Neutron diffraction from crystals of nucleosome core particles

1980 ◽  
Vol 290 (1043) ◽  
pp. 635-638 ◽  
Keyword(s):  
Neutron Diffraction ◽  
Molecular Mass ◽  
Micrococcal Nuclease ◽  
Core Particle ◽  
Base Pairs ◽  
Histone Protein ◽  
Nucleosome Core ◽  
The Core ◽  
Nucleosome Core Particles ◽  
Protein Molecules

The nucleosome is the basic repeating unit of chromatin (see review by Kornberg (1977)). It is a complex of histone protein molecules with a length of DNA, which digestion studies with the enzyme micrococcal nuclease have shown to be often about 200 base pairs in length but with quite wide variations between different cell species. With sufficient digestion, however, a ‘core’ particle is produced, which for all species so far investigated contains close to 145 base pairs of DNA associated with an octamer of pairs of the histones H3, H4, H2A and H2B. The molecular mass of the core particle is about 200000, roughly equally divided between DNA and protein.

scholarly journals Localization of testis-variant histones in rat testis chromatin

1982 ◽  
Vol 205 (1) ◽  
pp. 15-21 ◽  
Author(s):  
M R S Rao ◽  
B J Rao ◽  
J Ganguly
Keyword(s):  
Sedimentation Coefficient ◽  
Soluble Proteins ◽  
Micrococcal Nuclease ◽  
Base Pairs ◽  
Rat Testis ◽  
Nucleosome Core ◽  
The Core ◽  
Nucleosome Core Particles ◽  
Acid Solubility ◽  
Core Particles

Nucleosome core particles and oligonucleosomes were isolated by digesting rat testis nuclei with micrococcal nuclease to 20% acid-solubility, followed by fractionation of the digest on a Bio-Gel A-5m column. The core particles thus isolated were characterized on the basis of their DNA length of 151 +/- 5 base-pairs and sedimentation coefficient of 11.4S. Analysis of the acid-soluble proteins of the core particles indicated that histones TH2B and X2 are constituents of the core particles, in addition to the somatic histones H2A, H2B, H3 and H4. The acid-soluble proteins of the oligonucleosomes comprised all the histones, including both the somatic (H1, H2A, H2B, H3, H4 and X2) and the testis-specific ones (TH1 and TH2B). It was also observed that histones TH1 and H1 are absent from the core particles and were readily extracted from the chromatin by 0.6 M-NaCl, which indicated that both of them are bound to the linker DNA.

Helical repeat of DNA in the nucleosome core particle

2000 ◽  
Vol 28 (4) ◽  
pp. 373-376 ◽  
Author(s):  
R. Negri ◽  
M. Buttinelli ◽  
G. Panetta ◽  
V. De Arcangelis ◽  
E. Di Mauro ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Linker Histone ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
Apparent Paradox ◽  
Nucleosome Core ◽  
Nucleosome Core Particles ◽  
High Affinity Site ◽  
Hydroxyl Radical Cleavage ◽  
Radical Cleavage

Although the crystal structure of nucleosome core particle is essentially symmetrical in the vicinity of the dyad, the linker histone binds asymmetrically in this region to select a single high-affinity site from potentially two equivalent sites. To try to resolve this apparent paradox we mapped to base-pair resolution the dyads and rotational settings of nucleosome core particles reassembled on synthetic tandemly repeating 20 bp DNA sequences. In agreement with previous observations, we observed (1) that the helical repeat on each side of the dyad cluster is 10 bp maintaining register with the sequence repeat and (2) that this register changes by 2 bp in the vicinity of the dyad. The additional 2 bp required to effect the change in the rotational settings is accommodated by an adjustment immediately adjacent to the dyad. At the dyad the hydroxyl radical cleavage is asymmetric and we suggest that the inferred structural asymmetry could direct the binding of the linker histone to a single preferred site.

