylenediaminetetraacetic acid-10 mM tris(hydroxymethyl) aminomethane (pH 7.8). The ellipticity of chromatin shows a smaller decrease relative to the other nucleoproteins and protein-free DNA upon the addition of Mg2+ ions. Therefore, some structural elements of chromatin are apparently somewhat protected against the conformational change induced by these ions. The spectrum of chromatin becomes almost indistinguishable from that of H1-depleted chromatin in 0.2 mM MgCl2.(ABSTRACT TRUNCATED AT 250 WORDS)

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Section: Discussionsupporting

confidence: 60%

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confidence: 99%

Magnesium binding and conformational change of DNA in chromatin

Watanabe¹,

Iso²

1984

Biochemistry

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“…Only a part of DNA phosphates are participating in salt bridging with histones in nucleosomes. Titration of mono-, di-and trinucleosomes with polylysine (Doenecke, 1977) and that of core particles with Mn 2+ (Girardet & Lawrence, 1979) has revealed that about 50-60% DNA phosphate groups are not shielded with histones. Similarly, about 50% neutralization of DNA phosphates in cores by histones was evaluated on the basis of calculating the stoichiometry of the balance of charged groups in histones (lysine, arginine, aspartic and glutamic acids, NH 2 -and COOH-terminal residues) and DNA (Mirzabekov & Rich, 1979).…”

Section: H2amentioning

confidence: 99%

Nucleosomes structure and its dynamic transitions

Mirzabekov

1980

Quart. Rev. Biophys.

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The discovery of nucleosomes as a basic repeating unit of the chromatin structure organizing the major part of eukaryotic DNA greatly catalyzes the expansion of our knowledge on chromatin. Several lines of experimental evidence have led to the formulation of the nucleosome conception: the observation of chains of globular particles in electron micrographs of chromatin (Olins & Olins, 1974); the demonstration that DNA is released as a set of discrete sizes upon digestion of chromatin with endogenous nucleases (Hewish & Burgoyne, 1973); the isolation of discrete nucleoprotein particles upon digestion of chromatin with micrococcal nuclease (Rill & Van Holde, 1973).

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“…But do intercalating dyes bind in the same manner when DNA is wrapped around the histone octamer to form the nucleosome structure? The nucleosome differs from free DNA in its charge/mass ratio (Donecke, 1977; Mirzabekov & Rich, 1979; Girardet & Lawrence, 1979;McGhee & Felsenfeld, 1980), its average twist angle (Fasman, 1977;Simpson & Shindo;, and its solubility properties (Perry & Chalkley, 1982; Komaiko & Felsenfeld, 1985; Ausio, 1986).…”

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Binding of ethidium to the nucleosome core particle. 2. Internal and external binding modes

McMurray¹,

Small²,

Holde³

1991

Biochemistry

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We have previously reported that the binding of ethidium bromide to the nucleosome core particle results in a stepwise dissociation of the structure which involves the initial release of one copy each of H2A and H2B (McMurray & van Holde, 1986). In this report, we have examined the absorbance and fluorescence properties of intercalated and outside bound forms of ethidium bromide. From these properties, we have measured the extent of external, electrostatic binding of the dye versus internal, intercalation binding to the core particle, free from contribution by linker DNA. We have established that dissociation is induced by the intercalation mode of binding to DNA within the core particle DNA, and not by binding to the histones or by nonintercalative binding to DNA. The covalent binding of [3H]-8-azidoethidium to the core particle clearly shows that less than 1.0 adduct is formed per histone octamer over a wide range of input ratios. Simultaneously, analyses of steady-state fluorescence enhancement and fluorescence lifetime data from bound ethidium complexes demonstrate extensive intercalation binding. Combined analyses from steady-state fluorescence intensity with equilibrium dialysis or fluorescence lifetime data revealed that dissociation began when approximately 14 ethidium molecules are bound by intercalation to each core particle and less than 1.0 nonintercalated ion pair was formed per core particle.

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Experimental evidence for asymmetrical shielding of nucleosomal DNA by histones

Cited by 9 publications

References 30 publications

Magnesium binding and conformational change of DNA in chromatin

Magnesium binding and conformational change of DNA in chromatin

Nucleosomes structure and its dynamic transitions

Binding of ethidium to the nucleosome core particle. 2. Internal and external binding modes

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