DNA damage can alter the stability of nucleosomes: Effects are dependent on damage type

Mann, David B.; Springer, David L.; Smerdon, Michael J.

doi:10.1073/pnas.94.6.2215

Cited by 55 publications

(47 citation statements)

References 56 publications

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“…At present we do not have a definitive explanation for why TϽϾT repair is not stimulated by SWI/SNF. Based on structural considerations alone, it is safe to assume that the (6-4) photoproduct distorts the duplex more severely than does TϽϾT and hence would be more accessible to any protein approaching the nucleosome (20). However, there is no evidence that SWI/SNF has a higher affinity for damaged DNA.…”

Section: Discussionmentioning

confidence: 99%

Effect of Damage Type on Stimulation of Human Excision Nuclease by SWI/SNF Chromatin Remodeling Factor

Hara

Sancar

2003

Molecular and Cellular Biology

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To investigate the repair of different types of DNA lesions in chromatin, we prepared mononucleosomes containing an acetylaminofluorene-guanine adduct (AAF-G), a (6-4) photoproduct, or a cyclobutane pyrimidine dimer (CPD) and measured the repair of these lesions by reconstituted 6-factor human excision nuclease. We find that incorporation into nucleosomes inhibits the repair of CPD more severely than repair of the AAF-G adduct and the (6-4) photoproduct. Equally important, we find that SWI/SNF stimulates the removal of AAF-G and (6-4) photoproduct but not of CPD from nucleosomal DNA. These results shed new light on the low rate of repair of CPDs in human cells in vivo.Nucleotide excision repair (excision repair) removes a wide variety of structurally unrelated DNA lesions by dual incisions bracketing the lesion and spaced 24 to 32 nucleotides (nt) apart (30,32,41). The excision reaction is carried out by six repair factors, XPA, RPA, XPC, TFIIH, XPG, and XPF-ERCC1, in humans (5,24,25) and their counterparts in yeast (7). Although the excision nuclease removes all types of DNA lesions ranging from bases adducted to polyaromatic hydrocarbons (4, 12, 32) to simply methylated bases (13) and even undamaged nucleotides (3,8), these lesions are removed with widely differing rates (3,12,13). In particular, the rates of removal of the two major UV photoproducts, the cyclobutane pyrimidine dimer (PyrϽϾPyr) and the (6-4) photoproduct, are of interest because, arguably, these are the two most important lesions that the excision nuclease has to deal with in nature. Numerous in vivo studies have shown that (6-4) photoproducts are repaired at 10-to 20-fold-higher rates than is PyrϽϾPyr in human cells (22,42). Yet in vitro studies with human cell extracts (26) or 6-factor reconstituted human excision nuclease reveal only a two-to fivefold-higher rate of removal of (6-4) photoproduct than for cyclobutane thymine dimer (TϽϾT) (26, 27). There might be several factors contributing to the discrepancy between the in vivo and in vitro relative rates. One obvious factor is the nature of the substrates in the two systems. In vivo, the substrate is chromatin, whereas in vitro the substrate is typically naked DNA, and it has been shown recently that incorporation of a lesion into a nucleosome severely affects the rate of repair of the (6-4) photoproduct and the acetylaminofluorene-guanine (AAF-G) adduct (9, 10, 38). It was, therefore, conceivable that incorporation of the two photoproducts might have different effects on their rates of removal and the modulation of this rate by chromatin remodeling factors.Recently, we showed that incorporation of an AAF-G adduct into nucleosomes inhibited its rate of removal by the human excision nuclease to about 25% of the rate of excision from naked DNA and that this inhibition was partly overcome by the SWI/SNF chromatin remodeling factor (10). In the present study we have used AAF-G as a reference substrate to investigate the comparative effects of incorporation into nucleosomes on the rates of exci...