Reconstruction of complexes of histone and superhelical nuclear DNA

1981 ◽  
Vol 50 (1) ◽  
pp. 209-224
Author(s):  
J.M. Levin ◽  
P.R. Cook
Keyword(s):  
Nuclear Dna ◽  
Micrococcal Nuclease ◽  
Base Pairs ◽  
The Core ◽  
Ionic Detergent ◽  
Nuclear Rna ◽  
Core Histones ◽  
Non Destructive ◽  
Rna And Dna ◽  
General Method

When HeLa cells are lysed in solutions containing a non-ionic detergent and 2 M-NaCl, structures are released that retain many of the morphological features of nuclei. These nucleoids contain all the nuclear RNA and DNA but few of the proteins characteristic of chromatin. Their DNA is supercoiled and so intact. Using a simple and rapid procedure we have reconstructed nucleohistone complexes from nucleoids and the ‘core’ histones without breaking the DNA. We have probed the integrity and structure of the reconstructed complexes using a non-destructive fluorometric approach, which provides a general method for detecting agents that bind to DNA and alter its supercoiling. The superhelical status of the DNA in the reconstructed complexes is indistinguishable from that found in control nucleoids containing core histones. Experiments with micrococcal nuclease confirm that the DNA in the reconstructed complexes is organized into nucleosome-like structures. These, however, are spaced 145 base-pairs apart and not 200 base-pairs apart as is found in native chromatin.

The crystal structure of the nucleosome core particle by neutron diffraction

1984 ◽  
Vol 40 (a1) ◽  
pp. C20-C20
Author(s):  
G. Bentley ◽  
A. Lewit-Bentley ◽  
J. T. Finch ◽  
A. D. Podjarny ◽  
M. Roth
Keyword(s):  
Crystal Structure ◽  
Neutron Diffraction ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
Nucleosome Core

Identification of nonhistone chromatin proteins in chromatin subunits (or mononucleosomes) devoid of histone H1

1979 ◽  
Vol 57 (6) ◽  
pp. 666-672 ◽  
Author(s):  
P. K. Chan ◽  
C. C. Liew
Keyword(s):  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Sucrose Density Gradient ◽  
Polyacrylamide Gel ◽  
Micrococcal Nuclease ◽  
Dna Fragments ◽  
Base Pairs ◽  
The Core ◽  
Liver Chromatin ◽  
Chromatin Proteins

Rat liver chromatin was digested by micrococcal nuclease. Chromatin subunits (or mononucleosomes) were isolated by sucrose density gradient and subsequently fractionated by 6% polyacrylamide gel electrophoresis into two major components. One component (MN1) of the mononucleosomes had a higher mobility, contained histones H2A, H2B, H3, H4, and shorter DNA fragments (140 base pairs) while the other (MN2) contained all five histones and longer DNA fragments (180 base pairs). Both submononucleosomes (MN1 and MN2) were found to contain nonhistone chromatin proteins (NHCP). By electrophoresis in 15% sodium dodecyl sulfate – polyacrylamide gel, 9 and 11 major fractions of NHCP were identified in the submononucleosomes MN1 and MN2, respectively. It was also observed that treatment of mononucleosomes with 0.6 M NaCl removes most of these NHCP and histone H1 except for two major NHCP which remain in the core particles.

scholarly journals Dynamic networks observed in the nucleosome core particles couple the histone globular domains with DNA

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Xiangyan Shi ◽  
Chinmayi Prasanna ◽  
Aghil Soman ◽  
Konstantin Pervushin ◽  
Lars Nordenskiöld
Keyword(s):  
Dynamic Networks ◽  
Structural Features ◽  
Epigenetic Changes ◽  
Internal Dynamics ◽  
Histone Tails ◽  
Multiple Timescales ◽  
Nucleosome Core ◽  
The Core ◽  
Nucleosome Core Particles ◽  
Core Particles

Abstract The dynamics of eukaryotic nucleosomes are essential in gene activity and well regulated by various factors. Here, we elucidated the internal dynamics at multiple timescales for the human histones hH3 and hH4 in the Widom 601 nucleosome core particles (NCP), suggesting that four dynamic networks are formed by the residues exhibiting larger-scale μs-ms motions that extend from the NCP core to the histone tails and DNA. Furthermore, despite possessing highly conserved structural features, histones in the telomeric NCP exhibit enhanced μs-ms dynamics in the globular sites residing at the identified dynamic networks and in a neighboring region. In addition, higher mobility was observed for the N-terminal tails of hH3 and hH4 in the telomeric NCP. The results demonstrate the existence of dynamic networks in nucleosomes, through which the center of the core regions could interactively communicate with histone tails and DNA to potentially propagate epigenetic changes.

