Nucleosomes structure and its dynamic transitions

Mirzabekov, Andrei D.

doi:10.1017/s0033583500001670

Cited by 54 publications

(38 citation statements)

References 142 publications

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“…The histones probably are coiled around the macronucleosomic loop withoutside DNA strand. This assumption contradicts the hypothesis that DNA is wrapped around histones [16], but we believe that our scheme more precisely indicates the location of DNA mini-segments directly bound with certain type of histones in the nucleosomic loop.…”

contrasting

confidence: 90%

Compaction Principle and Approaches to Biopolymer Structure Deciphering

Shabalkin

Шабалкин

2010

Bull Exp Biol Med

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On the basis of a principle of maximum compaction of biopolymer structure in a limited space derived from the concept about the existence of three different types of dimers in the studied structure, we propose a hypothesis according to which side groups in macromolecules (nitrogenous bases in nucleic acids or R-groups in proteins) are specifically distributed in different points depending on geometrical shape of dimer bending in the biopolymer chain backbone. The latter provides the possibility of complete deciphering of biopolymer structure.

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contrasting

confidence: 90%

Compaction Principle and Approaches to Biopolymer Structure Deciphering

Shabalkin

Шабалкин

2010

Bull Exp Biol Med

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“…The location and assembly of the eight histones in these particles is approximately known. Cross-link experiments and association studies in solution have shown that a tetrameric unit (H32 , H42) which constitutes the central core of the octamer is easily formed and that strong dimers (H2A, H2B) and (H2B, H4) and weakly bound dimers (H2A, H4) and (H2B, H3) exist (1323,1327,1330). The heart-shaped appearance of the histone octamer (Figures 19-4, 19-5) is due to the disk-like arrangement of the (H3 2 , H42) tetramer which forms the center and lower tip of the heart and is associated with two (H2A, H2B) dimers producing the upper two tips (1330).…”

Section: Structure Of the Nucleosome Corementioning

confidence: 99%

“…Cross-link experiments and association studies in solution have shown that a tetrameric unit (H32 , H42) which constitutes the central core of the octamer is easily formed and that strong dimers (H2A, H2B) and (H2B, H4) and weakly bound dimers (H2A, H4) and (H2B, H3) exist (1323,1327,1330). The heart-shaped appearance of the histone octamer (Figures 19-4, 19-5) is due to the disk-like arrangement of the (H3 2 , H42) tetramer which forms the center and lower tip of the heart and is associated with two (H2A, H2B) dimers producing the upper two tips (1330). The octamer is probably stabilized by interaction of the hydrophobic C-terminal ends of the histones (Box 19-2) while their N-terminal ends, rich in arginine and lysine, are located at the periphery and interact with DNA wound around the core in nearly two negative helical supercoil turns.…”

Section: Structure Of the Nucleosome Corementioning

confidence: 99%

Principles of Nucleic Acid Structure

Saenger

1984

Springer Advanced Texts in Chemistry

5,969

312

6,279

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“…With our current appreciation of the nucleosome as the fundamental unit of chromatin condensation (1)(2)(3), it has been pertinent to ask whether or not there is a functional requirement for a particular nucleosomal array. This aspect of chromatin structure has been most often expressed in the concept of specific nucleosome positioning (or "phasing") at a few or many loci of the eukaryotic genome, perhaps in a cell-, tissue-, or development-specific manner.…”

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confidence: 99%

Cleavage of chromatin with methidiumpropyl-EDTA . iron(II).

Cartwright¹,

Hertzberg²,

Dervan³

et al. 1983

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

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Methidiumpropyl-EDTA-iron(II) [MPE-Fe(II)] cleaves double-helical DNA with considerably lower sequence specificity than micrococcal nuclease. Moreover, digestions with MPE-Fe(II) can be performed in the presence of certain metal chelators, which will minimize the action of many endogenous nucleases. Because of these properties MPE-Fe(II) would appear to be a superior tool for probing chromatin structure. We have compared the patterns generated from the 1.688 g/cm3 complex satellite, 5S ribosomal RNA, and histone gene sequences of Drosophila melanogaster chromatin and protein-free DNA by MPE-Fe(I) and micrococcal nuclease cleavage. MPE-Fe(II) at low concentrations recognizes the nucleosome array, efficiently introducing a regular series of single-stranded (and some doublestranded) cleavages in chromatin DNA. Subsequent S1 nuclease digestion of the purified DNA produces a typical extended oligonucleosome pattern, with a repeating unit of ca. 190 base pairs. Under suitable conditions, relatively little other nicking is observed. Unlike micrococcal nuclease, which has a noticeable sequence preference in introducing cleavages, MPE-Fe(II) cleaves protein-free tandemly repetitive satellite and 5S DNA sequences in a near-random fashion. The spacing of cleavage sites in chromatin, however, bears a direct relationship to the length of the respective sequence repeats. In the case of the histone gene sequences a faint, but detectable, MPE-Fe(H) cleavage pattern is observed on DNA, in some regions similar to and in some regions different from the strong chromatin-specified pattern. The results indicate that MPE-Fe(ll) will be very useful in the analysis of chromatin structure.With our current appreciation of the nucleosome as the fundamental unit of chromatin condensation (1-3), it has been pertinent to ask whether or not there is a functional requirement for a particular nucleosomal array. This aspect of chromatin structure has been most often expressed in the concept of specific nucleosome positioning (or "phasing") at a few or many loci of the eukaryotic genome, perhaps in a cell-, tissue-, or development-specific manner. Possible advantages of such positioning have been envisaged by many investigators, although no positive evidence for its actual functional importance in vivo has yet been presented. Numerous studies arguing for a specific or, conversely, for a random distribution of nucleosomes have been reported, and these have been reviewed (4-7). Many of these experiments have utilized micrococcal nuclease for generation of nucleosomal arrays. The DNA is purified subsequent to the nuclear digestion and the cleavage sites are mapped by reference to well-characterized restriction sites. Unfortunately, micrococcal nuclease has a marked sequence preference and introduces cleavages into purified DNA at quite specific and reproducible positions (8,9). In some cases these occur at exactly the same sites in chromatin, leading to uncertainty concerning which is chromatin specific and which is purely sequence specific....

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Nucleosomes structure and its dynamic transitions

Cited by 54 publications

References 142 publications

Compaction Principle and Approaches to Biopolymer Structure Deciphering

Compaction Principle and Approaches to Biopolymer Structure Deciphering

Principles of Nucleic Acid Structure

Cleavage of chromatin with methidiumpropyl-EDTA . iron(II).

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