Aspects of Nucleosomal Positional Flexibility and Fluidity

Caserta, Micaela; Verdone, Loredana; Mauro, Ernesto Di

doi:10.1002/1439-7633(20021202)3:12<1172::aid-cbic1172>3.0.co;2-y

Cited by 10 publications

(5 citation statements)

References 129 publications

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“…• DNA structure and packaging. AC n or AT n repeats can form Z-DNA [1,58], while repeats of several types can influence nucleosome formation [59,60].…”

Section: Box 1 Characteristic Properties Of Simple Sequence Repeats (mentioning

confidence: 99%

Simple sequence repeats as advantageous mutators in evolution

2006

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Simple sequence repeats (SSRs) often serve to modify genes with which they are associated. The influence of SSRs on gene regulation, transcription and protein function typically depends on the number of repeats, while mutations that add or subtract repeat units are both frequent and reversible. SSRs thus provide a prolific source of quantitative and qualitative variation. Over the past decade, researchers have found that this spontaneous variation has been tapped by natural and artificial selection to adjust almost every aspect of gene function. These studies support the hypothesis that SSRs, by virtue of their special mutational and functional qualities, have a major role in generating the genetic variation underlying adaptive evolution.

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“…• DNA structure and packaging. AC n or AT n repeats can form Z-DNA [1,58], while repeats of several types can influence nucleosome formation [59,60].…”

Section: Box 1 Characteristic Properties Of Simple Sequence Repeats (mentioning

confidence: 99%

Simple sequence repeats as advantageous mutators in evolution

2006

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“…As mentioned earlier, there is no shortage of nuclear proteins designed to modify chromatin structure. The difference between the dynamics of chromatin in live cells and in isolated nuclei at physiological ionic strength is likely due to the presence of chromatin remodeling factors in live cells (Caserta et al, 2002;Becker, 2002). Examples of such factors present in interphase nuclei, which often work through selective histone deacetylation (Tong et al, 1998), include ATP-dependent protein complexes like NURF (Hamiche et al, 1999), and various members of the SWI/ISWI family like Mi-2 and ACF which have been observed in X. laevis cells (Guschin et al, 2000a,b).…”

Section: Chromatin Dynamics In Live Cellsmentioning

confidence: 99%

The Connection between Chromatin Motion on the 100 nm Length Scale and Core Histone Dynamics in Live XTC-2 Cells and Isolated Nuclei

Davis

Bardeen

2004

Biophysical Journal

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The diffusive motion of DNA-containing chromatin in live cells and isolated nuclei is investigated using a two-photon standing wave fluorescence photobleaching experiment with 100 nm spatial resolution. The chromatin is labeled using the minor groove binding dye Hoechst 33342. In live cells, the mean diffusion rate is 5 x 10(-4) micro m2/s, with considerable cell-to-cell variation. This diffusion is highly constrained and cannot be observed in a standard, single beam fluorescence recovery after photobleaching experiment. To determine the chemical origin of the diffusion, we study motion in isolated nuclei and vary the strength of the histone-DNA interactions by changing the ionic strength and using chemical and photocross-linking experiments. At higher NaCl concentrations, we see increased chromatin diffusion as the histone-DNA interaction is weakened due to ionic screening, whereas photocross-linking the core histones to the DNA results in a complete absence of diffusive motion. These trends are consistent with the 100 nm scale motion being correlated with the interactions of histone proteins with the DNA. If chromatin diffusion is connected to the nucleosomal dynamics on much smaller length scales, this may provide a way to assay biochemical activity in vivo based on larger scale macromolecular dynamics observed via fluorescence microscopy.

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“…Nature has therefore constructed it in such a manner as to lack a preferred positional setting for most sequences of the double-stranded DNA that wraps around the central core of eight histone proteins (2,3). The rotational setting of DNA on the surface of the histone octamer defines which nucleotides are directed toward the solvent and which are occluded by the histones.…”

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confidence: 99%

Platinum anticancer drug damage enforces a particular rotational setting of DNA in nucleosomes

Danford

Wang²,

Wang³

et al. 2005

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

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We constructed two site-specifically modified nucleosomes containing an intrastrand cis-{Pt(NH3)2} 2؉ 1,3-d(GpTpG) cross-link, similar to one formed by the anticancer drugs carboplatin and cisplatin on DNA, and investigated their structures by hydroxyl radical footprinting and exonuclease III digestion. Hydroxyl radical footprinting demonstrated that the presence of the platinum cross-link selects out a specific rotational setting of DNA on the histone octamer core in each of two reconstituted nucleosomes in which the platinum positions differ by half a DNA helical turn. The {Pt(NH3)2} 2؉ cross-link is situated in a structurally similar location, with the undamaged strand projecting outward, forcing the DNA to adopt opposite rotational settings in its wrapping around the histone octamer in the two nucleosomes. Enzymatic digestion by exonuclease III of the nucleosome substrates revealed that the platinum cross-link affects the translational positioning of the DNA, forcing it into an asymmetric arrangement with respect to the core histone proteins. We suggest that these phasing phenomena may be central to the recognition and processing of platinum-DNA adducts in cancer cells treated with these drugs and possibly may be common to other DNA damaging events.cancer ͉ carboplatin ͉ chromatin ͉ DNA repair ͉ DNA structure T he anticancer drugs cisplatin and carboplatin form intrastrand cross-links on DNA that evoke their antineoplastic activity by inhibiting DNA and RNA polymerases while escaping resistance mechanisms including nucleotide excision repair (NER) (1). In the cell, recognition of the platinum lesion by the repair machinery in the context of chromatin may require exposure of the damaged DNA duplex to the exterior of the nucleosome.The nucleosome is the fundamental building block of chromatin. Nature has therefore constructed it in such a manner as to lack a preferred positional setting for most sequences of the double-stranded DNA that wraps around the central core of eight histone proteins (2, 3). The rotational setting of DNA on the surface of the histone octamer defines which nucleotides are directed toward the solvent and which are occluded by the histones.Determining where platinum-DNA cross-links are located within the nucleosome represents an important step in understanding their cellular recognition and processing. A key question is whether the platinum adduct or the DNA sequence determines the rotational setting of a DNA segment on the nucleosome and therefore how the platinum lesion is presented to the replication, transcription, and repair machinery of the cell. To answer this question, we prepared two nucleosomes in which a 1,3-d(GpTpG) cross-link was incorporated site-specifically near the center of the DNA molecule. The sites of platination were placed one-half turn of the DNA helix apart in the two nucleosomal DNA sequences. We then used high-resolution footprinting and exonuclease mapping experiments to reveal the rotational and translational settings of the platinated DNA in the two nucleosom...

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Aspects of Nucleosomal Positional Flexibility and Fluidity

Cited by 10 publications

References 129 publications

Simple sequence repeats as advantageous mutators in evolution

Simple sequence repeats as advantageous mutators in evolution

The Connection between Chromatin Motion on the 100 nm Length Scale and Core Histone Dynamics in Live XTC-2 Cells and Isolated Nuclei

Platinum anticancer drug damage enforces a particular rotational setting of DNA in nucleosomes

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