H3.cntdot.H4 tetramer directs DNA and core histone octamer assembly in the nucleosome core particle

Chromatin comprises nucleosomes as well as nonnucleosomal histone–DNA particles. Prenucleosomes are rapidly formed histone–DNA particles that can be converted into canonical nucleosomes by a motor protein such as ACF. Here we show that the prenucleosome is a stable conformational isomer of the nucleosome. It consists of a histone octamer associated with ∼80 base pair (bp) of DNA, which is located at a position that corresponds to the central 80 bp of a nucleosome core particle. Monomeric prenucleosomes with free flanking DNA do not spontaneously fold into nucleosomes but can be converted into canonical nucleosomes by an ATP-driven motor protein such as ACF or Chd1. In addition, histone H3K56, which is located at the DNA entry and exit points of a canonical nucleosome, is specifically acetylated by p300 in prenucleosomes relative to nucleosomes. Prenucleosomes assembled in vitro exhibit properties that are strikingly similar to those of nonnucleosomal histone–DNA particles in the upstream region of active promoters in vivo. These findings suggest that the prenucleosome, the only known stable conformational isomer of the nucleosome, is related to nonnucleosomal histone–DNA species in the cell.

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How does the histone code work?

Biochemistry and Cell Biology ◽

10.1139/o05-137 ◽

2005 ◽

Vol 83 (4) ◽

pp. 468-476 ◽

Cited By ~ 136

Author(s):

Michael S Cosgrove ◽

Cynthia Wolberger

Keyword(s):

Chromatin Structure ◽

Histone Code ◽

Globular Domain ◽

Core Particle ◽

Nucleosome Core Particle ◽

Histone Tails ◽

Post Translational Modifications ◽

Nucleosome Core ◽

Histone Octamer ◽

Nucleosome Dynamics

Patterns of histone post-translational modifications correlate with distinct chromosomal states that regulate access to DNA, leading to the histone-code hypothesis. However, it is not clear how modification of flexible histone tails leads to changes in nucleosome dynamics and, thus, chromatin structure. The recent discovery that, like the flexible histone tails, the structured globular domain of the nucleosome core particle is also extensively modified adds a new and exciting dimension to the histone-code hypothesis, and calls for the re-examination of current models for the epigenetic regulation of chromatin structure. Here, we review these findings and other recent studies that suggest the structured globular domain of the nucleosome core particle plays a key role regulating chromatin dynamics.Key words: histones, histone code, modifications, epigenetic, chromatin, nucleosome, dynamics, regulated nucleosome mobility, core, archaeal, combinatorial switch, histone octamer.

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Faculty Opinions recommendation of Structure of RCC1 chromatin factor bound to the nucleosome core particle.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.4941956.4954054 ◽

2010 ◽

Author(s):

Yixian Zheng

Keyword(s):

Core Particle ◽

Nucleosome Core Particle ◽

Nucleosome Core

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Faculty Opinions recommendation of 3.9 Å structure of the nucleosome core particle determined by phase-plate cryo-EM.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.726675170.793526714 ◽

2016 ◽

Author(s):

Jose Valpuesta

Keyword(s):

Phase Plate ◽

Core Particle ◽

Nucleosome Core Particle ◽

Nucleosome Core

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Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions

The EMBO Journal ◽

10.1093/emboj/20.18.5207 ◽

2001 ◽

Vol 20 (18) ◽

pp. 5207-5218 ◽

Cited By ~ 274

Author(s):

Cindy L. White ◽

Robert K. Suto ◽

Karolin Luger

Keyword(s):

Core Particle ◽

Nucleosome Core Particle ◽

Nucleosome Core

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Helical repeat of DNA in the nucleosome core particle

Biochemical Society Transactions ◽

10.1042/bst0280373 ◽

2000 ◽

Vol 28 (4) ◽

pp. 373-376 ◽

Cited By ~ 2

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.

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