The structure of DNA in a nucleosome.

Hayes, Jeffrey J.; Tullius, Thomas D.; Wolffe, Alan P.

doi:10.1073/pnas.87.19.7405

Cited by 324 publications

(371 citation statements)

References 39 publications

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“…Band intensities were quantified using a Fuji phosporimager and ImageGauge software (Fuji). Hydroxyl radical cleavage of both free IL-2 promoter DNA and in vitro reconstituted chromatin substrates followed published procedures (46,48).…”

Section: Dnase I and Hydroxyl Radical Footprintingmentioning

confidence: 99%

The Human IL-2 Gene Promoter Can Assemble a Positioned Nucleosome That Becomes Remodeled Upon T Cell Activation

Attema

Reeves

Murray

et al. 2002

The Journal of Immunology

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Controlled production of the cytokine IL-2 plays a key role in the mammalian immune system. Expression from the gene is tightly regulated with no detectable expression in resting T cells and a strong induction following T cell activation. The IL-2 proximal promoter (+1 to −300) contains many well-defined transcriptional activation elements that respond to T cell stimulation. To determine the role of chromatin structure in the regulation of interleukin-2 gene transcription, nucleosome assembly across the IL-2 promoter region was examined using in vitro chromatin reconstitution assays. The IL-2 promoter assembles a nucleosome that is both translationally and rotationally positioned, spanning some of the major functional control elements. The binding of transcription factors to these elements, with the exception of the architectural protein HMGA1, was occluded by the presence of the nucleosome. Analysis of the chromatin architecture of the IL-2 gene in Jurkat T cells provided evidence for the presence of a similarly positioned nucleosome in vivo. The region encompassed by this nucleosome becomes remodeled following activation of Jurkat T cells. These observations suggest that the presence of a positioned nucleosome across the IL-2 proximal promoter may play an important role in maintaining an inactive gene in resting T cells and that remodeling of this nucleosome is important for gene activation.

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Section: Dnase I and Hydroxyl Radical Footprintingmentioning

confidence: 99%

The Human IL-2 Gene Promoter Can Assemble a Positioned Nucleosome That Becomes Remodeled Upon T Cell Activation

Attema

Reeves

Murray

et al. 2002

The Journal of Immunology

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“…14 It is possible to obtain detailed structural information of positioned nucleosome particles by hydroxyl radical footprinting. 15 Comparison of selectively platinated with sequence-identical unplatinated reference nucleosomes will allow a precise quantification of the structural deviation induced by the cisplatin adduct, and obtaining this information was the second goal of this study.…”

Section: Introductionmentioning

confidence: 99%

Cisplatin Damage Overrides the Predefined Rotational Setting of Positioned Nucleosomes

Ober

Lippard

2007

J. Am. Chem. Soc.

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Cisplatin and carboplatin are used successfully to treat various types of cancer. The drugs target the nucleosomes of cancer cells and form intrastrand DNA cross-links that are located in the major groove. We constructed two site-specifically modified nucleosomes containing defined intrastrand cis-{Pt(NH 3 ) 2 } 2+ 1,3-d(GpTpG) cross-links. Histones from HeLa-S3 cancer cells were transferred onto synthetic DNA duplexes having nucleosome positioning sequences. The structures of these complexes were investigated by hydroxyl radical footprinting. Employing nucleosome positioning sequences allowed us to quantify the structural deviation induced by the cisplatin adduct. Our experiments demonstrate that a platinum cross-link locally overrides the rotational setting predefined in the nucleosome positioning sequence such that the lesion faces toward the histone core. Identical results were obtained for two DNA duplexes in which the sites of platination differed by approximately half a helical turn. Additionally, we determined that cisplatin unwinds nucleosomal DNA globally by approximately 24°. The intrastrand cis-{Pt(NH 3 ) 2 } 2+ 1,3-d(GpTpG) cross-links are located in an area of the nucleosome that contains locally overwound DNA in undamaged reference nucleosomes. Because most nucleosome positions in vivo are defined by the intrinsic DNA sequence, the ability of cisplatin to influence the structure of these positioned nucleosomes may be of physiological relevance.

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“…The close association (Luger et al 1997) between the histone octamer and the DNA in a nucleosome might be expected merely on steric grounds to decrease the exposure of the DNA to • OH attack from the solvent. There is both experimental (Hayes et al 1990) and biophysical modeling (Bĕgusová et al 2000) evidence that this is the case in the nucleosome. A higher resolution system involving a specific binding site (the lac operator sequence) found protection at the DNA binding site against • OH attack by the lac repressor (Bĕgusová et al 2001).…”

Section: Discussionmentioning

confidence: 99%

“…To provide a better model system for chromatin, we have most recently used as a DNA substrate the minichromosomal form of the mammalian virus SV40. The SV40 minichromosome has found frequent use as a model for DNA in cellular chromatin (van Holde 1988, Riedinger et al 2002. It contains a closed-circular double-stranded DNA molecule 5243 bp in length associated with an approximately equal mass of histone proteins (Blasquez et al 1988).…”

Section: Introductionmentioning

confidence: 99%

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Kinetic behavior of the reaction between hydroxyl radical and the SV40 minichromosome

Aguilera

Milligan

2007

Radiation Physics and Chemistry

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Aqueous solutions containing the minichromosomal form of the virus SV40 and the radical scavenger DMSO were subjected to gamma-irradiation, and the resulting formation of single strand breaks (SSB) was quantified. Under the irradiation conditions, most SSBs were produced as a consequence of hydroxyl radical ( • OH) reactions. By controlling the competition between DMSO and the viral DNA substrate for • OH, we are able to estimate the rate coefficient for the reaction of • OH with the SV40 minichromosome. The results cannot be described adequately by homogeneous competition kinetics, but it is possible to describe the rate coefficient for the reaction as a function of the scavenging capacity of the solution. The experimentally determined rate coefficient lies in the range 1×10 9 -2×10 9 L mol −1 s −1 at 10 7 s −1 , and increases with increasing scavenging capacity.

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The structure of DNA in a nucleosome.

Cited by 324 publications

References 39 publications

The Human IL-2 Gene Promoter Can Assemble a Positioned Nucleosome That Becomes Remodeled Upon T Cell Activation

The Human IL-2 Gene Promoter Can Assemble a Positioned Nucleosome That Becomes Remodeled Upon T Cell Activation

Cisplatin Damage Overrides the Predefined Rotational Setting of Positioned Nucleosomes

Kinetic behavior of the reaction between hydroxyl radical and the SV40 minichromosome

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