Asymmetries in the nucleosome core particle at 2.5 Å resolution

Harp, Joel M.; Hanson, B. Leif; Timm, David E.; Bunick, Gerard J.

doi:10.1107/s0907444900011847

Cited by 212 publications

(221 citation statements)

References 51 publications

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“…1 APB H2AA12C Does Not Participate in Inter-nucleosomal Interactions-We next determined the extent to which a position near the first ␣-helix in H2A is able to mediate internucleosome interactions. This position is located at the junction of the H2A N-terminal tail and the histone fold domain, near the inside of the superhelical DNA gyre, and therefore is less likely to participate in inter-nucleosomal DNA binding (3,(5)(6)(7)58). Previous experiments have shown that irradiation of mononucleosomes containing H2A-A12C-APB results in crosslinks to DNA located ϳ40 bp to either side of the nucleosome dyad, consistent with the known structure of this complex (3,19).…”

Section: Resultsmentioning

confidence: 51%

“…This spool is formed primarily by the histone fold motif within each protein and additional structural elements adjacent to these domains (1,3). The structural details of these domains and their interactions with DNA have been well described (2)(3)(4)(5)(6)(7). Each nucleosome also includes a stretch of linker DNA, which joins nucleosome cores together in native chromatin, and, in most cases, a single linker histone (8).…”

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confidence: 99%

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Intra- and Inter-nucleosomal Protein-DNA Interactions of the Core Histone Tail Domains in a Model System

Zheng

Hayes

2003

Journal of Biological Chemistry

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The core histone tail domains are key regulators of eukaryotic chromatin structure and function and alterations in the tail-directed folding of chromatin fibers and higher order structures are the probable outcome of much of the post-translational modifications occurring in these domains. The functions of the tail domains are likely to involve complex intra-and inter-nucleosomal histone-DNA interactions, yet little is known about either the structures or interactions of these domains. Here we introduce a method for examining inter-nucleosome interactions of the tail domains in a model dinucleosome and determine the propensity of each of the four N-terminal tail domains to mediate such interactions in this system. Using a strong nucleosome "positioning" sequence, we reconstituted a nucleosome containing a single histone site specifically modified with a photoinducible cross-linker within the histone tail domain, and a second nucleosome containing a radiolabeled DNA template. These two nucleosomes were then ligated together and cross-linking induced by brief UV irradiation under various solution conditions. After cross-linking, the two templates were again separated so that cross-linking representing inter-nucleosomal histone-DNA interactions could be unambiguously distinguished from intra-nucleosomal cross-links. Our results show that the N-terminal tails of H2A and H2B, but not of H3 and H4, make internucleosomal histone-DNA interactions within the dinucleosome. The relative extent of intra-to inter-nucleosome interactions was not strongly dependent on ionic strength. Additionally, we find that binding of a linker histone to the dinucleosome increased the association of the H3 and H4 tails with the linker DNA region.

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Section: Resultsmentioning

confidence: 51%

mentioning

confidence: 99%

Intra- and Inter-nucleosomal Protein-DNA Interactions of the Core Histone Tail Domains in a Model System

Zheng

Hayes

2003

Journal of Biological Chemistry

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“…1B). Most residues involved in mediating the histone-histone interactions of H3 (14,22) are well conserved in Cid, consistent with their structural role. In contrast, the Loop 1 region of Cid, which is predicted to form an extensive DNA-interaction domain with Loop 2 of H4, is more variable (Fig.…”

Section: Resultsmentioning

confidence: 52%

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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“…For detailed atomistic modeling of functionalized gold NP-nucleosome interactions, we downloaded the structure of nucleosome core particle (NCP) resolved at 2.5 Å resolution [7]. In accordance with our roadmap-scheme (Fig.…”

Section: Resultsmentioning

confidence: 99%

Roadmap for Computer-Aided Modeling of Theranostics and Related Nanosystems

Uličný

Kožár

2018

EPJ Web Conf.

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Abstract. Detailed understanding of the interactions of novel metal-containing nanoparticles with biological membranes, macromolecules and other molecular targets of the living cell is crucial for the elucidation of the biological actions of such functionalized nanosystems. We present here the construction and modeling of thiolate-protected gold clusters and the prediction of their static and dynamic properties.

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Asymmetries in the nucleosome core particle at 2.5 Å resolution

Cited by 212 publications

References 51 publications

Intra- and Inter-nucleosomal Protein-DNA Interactions of the Core Histone Tail Domains in a Model System

Intra- and Inter-nucleosomal Protein-DNA Interactions of the Core Histone Tail Domains in a Model System

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

Roadmap for Computer-Aided Modeling of Theranostics and Related Nanosystems

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