Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites 1 1Edited by T. Richmond

Anderson, J. D.; Widom, Jonathan

doi:10.1006/jmbi.2000.3531

Cited by 271 publications

(287 citation statements)

References 17 publications

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“…50, and references therein). By monitoring salt-dependent changes in FRET between the ends of the DNA, we show that significant partial dissociation of DNA takes place with the (H2A-H2B) dimer and (H3-H4) 2 tetramer still firmly in place.…”

Section: Discussionmentioning

confidence: 99%

A New Fluorescence Resonance Energy Transfer Approach Demonstrates That the Histone Variant H2AZ Stabilizes the Histone Octamer within the Nucleosome

Park

Dyer

Tremethick

et al. 2004

Journal of Biological Chemistry

203

200

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Nucleosomes are highly dynamic macromolecular complexes that are assembled and disassembled in a modular fashion. One important way in which this dynamic process can be modulated is by the replacement of major histones with their variants, thereby affecting nucleosome structure and function. Here we use fluorescence resonance energy transfer between fluorophores attached to various defined locations within the nucleosome to dissect and compare the structural transitions of a H2A.Z containing and a canonical nucleosome in response to increasing ionic strength. We show that the peripheral regions of the DNA dissociate from the surface of the histone octamer at relatively low ionic strength, under conditions where the dimer-tetramer interaction remains unaffected. At around 550 mM NaCl, the (H2A-H2B) dimer dissociates from the (H3-H4) 2 tetramer-DNA complex. Significantly, this latter transition is stabilized in nucleosomes that have been reconstituted with the essential histone variant H2A.Z. Our studies firmly establish fluorescence resonance energy transfer as a valid method to study nucleosome stability, and shed new light on the biological function of H2A.Z.Chromatin is built from nucleosomes, the universally repeating protein-DNA complexes in all eukaryotic cells. The crystal structure of the nucleosome core particle (NCP) 1 (1) reveals an octameric histone core around which 147 base pairs of DNA are wrapped in 1.65 tight superhelical turns. The histone octamer itself is a modular assembly of two copies each of the four histone proteins H2A, H2B, H3, and H4. Two histone pairs, composed either of H2A and H2B, or H3 and H4, form stable heterodimers. In solution, two H3-H4 dimers form a tetramer in the shape of a flat, twisted horseshoe that binds the central 60 base pairs of the nucleosomal DNA around its outside (1, 2). One (H2A-H2B) dimer is tethered to each face of the (H3-H4) 2 tetramer-DNA complex, to complete a "helical ramp" for continued DNA binding (reviewed in Ref.3).The interaction between the two histone subcomplexes occurs via two spatially distinct interaction interfaces of quite different character (Fig. 1). A four-helix bundle structure (formed by H2B and H4) is characterized mainly by hydrophobic interactions, and buries 1000 Å 2 (1). The second, larger interface (1600 Å 2 ) is characterized mostly by direct and solvent-mediated hydrogen bonds between the "docking domain" of H2A, and the histone fold extensions of H3 and H4 (4). In addition, a small interface is formed between the L1 loops of the two H2A molecules, which may contribute to holding together the two gyres of the DNA superhelix at the back of the nucleosome (Fig. 1) (5). Under physiological conditions, the (H2A-H2B) dimer associates stably with the (H3-H4) 2 tetramer only in the presence of DNA (6). Each (H2A-H2B) dimer organizes 30 base pairs toward either end of the DNA. The penultimate 10 base pairs of nucleosomal DNA on either side are organized by a region of H3 that does not form an integral part of the (H3-H4) 2 tetramer, an...

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Section: Discussionmentioning

confidence: 99%

A New Fluorescence Resonance Energy Transfer Approach Demonstrates That the Histone Variant H2AZ Stabilizes the Histone Octamer within the Nucleosome

Park

Dyer

Tremethick

et al. 2004

Journal of Biological Chemistry

203

200

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“…Nucleosomes, the building blocks of eukaryotic chromatin, play a key role in the organization of the overall chromatin structure and participate in regulated gene functioning [Anderson and Widom 2000;Ehrenhofer-Murray 2004]. Chromatin can also be involved in protection of functionally important sequence sites.…”

Section: Introductionmentioning

confidence: 99%

Gene splice sites correlate with nucleosome positions

Kogan

Trifonov

2005

Gene

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Gene sequences in the vicinity of splice sites are found to possess dinucleotide periodicities, especially RR and YY, with the period close to the pitch of nucleosome DNA. This confirms previously reported finding about preferential positioning of splice junctions within the nucleosomes. The RR and YY dinucleotides oscillate counterphase, i.e., their respective preferred positions are shifted about half-period one from another, as it was observed earlier for AA and TT dinucleotides. Species specificity of nucleosome positioning DNA pattern is indicated by predominant use of the periodical GG(CC) dinucleotides in human and mouse genes, as opposed to predominant AA(TT) dinucleotides in Arabidopsis and C.elegans.

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“…The NCP must be a stable and yet dynamic structure, both maintaining eukaryotic DNA in a condensed state and also permitting regulated access to genetic information contained therein. Equilibrium accessibility of DNA in the NCP has been demonstrated by using restriction enzyme accessibility assays (3). As visualized by cryoelectron microscopy, variability in the amount of DNA associated with the histone octamer and in the angle of exit and entry of DNA from the NCP are also consistent with spontaneous peeling of DNA ends from the octamer surface (4).…”

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confidence: 95%

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA

Brower-Toland

Smith

Yeh

et al. 2002

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

452

465

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The dynamic structure of individual nucleosomes was examined by stretching nucleosomal arrays with a feedback-enhanced optical trap. Forced disassembly of each nucleosome occurred in three stages. Analysis of the data using a simple worm-like chain model yields 76 bp of DNA released from the histone core at low stretching force. Subsequently, 80 bp are released at higher forces in two stages: full extension of DNA with histones bound, followed by detachment of histones. When arrays were relaxed before the dissociated state was reached, nucleosomes were able to reassemble and to repeat the disassembly process. The kinetic parameters for nucleosome disassembly also have been determined.

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Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites 1 1Edited by T. Richmond

Cited by 271 publications

References 17 publications

A New Fluorescence Resonance Energy Transfer Approach Demonstrates That the Histone Variant H2AZ Stabilizes the Histone Octamer within the Nucleosome

A New Fluorescence Resonance Energy Transfer Approach Demonstrates That the Histone Variant H2AZ Stabilizes the Histone Octamer within the Nucleosome

Gene splice sites correlate with nucleosome positions

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA

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