Structure of the nucleosome core particle at 7 Å resolution

Richmond, Timothy J.; Finch, J.T.; Rushton, B.; Rhodes, Daniela; Klug, A.

doi:10.1038/311532a0

Cited by 1,035 publications

(653 citation statements)

References 52 publications

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“…Advanced studies might involve further peculiarities of DNA-DNA and DNA-histone interactions including the difference in their dielectric constants and possible specific/bridging interactions, sequence-dependent DNA deformability 76,77 and periodicity, 3 the influence of counterion condensation, 44 and, probably, DNA-DNA chiral interactions. 78 On a higher level of NCPs organization, the crystallization 5,6,79 and folding of interconnected NCP filaments into high-order (solenoidal) structures 80-83 might also involve DNA-DNA interactions. For instance, the folding into the 30 nm solenoidal fiber can be triggered by addition of multivalent cations, which presumably adsorb into DNA grooves making the DNA-DNA electrostatic interactions more favorable.…”

Section: Discussionmentioning

confidence: 99%

Simple Model for Overcharging of a Sphere by a Wrapped Oppositely Charged Asymmetrically Neutralized Polyelectrolyte: Possible Effects of Helical Charge Distribution

Cherstvy

Winkler

2005

J. Phys. Chem. B

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We investigate the complexation of a polyelectrolyte bendable rod with an oppositely charged spherical macroion. We take into account electrostatic bending of the rod and its asymmetric charge neutralization by sphere charges. The spontaneous curvature of the rod toward the sphere results in a substantial overcharging of such polyelectrolyte complex with a possible phase transition. Assuming a discrete helical charge distribution on the rod surface, we calculate the electrostatic energy of the helix and the electrostatic contribution to its bending and twisting elasticity. We show that the latter may change sign when the helical pitch is changed. For a DNA-relevant case, these corrections appear to be small compared to the corresponding mechanical elastic moduli. We discuss possible applications of our results to the description of overcharging of the nucleosome core particles.

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Section: Discussionmentioning

confidence: 99%

Simple Model for Overcharging of a Sphere by a Wrapped Oppositely Charged Asymmetrically Neutralized Polyelectrolyte: Possible Effects of Helical Charge Distribution

Cherstvy

Winkler

2005

J. Phys. Chem. B

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“…Besides its role in packing the genome, nucleosome occupancy at gene promoters inhibits transcription initiation (1), and nucleosomes play a critical role in epigenetic regulation (2). The overall organization of the nucleosome (the repeating subunit of chromatin (3)(4)(5)), as a disklike complex of eight histone proteins (two H2A$H2B dimers and an (H3$H4) 2 tetramer), surrounded by~200 basepairs of DNA, was known for several decades (6). However, it was not until 1997 that the nucleosome structure was resolved at atomic resolution (7), uncovering key, previously unknown details of the histone-histone and histone-DNA interactions.…”

Section: Introductionmentioning

confidence: 99%

Partially Assembled Nucleosome Structures at Atomic Detail

Rychkov

Ilatovskiy

Nazarov

et al. 2017

Biophysical Journal

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The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A$H2B)$(H3$H4) 2 , the tetrasome (H3$H4) 2 , and the disome (H3$H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Fö rster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo.

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“…In eukaryotic cells, DNA is severely compacted when it folds into chromosomes. The elementary structural unit of chromatin is the nucleosome [3,4,5,6], which consists of a histone protein core enveloped by DNA. At first level of organization, the chromatin fiber is built from a linear array of nucleosomes [7,8].…”

Section: Introductionmentioning

confidence: 99%

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Audit

Vaillant

Arnéodo

et al. 2004

Journal of Biological Physics

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Abstract. Analyses of genomic DNA sequences have shown in previous works that base pairs are correlated at large distances with scale-invariant statistical properties. We show in the present study that these correlations between nucleotides (letters) result in fact from long-range correlations (LRC) between sequence-dependent DNA structural elements (words) involved in the packaging of DNA in chromatin. Using the wavelet transform technique, we perform a comparative analysis of the DNA text and of the corresponding bending profiles generated with curvature tables based on nucleosome positioning data. This exploration through the optics of the so-called 'wavelet transform microscope' reveals a characteristic scale of 100 − 200 bp that separates two regimes of different LRC. We focus here on the existence of LRC in the small-scale regime ( 200 bp). Analysis of genomes in the three kingdoms reveals that this regime is specifically associated to the presence of nucleosomes. Indeed, small scale LRC are observed in eukaryotic genomes and to a less extent in archaeal genomes, in contrast with their absence in eubacterial genomes. Similarly, this regime is observed in eukaryotic but not in bacterial viral DNA genomes. There is one exception for genomes of Poxviruses, the only animal DNA viruses that do not replicate in the cell nucleus and do not present small scale LRC. Furthermore, no small scale LRC are detected in the genomes of all examined RNA viruses, with one exception in the case of retroviruses. Altogether, these results strongly suggest that small-scale LRC are a signature of the nucleosomal structure. Finally, we discuss possible interpretations of these small-scale LRC in terms of the mechanisms that govern the positioning, the stability and the dynamics of the nucleosomes along the DNA chain. This paper is maily devoted to a pedagogical presentation of the theoretical concepts and physical methods which are well suited to perform a statistical analysis of genomic sequences. We review the results obtained with the so-called waveletbased multifractal analysis when investigating the DNA sequences of various organisms in the three kingdoms. Some of these results have been announced in B. Audit et al. [1,2].

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Structure of the nucleosome core particle at 7 Å resolution

Cited by 1,035 publications

References 52 publications

Simple Model for Overcharging of a Sphere by a Wrapped Oppositely Charged Asymmetrically Neutralized Polyelectrolyte: Possible Effects of Helical Charge Distribution

Simple Model for Overcharging of a Sphere by a Wrapped Oppositely Charged Asymmetrically Neutralized Polyelectrolyte: Possible Effects of Helical Charge Distribution

Partially Assembled Nucleosome Structures at Atomic Detail

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

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