Unfolding of nucleosome cores dramatically changes the distribution of ultraviolet photoproducts in DNA

Brown, David W.; Libertini, Louis J.; Suquet, Christine; Small, Enoch W.; Smerdon, Michael J.

doi:10.1021/bi00091a001

Cited by 41 publications

(23 citation statements)

References 25 publications

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“…Indeed, there has long been evidence for a thermodynamically stable extended form of the nucleosome existing below Ϸ1 mM salt (38,39). Furthermore, UV photofootprinting studies indicate that the DNA in that structure is ''no longer bent to a significant degree,'' although it is still attached to histones (40). We suggest that the fluctuations we observe may represent temporary excursions into a similar open state that also can occur at higher salt concentrations.…”

Section: Dynamic Equilibrium Between Open and Closed States Of A Nucleo-mentioning

confidence: 62%

Fast, long-range, reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer

Tomschik

Zheng²,

Holde³

et al. 2005

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

127

108

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The nucleosome core particle, the basic repeated structure in chromatin fibers, consists of an octamer of eight core histone molecules, organized as dimers (H2A/H2B) and tetramers [(H3/H4) 2 ] around which DNA wraps tightly in almost two left-handed turns. The nucleosome has to undergo certain conformational changes to allow processes that need access to the DNA template to occur. By single-pair fluorescence resonance energy transfer, we demonstrate fast, long-range, reversible conformational fluctuations in nucleosomes between two states: fully folded (closed), with the DNA wrapped around the histone core, or open, with the DNA significantly unraveled from the histone octamer. The brief excursions into an extended open state may create windows of opportunity for protein factors involved in DNA transactions to bind to or translocate along the DNA.

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Section: Dynamic Equilibrium Between Open and Closed States Of A Nucleo-mentioning

confidence: 62%

Fast, long-range, reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer

Tomschik

Zheng²,

Holde³

et al. 2005

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

127

108

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“…The same modulation of CPD formation was observed in UV-irradiated isolated nucleosome cores (Gale et al, 1987) which is consistent with a preferential formation of CPDs at sites where the DNA minor groove faces the solution. A similar periodic CPD pattern generated in a DNA loop (Pehrson & Cohen, 1992) and a loss of the periodicity observed in unfolded nucleosomes (Brown et al, 1993) showed that DNA curvature is a major parameter for the modulation of CPD formation in nucleosomes. When polynucleosomes were reconstituted on irradiated calf thymus DNA, and nucleosome cores were isolated, the CPD distribution was similar to that of irradiated nucleosomes, demonstrating that CPDs were preferentially accommodated during nucleosome assembly on mixed-sequence DNA .…”

mentioning

confidence: 61%

Modulation of Cyclobutane Pyrimidine Dimer Formation in a Positioned Nucleosome Containing Poly(dA·dT) Tracts

Schieferstein

Thoma

1996

Biochemistry

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We have used a defined-sequence nucleosome to concomitantly investigate the generation and location of DNA lesions in nucleosomes and their influence on nucleosome positioning (translational and rotational setting). A 134 bp HISAT sequence from the yeast DED1 promoter, containing a polypyrimidine region (40 bp) with a T6-tract, two T5-tracts, and a T9-tract, was reconstituted in nucleosomes with a defined rotational setting. T-tracts adopt unusually rigid DNA structures in solution ("T-tract structure") and are hot spots of cyclobutane pyrimidine dimer (CPD) formation by UV light (254 nm). DNA was irradiated with UV light before or after reconstitution. The CPD yields and distribution were analyzed by cleavage with T4 endonuclease V. The rotational setting of nucleosomal DNA was characterized by DNase I digestion. With the exception of one T5-tract (1T5), the T6-, the 2T5-, and the T9-tracts formed T-tract structure in solution. T-tract structure was lost upon folding in nucleosomes, demonstrating a dominant constraint of DNA folding in nucleosomes over that of T-tract structure. CPD formation was strongly modulated by the nucleosome structure, but the CPD distribution differed from that reported for mixed-sequence DNA. CPD formation in the nucleosome had no effect on the rotational setting of nucleosomal DNA, but the rotational setting was affected when nucleosomes were assembled on damaged DNA. The toleration of DNA distortions imposed by CPDs in nucleosomes may have important implications for the recognition and repair of these damages in chromatin.

