A charged and contoured surface on the nucleosome regulates chromatin compaction

Chodaparambil, J.V.; Barbera, Andrew J.; Lu, Xu; Kaye, Kenneth M.; Hansen, Jeffrey C.; Luger, Karolin

doi:10.1038/nsmb1334

Cited by 107 publications

(130 citation statements)

References 15 publications

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“…These data suggest that this band represents interaction of the H4 tail domain with the H2A pocket previously observed in crystal structures of nucleosome core particles (27). These results are consistent with previous reports that the H4 tail binds to a pocket on the surface of H2A, generating an on May 9, 2018 by guest http://mcb.asm.org/ internucleosomal interaction to enhance folding of nucleosome arrays (10,13,33,49). Interestingly, although the nucleosome array is expected to exist as a completely extended structure with little or no internucleosome interactions in the absence of MgCl 2 (25,30,31), cross-linking between H4 and H2A was detectable under these conditions (Fig.…”

Section: Vol 29 2009 Interarray Interactions Of the H4 Tail In Chrosupporting

confidence: 82%

“…They further showed that the initial step in the process involves self-association of monomeric nucleosome arrays (55 S) into oligomeric structures approximately 10 times larger than the arrays (about 500 S), without appreciable accumulation of species of intermediate sizes. As the salt is increased further, these ϳ500-S structures continue to self-associate into extremely large complexes that sediment in excess of Ͼ Ͼ10,000 S. These observations provide a rigorous physicochemical basis for a simple microcentrifuge-based assay now routinely used to study self-association (5,10,25,30,33,43). Association of linker histones also pushes the equilibrium toward the largest species (8,30).…”

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confidence: 89%

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The H4 Tail Domain Participates in Intra- and Internucleosome Interactions with Protein and DNA during Folding and Oligomerization of Nucleosome Arrays

Kan

Caterino²,

Hayes³

2009

Molecular and Cellular Biology

156

151

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The condensation of nucleosome arrays into higher-order secondary and tertiary chromatin structures likely involves long-range internucleosomal interactions mediated by the core histone tail domains. We have characterized interarray interactions mediated by the H4 tail domain, known to play a predominant role in the formation of such structures. We find that the N-terminal end of the H4 tail mediates interarray contacts with DNA during self-association of oligonucleosome arrays similar to that found previously for the H3 tail domain. However, a site near the histone fold domain of H4 participates in a distinct set of interactions, contacting both DNA and H2A in condensed structures. Moreover, we also find that H4-H2A interactions occur via an intraas well as an internucleosomal fashion, supporting an additional intranucleosomal function for the tail. Interestingly, acetylation of the H4 tail has little effect on interarray interactions by itself but overrides the strong stimulation of interarray interactions induced by linker histones. Our results indicate that the H4 tail facilitates secondary and tertiary chromatin structure formation via a complex array of potentially exclusive interactions that are distinct from those of the H3 tail domain.Eukaryotic DNA is packaged with core histones and other nonhistone chromosomal proteins through multiple levels of increasingly condensed chromatin structures. Arrays of nucleosomes, which form the primary repeating structure of chromatin, fold into secondary chromatin structures such as the 30-nm-diameter chromatin fiber (21, 37, 45). Chromatin fibers and other secondary structures are further condensed into higher-order tertiary chromatin structures such as the 100-to 130-nm-diameter chromonema observed by Belmont and Bruce (7). While models (solenoid, twisted-ribbon, and crossed-linker) have been proposed for the 30-nm-diameter chromatin fiber, to date no definitive model has been broadly accepted (38). Moreover, only very limited structural information is available with regard to tertiary and higher-order chromatin structures (see references 21, 30, and 45 and see below).Although the molecular mechanisms behind the formation of secondary and tertiary chromatin structures remain unclear, work employing model systems has shown that in vitro reconstituted nucleosome arrays containing only DNA and core histone proteins undergo the same initial salt-dependent condensations as native chromatin (17, 21). In solutions containing physiological concentrations of mono-and divalent cations, nucleosome arrays spontaneously fold into structures with the same hydrodynamic shape as the 30-nm-diameter chromatin fiber and reversibly self-associate into larger assemblies with characteristics of native tertiary chromatin structures (21, 45).

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Section: Vol 29 2009 Interarray Interactions Of the H4 Tail In Chrosupporting

confidence: 82%

mentioning

confidence: 89%

The H4 Tail Domain Participates in Intra- and Internucleosome Interactions with Protein and DNA during Folding and Oligomerization of Nucleosome Arrays

Kan

Caterino²,

Hayes³

2009

Molecular and Cellular Biology

156

151

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“…This finding supports the idea that access to the H4 tail after DNA damage is restricted through interaction of H4 with the acidic patch on the nucleosome surface. Because the H4 tail and GFP-LANA both bind to this acidic patch (30,31), displacement of the H4 tail, either by LANA peptide or Anp32e (which removes H2A.Z and eliminates the acidic patch) will promote H4Ac after DNA damage.…”

