Crystal structure of the nucleosome core particle at 16 Å resolution

Bentley, G.A.; Lewit-Bentley, Anita; Finch, J.T.; Podjarny, A.; Roth, M.

doi:10.1016/0022-2836(84)90382-6

Cited by 85 publications

(48 citation statements)

References 22 publications

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“…Each individual histone octamer is comprised of two copies of H2A/H2B dimer cores and H3/H4 tetramers, which wrap around 146 base pairs of DNA. 83,84 Repeating histone units make up the composition of nucleosomes and nucleosomes make up higher order chromatin. Histone octamer components contain a structured domain and an unstructured N-terminal tail of varying length that protrudes outward from the nucleosome, being readily subject to modifications known as "histone marks."…”

Section: Histone Modificationsmentioning

confidence: 99%

Basic concepts of epigenetics

Mazzio

Soliman²

2012

Epigenetics

204

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Section: Histone Modificationsmentioning

confidence: 99%

Basic concepts of epigenetics

Mazzio

Soliman²

2012

Epigenetics

204

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“…As shown in Figure 4A ( Bentley et al, 1984) and by X-ray diffraction at a resolution of 25 A (Finch et al, 1981) have not yet made it possible to visualize the relative positions and orientations of the different histones inside core particles. Little information is therefore available concerning the orientation of discrete histone domains and of the mobile histone tails which are known to play a key role in the stability of the nucleoprotein (Allan et al, 1982;Grigoryev and Krasheninnikov, 1982).…”

Section: Accessibility Of Various Histone Regions In Native or Hj/h5-mentioning

confidence: 99%

Use of histone antibodies for studying chromatin topography and the phosphorylation of chromatin subunits.

Muller¹,

Mazen²,

Martinage³

et al. 1984

The EMBO Journal

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Polyclonal and monoclonal antibodies specific for histones as well as sera directed against synthetic peptides of histones were used to probe the topography of chromatin subunits. In native chromatin, the regions corresponding to residues 130 -135 of H3 and 6-18 of H2B were found to be exposed and able to interact with antibodies whereas the regions 26-35 and 36-43 of H2B and 80-89 and 85-102 of H4 were not. In vitro phosphorylation of H3 and H5 in native chromatin or of H3 in H1/H5-depleted chromatin led to a marked drop in the binding of antibodies specific for residues 130-135 of H3 and 6-18 of H2B. Phosphorylation of H1/H5-depleted chromatin also altered the degree of exposure of certain H2A epitopes but it did not affect the surface accessibility of residues 1-11 of H2B.

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“…The method has met with several successes in the low-resolution study of several large biological assemblies (e.g. Bentley, Lewit-Bentley, Finch, Podjarny & Roth, 1984) but its use has not been extended to higher resolution, for need of an adequate treatment of the effects of density non-uniformities within the macromolecule. The most recent statistical treatment, due to Roth (1987), is based on Wilson's statistics, and hence does not produce any phase relations between the structure factors belonging to different reflexions.…”

Section: Application To the Contrast-variation Methodsmentioning

confidence: 99%

“…It is then possible to use a series of contrast-variation measurements to determine the moduli of the protein and solvent structure factors and the absolute value of the angle between them (Roth, Lewit-Bentley & Bentley, 1984); but no method so far exists to determine the actual absolute phases.…”

Section: (F)=[(j~= Nflj)-[u/(d-u)]nofo](#mentioning

confidence: 99%

A Bayesian statistical theory of the phase problem. I. A multichannel maximum-entropy formalism for constructing generalized joint probability distributions of structure factors

Bricogne¹

1988

Acta Cryst Sect A

150

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In this first of three papers on a full Bayesian theory of crystal structure determination, it is shown that all currently used sources of phase information can be represented and combined through a universal expression for the joint probability distribution of structure factors. Particular attention is given to situations arising in macromolecular crystallography, where the proper treatment of non-uniform distributions of atoms is absolutely essential. A procedure is presented, in stages of gradually increasing complexity, for constructing the joint probability distribution of an arbitrary collection of structure factors. These structure factors may be gathered from one or several crystal forms of an unknown molecule, each comprising one or several isomorphous structures related by substitution operations, possibly containing solvent regions and known fragments, and/or obeying a set of non-crystallographic symmetries. This universal joint probability distribution can be effectively approximated by the saddlepoint method, using maximum-entropy distributions of atoms [Bricogne (1984). Acta Cryst. A40, 410-445] and a generalization of structure-factor algebra. Atomic scattering factors may assume arbitrary complex values, so that this formalism applies to neutron as well as to X-ray diffraction methods. This unified procedure will later be extended by the construction of conditional distributions allowing phase extension, and of likelihood functions capable of detecting and characterizing all potential sources of phase information considered so far, thus completing the formulation of a full Bayesian inference scheme for crystal structure determination.

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Crystal structure of the nucleosome core particle at 16 Å resolution

Cited by 85 publications

References 22 publications

Basic concepts of epigenetics

Basic concepts of epigenetics

Use of histone antibodies for studying chromatin topography and the phosphorylation of chromatin subunits.

A Bayesian statistical theory of the phase problem. I. A multichannel maximum-entropy formalism for constructing generalized joint probability distributions of structure factors

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