Orientation of the nucleosome within the higher order structure of chromatin

McGhee, James D.; Rau, Donald C.; Charney, Elliot; Felsenfeld, Gary

doi:10.1016/0092-8674(80)90157-9

Cited by 238 publications

(129 citation statements)

References 32 publications

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“…However, the s20,w of this latter control sample is -25% lower than that of the sane chronatin preparation which has not been exposed to 0.35 M NaCl. HMG 14/17 do not prevent bulk chronatin condensation as monitored by electric dichroism Electric dichroism can be used to monitor the chromatin filament t solenoid transition induced by Mg+ ions (11). Several of the data points in Fig.…”

Section: Methodsmentioning

confidence: 99%

“…Chromatin fractions obtained from adult chicken erythrocytes were prepared as described previously (11). Erythrocyte nuclei from 14 day chicken embryos were prepared as described in (12), including centrifugation through 2 M sucrose, resuspended at an A260 =100 (or in one case, 200) in 100 mM NaCl, 50 mM Tris HC1, pH 8.0, 2 mM MgC12, 1 mM CaC12, 5 mM Na butyrate, 0.1 mM PMSF and digested to 0.1-0.5% acid solubility with 0.01 units of micrococcal nuclease for 30 minutes at 37dC (nuclease units as defined in (13)).…”

Section: Methodsmentioning

confidence: 99%

“…ref 10), or by changes in electric dichroism properties induced by increasing divalent ions (11). We …”

Section: Introductionmentioning

confidence: 99%

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The high mobility group proteins, HMG 14 and 17, do not prevent the formation of chromatin higher order structure

McGhee¹,

Rau²,

Felsenfeld³

1982

Nucl Acids Res

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The high mobility group proteins, HMG 14 and 17, have been associated with the chromatin of active genes (refs 1-8), although how they function is not known. We use sedimentation and electric dichroism to investigate the effect of HMG 14 and 17 on the condensation of chicken erythrocyte chromatin into higher order structure. We find no evidence that excess HMG 14 and 17 induce an extended configuration, either in bulk chromatin or in the chromatin of the chicken 3-globin gene.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

The high mobility group proteins, HMG 14 and 17, do not prevent the formation of chromatin higher order structure

McGhee¹,

Rau²,

Felsenfeld³

1982

Nucl Acids Res

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“…Our results may be interpreted in terms of supranucleosomal organization of chromatin. Data in favor of nucleosome alternation in compact chromatin appeared in [12]. In spite of the alternation all linkers are accessible to micrococcal nuclease; therefore micrococcal nuclease does not induce the formation of nucleodisomes.…”

Section: Resultsmentioning

confidence: 99%

On the mechanism of nucleodisome splitting off by nucleases

Поспелов

Svetlikova

1982

FEBS Letters

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“…Moreover, our current understanding of chromatin organization is at a stage much like that which preceded the rapid buildup of knowledge about detailed DNA structure. The solution properties of DNA, which were once interpreted in terms of the stacking interactions of bases, resemble the features of strong internucleosomal association in chromatin detected with modern force-extension technology (50) or classic electric dichroism measurements (51). Classic polymer studies of chromatin offer the same sort of insights into overall macromolecular structure as did early studies of DNA, including how the composition and number of side groups (nucleosomes as opposed to bases) influence global chain dimensions (52).…”

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confidence: 86%

Contributions of Sequence to the Higher-Order Structures of DNA

Todolli

Perez

Clauvelin

et al. 2017

Biophysical Journal

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One of the critical unanswered questions in genome biophysics is how the primary sequence of DNA bases influences the global properties of very-long-chain molecules. The local sequence-dependent features of DNA found in high-resolution structures introduce irregularities in the disposition of adjacent residues that facilitate the specific binding of proteins and modulate the global folding and interactions of double helices with hundreds of basepairs. These features also determine the positions of nucleosomes on DNA and the lengths of the interspersed DNA linkers. Like the patterns of basepair association within DNA, the arrangements of nucleosomes in chromatin modulate the properties of longer polymers. The intrachromosomal loops detected in genomic studies contain hundreds of nucleosomes, and given that the simulated configurations of chromatin depend on the lengths of linker DNA, the formation of these loops may reflect sequence-dependent information encoded within the positioning of the nucleosomes. With knowledge of the positions of nucleosomes on a given genome, methods are now at hand to estimate the looping propensities of chromatin in terms of the spacing of nucleosomes and to make a direct connection between the DNA base sequence and larger-scale chromatin folding.Despite the astonishing amount of information now known about the sequential makeup and spatial organization of genomic DNA, there is much to learn about how the vast numbers of basepairs in these systems contribute to the three-dimensional architectures and workings of long, spatially constrained, double-helical molecules. New biochemical and imaging methodologies, such as proximity-based ligation and fluorescence in situ hybridization (1-3), have shed light on the large-scale organization of genomic DNA, enabling investigators to pinpoint DNA elements in close spatial proximity and follow the course of these associations during cellular processes. The resulting measurements have motivated the study of long genomes in terms of simple polymer models (4,5), which have in turn illuminated the physical nature of the contacted elements and pointed to mechanisms potentially governing genome architecture and dynamics. Although these models are appropriate for the very large scale of the experimental data, they rest on the assumption that the chemical makeup of DNA does not matter, and thus provide no link between the primary sequence of bases and the tertiary structures and interactions of genomic folds.At the other extreme of chain length, the detailed molecular structures of DNA with only tens of basepairs point to various sequence-dependent spatial and energetic codes underlying the three-dimensional organization of the double helix and its susceptibility to interactions with proteins and other molecules (6). The structural data also include more than 100 crystallographic examples of the tight, superhelical wrapping of~150 DNA basepairs (bp) around the core of the histone proteins in the nucleosome core particle, the fundamental packagi...

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Orientation of the nucleosome within the higher order structure of chromatin

Cited by 238 publications

References 32 publications

The high mobility group proteins, HMG 14 and 17, do not prevent the formation of chromatin higher order structure

The high mobility group proteins, HMG 14 and 17, do not prevent the formation of chromatin higher order structure

On the mechanism of nucleodisome splitting off by nucleases

Contributions of Sequence to the Higher-Order Structures of DNA

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