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Section: Discussionmentioning

confidence: 99%

Effect of Damage Type on Stimulation of Human Excision Nuclease by SWI/SNF Chromatin Remodeling Factor

Hara

Sancar

2003

Molecular and Cellular Biology

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“…However, in the slower, second phase, the damaged nucleosomes were digested at a 3.5-fold higher rate than the control nucleosomes. It has been reported that DNA damage can alter the stability of nucleosomes, and it may decrease or increase the stability depending on the type of lesion; it was found that while UV damage made nucleosomes unstable, benzo[a]pyrene-G adducts increased nucleosome stability (26). Thus, it appears that the AAF-G adduct, at least at the specific position at which it is located within our nucleosomes, has more of a UV lesion-type destabilizing effect, as measured by accessibility to a restriction endonuclease.…”

Section: Discussionmentioning

confidence: 99%

The SWI/SNF Chromatin-Remodeling Factor Stimulates Repair by Human Excision Nuclease in the Mononucleosome Core Particle

Hara

Sancar

2002

Molecular and Cellular Biology

137

131

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To investigate the role of chromatin remodeling in nucleotide excision repair, we prepared mononucleosomes with a 200-bp duplex containing an acetylaminofluorene-guanine (AAF-G) adduct at a single site. DNase I footprinting revealed a well-phased nucleosome structure with the AAF-G adduct near the center of twofold symmetry of the nucleosome core. This mononucleosome substrate was used to examine the effect of the SWI/SNF remodeling complex on the activity of human excision nuclease reconstituted from six purified excision repair factors. We found that the three repair factors implicated in damage recognition, RPA, XPA, and XPC, stimulate the remodeling activity of SWI/SNF, which in turn stimulates the removal of the AAF-G adduct from the nucleosome core by the excision nuclease. This is the first demonstration of the stimulation of nucleotide excision repair of a lesion in the nucleosome core by a chromatin-remodeling factor and contrasts with the ACF remodeling factor, which stimulates the removal of lesions from internucleosomal linker regions but not from the nucleosome core.Nucleotide excision repair (excision repair) is a multistep and all-purpose repair system which removes all DNA lesions, including UV photoproducts and alkylated and oxidized bases, from DNA (32, 52). The basic steps of this repair system include damage recognition, dual incision, excision (12), repair synthesis, and ligation. The excision of damage in human cells by dual incision is carried out by six repair factors, RPA, XPA, XPC, TFIIH, XPG, and XPF-ERCC1 (4,29,30). Similarly, the Saccharomyces cerevisiae homologs of these six factors are necessary and sufficient for dual incision (8). The basic enzymology of excision repair in both mammalian and yeast cells has been determined in considerable detail with naked DNA substrates (4,8,29,30,48). However, the natural substrate of this repair system in vivo is chromatin, and there have been only limited studies on the molecular mechanisms of excision repair of DNA damage in the nucleosome or chromatin in vitro (9,17,23,45).The nucleosome is the fundamental repeating unit of chromatin and constitutes the first order of DNA compaction in the nucleus. A nucleosome consists of two structurally different parts, the core particle and the linker. The nucleosome core particle consists of about 145 bp of DNA wrapped around the histone octamer. The nucleosome core particles are joined by the linker, consisting of approximately 50 bp of DNA associated with a linker histone to form the "beads-on-a-string" structure (16, 50). Packaging of DNA into the nucleosome has strong negative effects on essentially all DNA transactions, including replication, recombination, repair, and transcription (16, 41, 44); these effects have been best characterized with respect to transcriptional regulation. The development of an in vitro excision repair assay (12) and the reconstitution of the excision reaction in a defined six-factor system (29) have provided the opportunity to investigate the effect of DNA compaction in ...