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“…We note that an intense DNase I cut site, but not hydroxyl radical cut site, also occurs at Ϫ31, being strong in both naked 5 S rDNA and the 5 S nucleosome (star in Fig. 2B, lanes [5][6][7][8]. This reflects the strong sequence specificity of DNase I (28).…”

Section: Characterization Of Reconstituted 5 S Rdnamentioning

confidence: 81%

Nucleotide Excision Repair of the 5 S Ribosomal RNA Gene Assembled into a Nucleosome

Liu¹,

Smerdon

2000

Journal of Biological Chemistry

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A-175-base pair fragment containing the Xenopus borealis somatic 5 S ribosomal RNA gene was used as a model system to determine the effect of nucleosome assembly on nucleotide excision repair (NER) of the major UV photoproduct (cyclobutane pyrimidine dimer (CPD)) in DNA. Xenopus oocyte nuclear extracts were used to carry out repair in vitro on reconstituted, positioned 5 S rDNA nucleosomes. Nucleosome structure strongly inhibits NER at many CPD sites in the 5 S rDNA fragment while having little effect at a few sites. The time course of CPD removal at 35 different sites indicates that >85% of the CPDs in the naked DNA fragment have t1 ⁄2 values <2 h, whereas <26% of the t1 ⁄2 values in nucleosomes are <2 h, and 15% are >8 h. Moreover, removal of histone tails from these mononucleosomes has little effect on the repair rates. Finally, nucleosome inhibition of repair shows no correlation with the rotational setting of a 14-nucleotide-long pyrimidine tract located 30 base pairs from the nucleosome dyad. These results suggest that inhibition of NER by mononucleosomes is not significantly influenced by the rotational orientation of CPDs on the histone surface, and histone tails play little (or no) role in this inhibition.In eukaryotic cells DNA is associated with histone proteins in the structural hierarchy of chromatin, required to package the enormous length of DNA into the small volume of a nucleus. The fundamental unit of this hierarchy is the nucleosome core, which consists of 147 bp 1 of DNA wrapped in 1.65 lefthanded superhelical turns around an octamer of 2 each of the 4 core histones, H2A, H2B, H3, and H4 (1). This subunit is linked to adjacent nucleosome cores by less tightly bound linker DNA, and the entire unit repeats every 170 -240 bp (2, 3).It is believed that DNA damage and DNA processing events in eukaryotic cells such as DNA repair and transcription are modulated by the packaging of DNA into chromatin (4, 5). A clear example of chromatin modulation of DNA damage is observed with formation of UV photoproducts (6). The major UV photoproduct in DNA (cis-syn-cyclobutane pyrimidine dimer (CPD)) forms with a striking 10.3-base average periodicity in mixed sequence nucleosome cores (7). This periodic pattern of CPD formation reflects the bending of DNA molecules on the histone surface (8 -10), where the periodic compression of the minor grove of DNA may modulate the [2 ϩ 2]cyclo addition of adjacent 5-6 double bonds after UV photon absorption (11, 12). Indeed, CPDs cause an overall bend of 7°-9°in the long axis of a double-strand DNA molecule (13,14), with possibly significant distortion of the phosphodiester backbone on each side of the CPD site (15), and this may be facilitated by compression of the minor groove of adjacent pyrimidines.DNA repair in chromatin has been extensively examined in human diploid fibroblasts, where two distinct phases exist in the time course of repair in the genome overall (6, 16). There is an early rapid phase (lasting 3-6 h after irradiation) and a late slow phase starting betw...

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Unfolding of nucleosome cores dramatically changes the distribution of ultraviolet photoproducts in DNA

Cited by 41 publications

References 25 publications

Fast, long-range, reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer

Fast, long-range, reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer

Modulation of Cyclobutane Pyrimidine Dimer Formation in a Positioned Nucleosome Containing Poly(dA·dT) Tracts

Nucleotide Excision Repair of the 5 S Ribosomal RNA Gene Assembled into a Nucleosome

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