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

Abstract

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 ...

Chromatin disassembly and reassembly during DNA repair

“…In vitro, the ATP-dependent chromatin remodeler ACF can facilitate the dual incision step of NER within the linker DNA of a dinucleosomal template, although not within the nucleosome core particle [9]. Similarly, the ATP dependent chromatin remodeler SWI/ SNF can facilitate repair within the nucleosome core particle by a reconstituted human NER system [57]. It is possible that the addition of histone chaperones may further increase the efficiency of NER in vitro by their ability to unpackage chromatin, but this has not yet been experimentally demonstrated.…”

The SWI/SNF complex and cancer

“…BAF47-deficient cells are hypersensitive to genotoxic stress (Klochendler-Yeivin et al, 2006), and re-expression of BRG1 in BRG1-deficient SW13 cells renders the cells resistant to ultravioletinduced DNA damage (Gong et al, 2008). SWI/SNF facilitates the repair of cyclobutane pyrimidine dimers (Gaillard et al, 2003) and acetylaminofluorene-guanine adducts (Hara and Sancar, 2002) in a nucleosomal context. Studies carried out in vivo indicate that SWI/ SNF is recruited to double-strand break sites (Chai et al, 2005), and the inactivation of the SWI/SNF complex results in inefficient DNA double-strand break repair in vivo (Park et al, 2006).…”

INO80 chromatin remodeling complex promotes the removal of UV lesions by the nucleotide excision repair pathway

“…Biochemical studies showed that nucleosome assembly on in vitro NER substrate was severely inhibitory to the dual incision in either cell-extractbased or reconstituted assays (16)(17)(18). This inhibition can be mitigated by the presence of the yeast SWI/SNF complex in the reaction (19,20), which suggests that chromatin reconfiguration is likely a necessary step preceding NER. However, which ATPdependent remodeling complex or complexes provide the principal in vivo remodeling activity in aiding NER is unknown.…”