Section: Resultsmentioning

confidence: 99%

“…To test this hypothesis, we used the LANA protein of Kaposi's sarcoma herpes virus (27). LANA protein binds tightly to the acidic patch (30,31), using the same acidic amino acids to which the H4 tail binds. The 23 amino acid domain of LANA, which binds to the acidic patch, and a control, in which an essential arginine was mutated to glycine (30), were fused to GFP and expressed in cells (Fig.…”

Section: Resultsmentioning

confidence: 99%

Histone chaperone Anp32e removes H2A.Z from DNA double-strand breaks and promotes nucleosome reorganization and DNA repair

Gürsoy-Yüzügüllü

Ayrapetov

Price

2015

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

127

155

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The repair of DNA double-strand breaks (DSBs) requires open, flexible chromatin domains. The NuA4–Tip60 complex creates these flexible chromatin structures by exchanging histone H2A.Z onto nucleosomes and promoting acetylation of histone H4. Here, we demonstrate that the accumulation of H2A.Z on nucleosomes at DSBs is transient, and that rapid eviction of H2A.Z is required for DSB repair. Anp32e, an H2A.Z chaperone that interacts with the C-terminal docking domain of H2A.Z, is rapidly recruited to DSBs. Anp32e functions to remove H2A.Z from nucleosomes, so that H2A.Z levels return to basal within 10 min of DNA damage. Further, H2A.Z removal by Anp32e disrupts inhibitory interactions between the histone H4 tail and the nucleosome surface, facilitating increased acetylation of histone H4 following DNA damage. When H2A.Z removal by Anp32e is blocked, nucleosomes at DSBs retain elevated levels of H2A.Z, and assume a more stable, hypoacetylated conformation. Further, loss of Anp32e leads to increased CtIP-dependent end resection, accumulation of single-stranded DNA, and an increase in repair by the alternative nonhomologous end joining pathway. Exchange of H2A.Z onto the chromatin and subsequent rapid removal by Anp32e are therefore critical for creating open, acetylated nucleosome structures and for controlling end resection by CtIP. Dynamic modulation of H2A.Z exchange and removal by Anp32e reveals the importance of the nucleosome surface and nucleosome dynamics in processing the damaged chromatin template during DSB repair.

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“…Therefore, the reduction in silencing and changes in heterochromatin caused by LRS mutations are probably not a result of SIR dissociation from HML. As the solvent-accessible surface is involved in higher-order chromatin formation (Chodaparambil et al 2007;Zhou et al 2007), it is possible that LRS contributes to silencing by aiding the formation of high-order heterochromatin structure.…”

Section: Resultsmentioning

confidence: 99%

Differential Contributions of Histone H3 and H4 Residues to Heterochromatin Structure

Olsen

Zhang

et al. 2011

Genetics

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Transcriptional silencing in Saccharomyces cerevisiae is mediated by heterochromatin. There is a plethora of information regarding the roles of histone residues in transcriptional silencing, but exactly how histone residues contribute to heterochromatin structure is not resolved. We address this question by testing the effects of a series of histone H3 and H4 mutations involving residues in their aminoterminal tails, on the solvent-accessible and lateral surfaces of the nucleosome, and at the interface of the H3/H4 tetramer and H2A/H2B dimer on heterochromatin structure and transcriptional silencing. The general state, stability, and conformational heterogeneity of chromatin are examined with a DNA topology-based assay, and the primary chromatin structure is probed by micrococcal nuclease. We demonstrate that the histone mutations differentially affect heterochromatin. Mutations of lysine 16 of histone H4 (H4-K16) and residues in the LRS (loss of rDNA silencing) domain of nucleosome surface markedly alter heterochromatin structure, supporting the notion that H4-K16 and LRS play key roles in heterochromatin formation. Deletion of the aminoterminal tail of H3 moderately alters heterochromatin structure. Interestingly, a group of mutations in the globular domains of H3 and H4 that abrogate or greatly reduce transcriptional silencing increase the conformational heterogeneity and/or reduce the stability of heterochromatin without affecting its overall structure. Surprisingly, yet another series of mutations abolish or reduce silencing without significantly affecting the structure, stability, or conformational heterogeneity of heterochromatin. Therefore, histone residues may contribute to the structure, stability, conformational heterogeneity, or other yet-to-be-characterized features of heterochromatin important for transcriptional silencing.

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A charged and contoured surface on the nucleosome regulates chromatin compaction

Cited by 107 publications

References 15 publications

The H4 Tail Domain Participates in Intra- and Internucleosome Interactions with Protein and DNA during Folding and Oligomerization of Nucleosome Arrays

The H4 Tail Domain Participates in Intra- and Internucleosome Interactions with Protein and DNA during Folding and Oligomerization of Nucleosome Arrays

Histone chaperone Anp32e removes H2A.Z from DNA double-strand breaks and promotes nucleosome reorganization and DNA repair

Differential Contributions of Histone H3 and H4 Residues to Heterochromatin Structure

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