Chromatin Remodeling Activities Act on UV-damaged Nucleosomes and Modulate DNA Damage Accessibility to Photolyase

Abstract

Nucleosomes inhibit DNA repair in vitro, suggesting that chromatin remodeling activities might be required for efficient repair in vivo. To investigate how structural and dynamic properties of nucleosomes affect damage recognition and processing, we investigated repair of UV lesions by photolyase on a nucleosome positioned at one end of a 226-bp-long DNA fragment. Repair was slow in the nucleosome but efficient outside. No disruption or movement of the nucleosome was observed after UV irradiation and during repair. However, incubation with the nucleosome remodeling complex SWI/SNF and ATP altered the conformation of nucleosomal DNA as judged by UV photo-footprinting and promoted more homogeneous repair. Incubation with yISW2 and ATP moved the nucleosome to a more central position, thereby altering the repair pattern. This is the first demonstration that two different chromatin remodeling complexes can act on UV-damaged nucleosomes and modulate repair. Similar activities might relieve the inhibitory effect of nucleosomes on DNA repair processes in living cells.

Suppressed catalytic activity of base excision repair enzymes on rotationally positioned uracil in nucleosomes

“…50 for review). Finally, previous work has demonstrated that protected lesions in nucleosomal DNA can be exposed to nucleotide excision repair enzymes or UV photolyase by the addition of ATP-dependent remodeling factors in vitro (51)(52)(53). Although no direct interaction has been shown between pol ␤ and a nucleosome remodeling factor, proteins such as XRCC1, WRN, and͞or PARP may mediate such an interaction.…”

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).…”

Chromatin dynamics coupled to DNA repair

“…In vitro studies showed that the SWI/SNF complex enhances the incision and excision steps by purified NER proteins in reconstituted nucleosomes with DNA containing UV-induced lesions. 118,119 SWI/SNF also appears to act in vivo during NER, where it is at least partially responsible for increasing DNA accessibility in the repressed MFA2 promoter following UV treatment. 120,121 Snf6 and Snf5, two subunits of the SWI/SNF complex, interact with NER damage recognition Rad4-Rad23 proteins.…”