A nonuniform distribution of excision repair synthesis in nucleosome core DNA

Lan, Suey Y.; Smerdon, Michael J.

doi:10.1021/bi00347a041

Cited by 43 publications

(23 citation statements)

References 38 publications

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“…5 and 6), it is important to understand the influence of this packaging on the distribution of UV photoproducts, especially since the location of these lesions may be a significant factor in determining their removal by repair enzymes (7)(8)(9). Several studies have indicated that, at the level of total genomic DNA, PD form randomly (8)(9)(10), indicating that there is no significant bias between large domains of chromatin.…”

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confidence: 99%

“…Using exonuclease III as a probe, it was determined that the 5' and 3' end regions of core DNA are markedly enhanced in repair-incorporated nucleotides. A best-fit analysis of the data indicated that an "50-base central region of core DNA (between positions 62 and 114 from the 5' end) could be devoid of newly synthesized repair patches (7). Since this nonuniform distribution could result from either less efficient repair in the central region of nucleosomes or a nonuniform distribution of UV-induced lesions in core DNA, it was of immediate interest to "map" the location of these lesions within core DNA at the single nucleotide level.…”

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confidence: 99%

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UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases.

Gale

Nissen²,

Smerdon³

1987

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

197

150

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a DNase I cut site was incorrectly given as a 3' phosphate. The liberation of fragments with 3' hydroxyls by this enzyme makes the charge of these fragments the same as that of those liberated by T4 polymerase-exonuclease. The latter fragments differ only by the presence of a PD (cyclobutane pyrimidine dimer) at the 3' end.Proc. Natl. Acad. Sci. USA Vol. 84, pp. 6644-6648, October 1987 Biochemistry UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases (UV photoproduct ABSTRACTWe have determined the distribution of the major UV-induced photoproducts in nucleosome core DNA using the 3'-*5' exonuclease activity of T4 DNA polymerase, which has been shown to stop digestion immediately 3' to UV-induced pyrimidine dimers. This assay is extremely sensitive since all DNA fragments without photoproducts (background) are reduced to small oligonucleotides, which can be separated from those fragments containing photoproducts. The results show that the distribution of UV-induced photoproducts (primarily cyclobutane dipyrimidines) is not uniform throughout core DNA but displays a striking 10.3 (± 0.1) base periodicity. Furthermore, this characteristic distribution of photoproducts was obtained regardless of whether nucleosome core DNA was isolated from UV-irradiated intact chromatin fibers, histone H1-depleted chromatin fibers, isolated mononucleosomes, or cells in culture. The yield of pyrimidine dimers along the DNA seems to be modulated in a manner that reflects structural features of the nucleosome unit, possibly core histone-DNA interactions, since this pattern was not obtained for UV-irradiated core DNA either free in solution or bound tightly to calcium phosphate crystals. Based on their location relative to DNase I cutting sites, the sites of maximum pyrimidine dimer formation in core DNA mapped to positions where the phosphate backbone is farthest from the core histone surface. These results indicate that within the core region of nucleosomes, histone-DNA interactions significantly alter the quantum yield of cyclobutane dipyrimidines, possibly by restraining conformational changes in the DNA helix required for formation of these photoproducts.Irradiation by UV light produces a variety of lesions in cellular DNA, which, if unrepaired, may have lethal, mutagenic, or carcinogenic effects (1). The major lesion produced is the cyclobutane pyrimidine dimer (PD) formed between adjacent pyrimidines (2, 3), and the photochemistry of the formation of this lesion has been studied in detail (3). Several other photoproducts are also formed to a lesser extent. Among these are the pyrimidine-pyrimidone(6-4) adducts, which may play an important biological role since they have been shown to correlate with some mutational "hot spots" in specific DNA sequences (4).Since the "target" for PD formation in intact cells is DNA folded into the compact structure of chromatin (for reviews on chromatin structure, see refs. 5 and 6), it is important to understand the influence of...

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confidence: 99%

mentioning

confidence: 99%

UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases.

