Changes in chromatin structure induced by EDTA treatment and partial removal of histone H1

Vengerov, Yu. Yu.; Попенко, В. И.

doi:10.1093/nar/4.9.3017

Cited by 18 publications

(9 citation statements)

References 10 publications

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“…3. In this Nucleic Acids Research manner evaluated cross section diameters of 25 to 29 nm for quarterny structure agree well with electronmicroscopic and neutron or X-ray scattering data of other authors (6, 22, 23, 24, 25,26,27,28,29). The diameters obtained from the outer slopes of the scattering curves (Table I, column 4, side right) in general are less than 9 nm.…”

Section: Discussionsupporting

confidence: 90%

Studies on the structure of isolated chromatin in three different solvents

et al. 1979

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Properties of calf thymus chromatin, prepared by mild procedures, have been studied in various solvents. In 0.2 mM EDTA s-values ranged from 20 to 30 S and intrinsic viscosities from 5 to 24 dl/g. Dialysis against 0.15 M NaCl or 0.2 mM MgCl2 changed these values to 80 to 100 S and 0.2 to 5 dl/g, respectively, indicating an essentially more compact structure. In 0.2 mM EDTA X-ray scattering yielded a cross section diameter of 9 nm, which is associated with the tertiary structure of chromatin fiber (M/L = 21200 Dalton/nm). By dialysis against 0.15 M NaCl or 0.2 mM MgCl2 part of the material spontaneously formed quarterny structures (cross section diameters 25-29 nm). The rest of the material with cross section diameters less than 9 nm is supposed to be more strongly sheared tertiary structure which seems to be unable to form quarterny structure due to artificial conformational changes.

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Section: Discussionsupporting

confidence: 90%

Studies on the structure of isolated chromatin in three different solvents

et al. 1979

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“…The freshly isolated chromatin was used for transmission electron microscopy examination using the preparation method described by Vengerov and Popenko [27] with minor modifications. In brief, chromatin was diluted to a final concentration ,5 mg/mL in TE buffer containing 0.25 M ammonium acetate.…”

Section: Electron Microscopymentioning

confidence: 99%

Proteome and phosphoproteome analysis of chromatin associated proteins in rice (Oryza sativa)

Tan

Chitteti

et al. 2007

Proteomics

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The eukaryotic chromatin/chromosome stores genomic information, controls genetic material distribution, and plays an essential role in the establishment and maintenance of spatial and temporal gene expression profile. Despite over a century of research, the protein composition and higher level structure of chromatin still remain obscure, particularly in plants. In this report, we have developed a protocol for chromatin purification from rice suspension cells and examined proteins copurified with chromatin using both 2-DE gel and shotgun approaches. Nine hundred seventy-two distinct protein spots have been resolved on 2-DE gels and 509 proteins have been identified by MALDI-MS/MS following gel excision, which correspond to 269 unique proteins. When the chromatin copurified proteins are examined using shotgun method, a large number of histone variants in addition to the four common core histones have been identified. Other proteins identified include nucleosome assembly proteins, high mobility group proteins, histone modification proteins, transcription factors, and a large number of hypothetical and function unknown proteins. Furthermore, putative phosphoproteins copurified with chromatin have been examined using Pro-Q Diamond phosphoprotein stain and followed by MALDI-MS/MS. Our studies have provided valued new insight into chromatin composition in plants.

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“…1 the original quaternary structure. An outer diameter of about 25-30 nm for the higher-order chromatin fiber is often deduced from observations by electron microscopy [22,26,291, although procedures like drying and staining may reduce the original dimensions [16,28]. In contrast, chromatin in solution is perfectly hydrated and therefore data of soluble chromatin should be a very good approximation to the original state within the cell nuclei.…”

Section: For Chromatin From F K T I O T Zmentioning

confidence: 99%

Structural Investigations on Isolated Chromatin of Higher‐Order Organisation

Brust

Harbers

1981

European Journal of Biochemistry

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Chromatin of a high structural order was prepared by a method avoiding drastic mechanical stress, as well as strong changes of the ionic strength, and was investigated by small-angle X-ray scattering. The results obtained support the idea that the quaternary structure of completely hydrated chromatin in solution is a solenoid with a diameter of about 32-34 nm. Gel chromatography of this chromatin yields solutions containing mainly quaternary structures with differing portions of tertiary structure. Decrease of the ionic strength results in an increase of loosening and unfolding of quaternary structures. Reconstitution by readjustment of the physiological ionic strength indicates slight differences between reconstituted and original higher-order structures.Chromatin structure appears to be a hierarchical one. The elementary subunit is the nucleosome [I -61 of which the over all shape is well known now. Some details about the arrangement of D N A and histones within the nucleosome are established [7-111 and several models of primary organization of nucleosomes are discussed [8,12 -The next level of organization is the tertiary structure of chromatin which appears to be an arrangement of nucleosomes like 'beads on a string' or tightly packed like a rod with a diameter of about 10-11 nm in solvents of low ionic strength [1,16]. In solvents of higher ionic strength part of the chromatin is organized in a higher-order conformation [ 16 -321 forming a quaternary structure. In electron micrographs this sometimes appears as a 'knobby' fiber of about 25 -30 nm in diameter. However, whether the quaternary structure is organized in the form of 'superbeads' [26,27, 32-34] containing 6-12 nucleosomes or as a solenoid [17,[29][30][31] is still an open question [16].In order to investigate chromatin in solution it has first to be isolated. Even with mild methods avoiding shear and mechanical stress, one can obtain isolated chromatin only as a fragmentary material. A procedure often applied is the lysis of the cell nuclei in 0.2 mM EDTA [38]. In this solvent chromatin appears as a string of nucleosomes, i.e. the tertiary structure. Increasing the ionic strength of the solvent leads to reconstitution of higher-order structures. These quaternary structures appear to be very similar to the original ones in intact cell nuclei; however, it is not known how far they are really identical. By avoiding drastic changes of ionic strength during lysis of the nuclei it is possible to obtain solutions of chromatin having a highly preserved structural order [39,40]. For our structural studies applying small-angle X-ray scattering higher-order chromatin was obtained by a modification of the method of Rees et al. [39,41]. By enzymatic autolysing of the cell nuclei chromatin with a very high sedimentation coefficient can be isolated. Purification of this chromatin by gel chromatography results in solutions containing native quaternary structure and still a certain amount of tertiary structure. This accumulation of quaternary structure material ...

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Changes in chromatin structure induced by EDTA treatment and partial removal of histone H1

Cited by 18 publications

References 10 publications

Studies on the structure of isolated chromatin in three different solvents

Studies on the structure of isolated chromatin in three different solvents

Proteome and phosphoproteome analysis of chromatin associated proteins in rice (Oryza sativa)

Structural Investigations on Isolated Chromatin of Higher‐Order Organisation

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