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“…2 and 3) suggest that the observed changes in ⌬⌬G can be largely attributed to accommodating conformational changes that preserve interactions between histones and the DNA phosphate backbone. Finally, it is interesting to note that some DNA lesions can also increase DNA affinity for histone octamers (29).…”

Section: Discussionmentioning

confidence: 99%

“…1) (28). Thus, there is an energy penalty in burying CPD lesions on the histone surface (29). At this point, it remains to be seen whether CPDs change the DNA rotational setting on all nucleosome surfaces regardless of location or sequence and whether such a change can affect repair of this damage.…”

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confidence: 99%

Accommodation and Repair of a UV Photoproduct in DNA at Different Rotational Settings on the Nucleosome Surface

Svedružić

Wang²,

Kosmoski³

et al. 2005

Journal of Biological Chemistry

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Cyclobutane-thymine dimers (CTDs), the most common DNA lesion induced by UV radiation, cause 30°bending and 9°unwinding of the DNA helix. We prepared site-specific CTDs within a short sequence bracketed by strong nucleosome-positioning sequences. The rotational setting of CTDs over one turn of the helix near the dyad center on the histone surface was analyzed by hydroxyl radical footprinting. Surprisingly, the position of CTDs over one turn of the helix does not affect the rotational setting of DNA on the nucleosome surface. Gel-shift analysis indicates that one CTD destabilizes histone-DNA interactions by 0.6 or 1.1 kJ/mol when facing away or toward the histone surface, respectively. Thus, 0.5 kJ/mol energy penalty for a buried CTD is not enough to change the rotational setting of sequences with strong rotational preference. The effect of rotational setting on CTD removal by nucleotide excision repair (NER) was examined using Xenopus oocyte nuclear extracts. The NER rates are only 2-3 times lower in nucleosomes and change by only 1.5-fold when CTDs face away or toward the histone surface. Therefore, in Xenopus nuclear extracts, the rotational orientation of CTDs on nucleosomes has surprisingly little effect on rates of repair. These results indicate that nucleosome dynamics and/or chromatin remodeling may facilitate NER in gaining access to DNA damage in nucleosomes.In eukaryotes, DNA is organized in chromatin structures within the cell nucleus. The chromatin serves a dual purpose, tight DNA packing within the nucleus and organization of dynamic processes such as DNA transcription, replication, and repair. Of these, DNA repair protects genomic integrity from DNA-damaging agents and is vital for cell survival (1). Indeed, occasional failures in DNA repair can lead to aging and to multiple diseases, including cancer (2, 3). When DNA is irradiated with UV light, adjacent pyrimidines can form stable covalent bonds, yielding cis-syn cyclobutane-pyrimidine dimers (CPDs).5 A common UV lesion caused by exposure to direct sunlight, CPDs can lead to skin cancer, one of the most common forms of cancer (4). The CPD lesion can stall DNA replication (5) and transcription (6) and disrupt DNA interactions with other proteins that regulate gene expression (6). Each of these events can lead to genetic instability.The effect of chromatin structure on repair of UV damage was first implicated by the findings of Wilkins and Hart (7). These authors showed that UV-induced lesions in permeable human cells are removed more slowly from DNA that is less accessible to lesion-specific nucleases in chromatin. It was then found that newly repaired DNA in UVirradiated human fibroblasts is initially more accessible to exogenous nucleases than bulk DNA in chromatin (8) and that nucleosome rearrangement occurs in these regions (9). Studies with a yeast mini-chromosome showed that repair of CPDs is faster in nucleosome-free segments of DNA, being highest in the transcribed strand of a selectable gene and correlating with transcription rate in diff...

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DNA damage can alter the stability of nucleosomes: Effects are dependent on damage type

Cited by 55 publications

References 56 publications

Effect of Damage Type on Stimulation of Human Excision Nuclease by SWI/SNF Chromatin Remodeling Factor

Effect of Damage Type on Stimulation of Human Excision Nuclease by SWI/SNF Chromatin Remodeling Factor

The SWI/SNF Chromatin-Remodeling Factor Stimulates Repair by Human Excision Nuclease in the Mononucleosome Core Particle

Accommodation and Repair of a UV Photoproduct in DNA at Different Rotational Settings on the Nucleosome Surface

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