Reconstituted histone-DNA complexes

1978 ◽  
Vol 283 (997) ◽  
pp. 259-268 ◽  
Keyword(s):  
Dna Sequences ◽  
Micrococcal Nuclease ◽  
Nucleotide Pair ◽  
Nucleosome Core ◽  
Nucleosome Core Particles ◽  
Calf Thymus ◽  
Nuclease Digestion ◽  
Preferential Binding ◽  
One Step ◽  
Pair Fragment

Complexes of λdv 21 plasmid DNA with calf thymus histones are reconstituted in the presence and absence of urea, and, in the absence of urea, at 4 and 37 °C. It has been concluded previously on the basis of restriction nuclease digestion of complexes reconstituted in the presence of urea that the preferential binding of individual histones to certain DNA sequences is abolished, by specific histone-histone interactions, when a mixture of the four small histones is used (Steinmetz, Streeck & Zachau 1975 Nature, Lond. 258, 447). This conclusion holds also for the other conditions tested here. An exception is the pair of arginine-rich histones (H3-H4) which appears to bind specifically when reconstituted in the absence of urea by a one step dialysis procedure and non-specifically when the salt is removed by a stepwise dialysis procedure. The subunits which are formed when the four small histones are present simultaneously are very similar to nucleosome core particles according to the fragment patterns obtained with micrococcal nuclease. Protection of 155, 285, 420, 560 etc. nucleotide pairs is observed. When histone H1 is present in addition to the four small histones a 175 nucleotide pair fragment is protected, but no 200 nucleotide pair fragment or multiples thereof were formed under our conditions.

scholarly journals The effect of linker DNA on the structure and interaction of nucleosome core particles

Soft Matter ◽  
2018 ◽  
Vol 14 (45) ◽  
pp. 9096-9106 ◽  
Author(s):  
Yen-Chih Huang ◽  
Chun-Jen Su ◽  
Nikolay Korolev ◽  
Nikolay V. Berezhnoy ◽  
Sai Wang ◽  
...  
Keyword(s):  
Small Angle ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
X Ray ◽  
Nucleosome Core ◽  
Nucleosome Core Particles ◽  
X Ray Scattering ◽  
Nucleosomal Dna ◽  
The Impact

Small angle X-ray scattering reveals linker DNA-induced partial unwrapping of nucleosomal DNA on the nucleosome core particle (NCP) and the impact on NCP interaction demonstrating the crucial role of linker DNA.

Structure determination of the nucleosome core particle by selenium SAD phasing

2019 ◽  
Vol 75 (10) ◽  
pp. 930-936
Author(s):  
Mika Saotome ◽  
Naoki Horikoshi ◽  
Kazuki Urano ◽  
Tomoya Kujirai ◽  
Hidetaka Yuzurihara ◽  
...  
Keyword(s):  
Molecular Replacement ◽  
Base Pairs ◽  
Simple Method ◽  
X Ray Crystallography ◽  
Nucleosome Core ◽  
Nucleosome Core Particles ◽  
Experimental Phasing ◽  
Eukaryotic Species ◽  
Sad Phasing

The eukaryotic genome is compacted inside the nucleus of the cell in the form called chromatin. The fundamental unit of chromatin is the nucleosome, which contains four types of histones (H3, H4, H2A and H2B) and approximately 150 base pairs of DNA wrapped around the histone complex. The structure of the nucleosome is highly conserved across several eukaryotic species, and molecular replacement has been the primary phasing method used to solve nucleosome structures by X-ray crystallography. However, there is currently no simple, widely applicable experimental phasing method for the nucleosome. In the present study, it is demonstrated that selenomethionine-incorporated histones H3, H2A and H2B can be reconstituted into nucleosomes and crystallized for structural determination. Unexpectedly, it was found that the nucleosome can be phased with a relatively small number of Se atoms. The structures of nucleosome core particles containing 12 and 16 Se atoms were solved by SAD phasing at 2.5 and 2.4 Å resolution, respectively. The present study demonstrates a simple method for determining nucleosome structures by experimental phasing, which may be particularly useful for noncanonical structures that cannot be solved by molecular replacement.

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