ATP-Dependent Chromatin Remodeling Is Required for Base Excision Repair in Conventional but Not in Variant H2A.Bbd Nucleosomes

Abstract

In eukaryotes, base excision repair (BER) is responsible for the repair of oxidatively generated lesions. The mechanism of BER on naked DNA substrates has been studied in detail, but how it operates on chromatin remains unclear. Here we have studied the mechanism of BER by introducing a single 8-oxo-7,8-dihydroguanine (8-oxoG) lesion in the DNA of reconstituted positioned conventional and histone variant H2A.Bbd nucleosomes. We found that 8-oxoguanine DNA glycosylase, apurinic/apyrimidinic endonuclease, and polymerase ␤ activities were strongly reduced in both types of nucleosomes. In conventional nucleosomes SWI/SNF stimulated the processing of 8-oxoG by each one of the three BER repair factors to efficiencies similar to those for naked DNA. Interestingly, SWI/SNF-induced remodeling, but not mobilization of conventional nucleosomes, was required to achieve this effect. A very weak effect of SWI/SNF on the 8-oxoG BER removal in H2A.Bbd histone variant nucleosomes was observed. The possible implications of our data for the understanding of in vivo mechanisms of BER are discussed.Eukaryotic cells are constantly subjected to oxidative stress. The reactive oxygen species generated during cell metabolism react with the nucleobases and damage DNA at any moment of the cell life. 8-Oxo-7,8-dihydroguanine (8-oxoG), the major reactive oxygen species-induced oxidative lesion, is repaired by the base excision repair (BER) pathway (27). The first step in the BER pathway is the recognition and the removal of 8-oxoG by 8-oxoguanine DNA glycosylase (OGG1), a bifunctional Nglycosylase which exhibits both a glycosylase and an apurinic/ apyrimidinic (AP) lyase activity (38, 44). The DNA nicked by OGG1 at the site of the lesion (3Ј to the lesion) is then processed by an apurinic/apyrimidinic endonuclease (APE1), which creates a free 3Ј-hydroxyl group required for the gap filling by polymerase ␤ (Pol ␤). Finally, the 8-oxoG repair is completed by ligation of the nick by DNA ligase III (for a review, see reference 28).DNA in the eukaryotic cell is packaged into chromatin. The first level of chromatin organization, the nucleosome, consists of an octamer of core histones (two each of H2A, H2B, H3, and H4) around which ϳ150 bp of DNA is wrapped into two superhelical turns (45). In addition to the conventional histones, eukaryotic cells express histone variants, which are incorporated into chromatin and form variant nucleosomes (45). Histone variants are nonallelic isoforms of conventional histones and show various degrees of homology to their conventional counterparts (39). The recently identified histone variant H2A.Bbd (Barr body deficient), which exhibited only 48% identity with H2A, is found to be localized in transcriptionally active regions of the nucleus (8). H2A.Bbd nucleosomes have a more relaxed structure, they are less stable and more easily transcribed than conventional nucleosomes (14), and they are resistant to remodeling by SWI/SNF (3).The repair proteins catalyzing the different steps in BER on naked DNA substrates have ...

The role of Cockayne Syndrome group B (CSB) protein in base excision repair and aging

“…In accord with this, CSB have been reported to mediate ATPase dependent nucleosome remodeling of a mononucleosome, which did not result in core histone release (Citterio et al, 2000). Release of histones is, however, not needed for chromatin remodeling to have an effect on DNA repair, since chromatin remodelers that do not release histones but only open up the chromatin structure have a positive effect on BER (Menoni et al, 2007).…”

Nucleosome Disruption by DNA Ligase III-XRCC1 Promotes Efficient Base Excision Repair

“…Chromatin remodeling agents and histone chaperones facilitate most processes involving chromatin, and the other DNA repair pathways-nucleotide excision repair, mismatch repair, nonhomologous end-joining and homologous recombination-mediated repair-are all thought to require local disruption of nucleosomes (e.g., see references 18 and 38). As detailed in Discussion, we and others have reported that at least some steps in BER can occur without requiring or inducing nucleosome disruption (3,22,32,(35)(36)(37)43). However, there is not yet a clear consensus on whether BER in its entirety, or a subset of specific steps in BER, requires disruption of nucleosomes; nor is it clear which if any of the known chromatin remodeling factors facilitate BER in vivo.…”

The SWI/SNF complex and cancer

“…BRM and BRG1 are linked to DNA repair SWI/SNF complex plays an important role in DNA repair (Wuebbles and Jones, 2004;Morrison and Shen, 2006;Menoni et al, 2007;Osley et al, 2007). DNA repair proteins such as p53, BRCA1 and Fanconi anemia proteins associate with the SWI/SNF complex and are functionally dependent on it (Bochar et al, Otsuki et al, 2001;Lee et al, 2002;Wang et al, 2007).…”