Gale

Nissen²,

Smerdon³

1987

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

197

150

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“…Despite this important clinical implication, differential repair in mammalian genomes is not completely understood; in particular, the mechanistic basis of damage-specific and sequence-dependent hierarchies of excision remains obscure. Undoubtedly, DNA repair is influenced by local chromatin compaction (14,15); however, at least in the human p53 gene, no clear correlation between the pattern of DNase I or micrococcal nuclease cleavage and the repair efficiency of UV-induced lesions could be detected (16). In view of these findings, we elaborated on the hypothesis that site-specific changes in DNA conformation may contribute significantly to the observed excision repair variability (17,18).…”

Section: Mammalian Nucleotide Excision Repair (Ner)mentioning

confidence: 98%

Stereoselectivity of Human Nucleotide Excision Repair Promoted by Defective Hybridization

Heß¹,

Naegeli²,

Capobianco³

1998

Journal of Biological Chemistry

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To assess helical parameters that dictate fast or slow removal of carcinogen-DNA adducts, we probed human nucleotide excision repair (NER) activity with DNA containing L-deoxyriboses. Unlike natural lesions such as pyrimidine dimers or base adducts, L-deoxyribonucleosides (the mirror images of normal D-deoxyribonucleosides) involve neither the addition nor the loss of covalent bonds or functional groups and hence exclude modulation of repair efficiency by adduct chemistry and size. Previous studies showed that single L-deoxyribonucleosides distort DNA backbones but are accommodated in the double helix with intact hydrogen bonding between complementary strands. Here, we found that such single L-enantiomers are rejected as excision repair substrates in a NER-proficient cell extract. However, the same L-deoxyribose moiety stimulates NER activity upon incorporation into a nonhybridizing site of one or, more effectively, two base mismatches. In contrast to single L-deoxyriboses, multiple consecutive Ldeoxyriboses interfere with normal hybridization; in this case, the intrinsic derangement of base pairing was sufficient to promote the excision of a cluster of three adjacent L-deoxyribonucleosides without any requirement for mismatches. Thus, using stereoselective substrates, we demonstrate the participation of a recognition subunit that guides human NER activity to sites of defective Watson-Crick strand pairing. This conformational sensor detects labile hydrogen bonds irrespective of the type of deoxyribonucleotide modification. Mammalian nucleotide excision repair (NER)1 eliminates DNA damage with several overlapping levels of heterogeneity. Active genes are processed faster than inactive loci, and the template strand of RNA polymerase II-transcribed genes is repaired faster than the coding strand (1-5). However, excision efficiencies may also vary in a damage-specific manner. For example, UV-induced cyclobutane pyrimidine dimers are processed at lower rates than the less frequently occurring pyrimidine(6 -4)pyrimidone lesions (6 -8). Additionally, a sequence-dependent variability occurs between closely related genomic sites. Along the p53 or phosphoglycerate kinase 1 gene of UV-irradiated human fibroblasts, repair rates of cyclobutane pyrimidine dimers differ substantially with nucleotide position (9, 10). In the nontranscribed strand of these genes, some sites are less than 5% repaired within 24 h after irradiation, whereas other neighboring positions are repaired with up to 90% efficiency during the same period. Similarly, an analysis of repair kinetics along the nontranscribed strand of the human hypoxanthine phosphoribosyltransferase (HPRT) gene shows that excision repair in response to guanine adducts of benzo-[a]pyrene diol-epoxide varies by more than 1 order of magnitude (11). The excision of 1-nitrosopyrene-induced guanine adducts in the same region of the HPRT gene is equally variable but displays a distinctly different repair pattern (12).In some cases, sites that are slowly repaired coincide with critical...

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“…There is an early rapid phase (lasting 3-6 h after irradiation) and a late slow phase starting between 5 and 16 h after irradiation, depending on the cell strain. It was shown that repair synthesis is randomly distributed in nucleosome core DNA during the late repair phase, whereas there is a distinct bias toward the 5Ј ends of core DNA during the early repair phase (17,18). Surprisingly, during each of these phases, CPDs are repaired at almost equal rates on the inner and outer faces of the DNA helix, relative to the histone surface (18).…”

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confidence: 99%

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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A nonuniform distribution of excision repair synthesis in nucleosome core DNA

Cited by 43 publications

References 38 publications

UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases.

UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases.

Stereoselectivity of Human Nucleotide Excision Repair Promoted by Defective Hybridization

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

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