Preferential interaction of the core histone tail domains with linker DNA

Angelov, Dimitar; Vitolo, Joseph M.; Mutskov, Vesco; Dimitrov, Stéfan; Hayes, Jeffrey J.

doi:10.1073/pnas.121171498

Cited by 103 publications

(99 citation statements)

References 36 publications

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“…Even in the absence of SPKK motifs, conventional histone tails interact extensively with the linker DNA (38). When found in H2A C-terminal or H2B N-terminal histone tails, SPKK-containing motifs confer an additional protection of 16 bp of linker DNA in reconstitution experiments (30,39).…”

Section: Discussionmentioning

confidence: 99%

Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone

Malik

Vermaak

Henikoff

2002

Proc. Natl. Acad. Sci. U.S.A.

113

110

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All eukaryotes contain centromere-specific histone H3 variants (CenH3s), which replace H3 in centromeric chromatin. We have previously documented the adaptive evolution of the Drosophila CenH3 (Cid) in comparisons of Drosophila melanogaster and Drosophila simulans, a divergence of Ϸ2.5 million years. We have proposed that rapidly changing centromeric DNA may be driving CenH3's altered DNA-binding specificity. Here, we compare Cid sequences from a phylogenetically broader group of Drosophila species to suggest that Cid has been evolving adaptively for at least 25 million years. Our analysis also reveals conserved blocks not only in the histone-fold domain but also in the N-terminal tail. In several lineages, the N-terminal tail of Cid is characterized by subgroup-specific oligopeptide expansions. These expansions resemble minor groove DNA binding motifs found in various histone tails. Remarkably, similar oligopeptides are also found in N-terminal tails of human and mouse CenH3 (Cenp-A). The recurrent evolution of these motifs in CenH3 suggests a packaging function for the N-terminal tail, which results in a unique chromatin organization at the primary constriction, the cytological marker of centromeres.

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Section: Discussionmentioning

confidence: 99%

Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone

Malik

Vermaak

Henikoff

2002

Proc. Natl. Acad. Sci. U.S.A.

113

110

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“…1). Clearly, the histone tails are flexible and rearrange to different locations depending on the context in which they are isolated or assembled (64,65; reviewed in refs. 22 and 60).…”

Section: Discussionmentioning

confidence: 99%

Electrostatic mechanism of nucleosomal array folding revealed by computer simulation

Sun

Zhang

Schlick

2005

Proc. Natl. Acad. Sci. U.S.A.

111

113

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Although numerous experiments indicate that the chromatin fiber displays salt-dependent conformations, the associated molecular mechanism remains unclear. Here, we apply an irregular Discrete Surface Charge Optimization (DiSCO) model of the nucleosome with all histone tails incorporated to describe by Monte Carlo simulations salt-dependent rearrangements of a nucleosomal array with 12 nucleosomes. The ensemble of nucleosomal array conformations display salt-dependent condensation in good agreement with hydrodynamic measurements and suggest that the array adopts highly irregular 3D zig-zag conformations at high (physiological) salt concentrations and transitions into the extended ''beads-on-a-string'' conformation at low salt. Energy analyses indicate that the repulsion among linker DNA leads to this extended form, whereas internucleosome attraction drives the folding at high salt. The balance between these two contributions determines the salt-dependent condensation. Importantly, the internucleosome and linker DNA-nucleosome attractions require histone tails; we find that the H3 tails, in particular, are crucial for stabilizing the moderately folded fiber at physiological monovalent salt.chromatin modeling ͉ irregular 3D zig-zag ͉ Discrete Surface Charge Optimization model C hromatin folding and the dynamic interplay between chromatin structures and various cellular factors directly regulate fundamental gene expression and silencing processes (1-4). Extensive studies have probed the structural and dynamic properties of chromatin and the molecular mechanisms that determine these properties (5-8). Nonetheless, questions remain concerning how a chain of nucleosomes connected by linker DNA folds into a condensed 30-nm chromatin fiber under physiological conditions (9) and what the exact arrangements of nucleosomes in the 30-nm fiber are (6). Two principal architectures of fiber arrangement proposed are the solenoid and zig-zag models. They differ significantly in how the linker DNA is arranged within the condensed chromatin fiber. In the solenoid model, the linker DNA is bent such that the consecutive nucleosomes interact with each other and form a helix (10-14); in the zig-zag model, the linker DNA remains straight and crosses the fiber axis so that the consecutive nucleosomes appear at the opposite side of the fiber axis (5, 15-18).The structure of chromatin strongly depends on the salt environment, both in terms of the valence of the ions and their concentration in solution (1). At low salt concentrations, chromatin adopts the extended ''beads-on-a-string'' conformation, whereas at high salt concentrations it folds into compact forms. In the presence of linker histones (H1 or H5) under physiological salt conditions, chromatin forms the folded 30-nm fiber. The histone tails are known to be crucial for the folding of chromatin fibers (19-21; reviewed in ref. 22). The tail domains, accounting for Ϸ50% of the positive charges of the histone octamer, are located at the N-terminal portions of H2A, H2B, H3, and H4, and ...

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“…H3 tails not only penetrate the small groove near SHL^7 (Figure 5(b)), but interact over a significant distance along the DNAs through their highly charged distal domains (see Introduction). 17 In this model, the untwisting achieved by H2B tails near SHL^5, in altering the rotational orientation of the two distal , 20 bp stretches, modifies at a distance H3 tail interactions with the small groove at SHL^7 (Figure 5(c)) and/or further away. This will in turn alter the trajectories of entering and exiting DNAs, making them less divergent than in the "no-untwisting" situation when viewed from the superhelix axis.…”

Section: Nucleosome Dynamics and Loop End Conditionsmentioning

confidence: 99%