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

Abstract

The creation of accessible DNA in the context of chromatin is a key step in many DNA functions. To reveal how ATP-dependent chromatin remodeling activities impact DNA repair, we constructed mammalian genetic models for the INO80 chromatin remodeling complex and investigated the impact of loss of INO80 function on the repair of UV-induced photo lesions. We showed that deletion of two core components of the INO80 complex, INO80 and ARP5, significantly hampered cellular removal of UV-induced photo lesions but had no significant impact on the transcription of nucleotide excision repair (NER) factors. Loss of INO80 abolished the assembly of NER factors, suggesting that prior chromatin relaxation is important for the NER incision process. Ino80 and Arp5 are enriched to UV-damaged DNA in an NER-incision-independent fashion, suggesting that recruitment of the remodeling activity likely takes place during the initial stage of damage recognition. These results demonstrate a critical role of INO80 in creating DNA accessibility for the NER pathway and provide direct evidence that repair of UV lesions and perhaps most bulky adduct lesions requires chromatin reconfiguration.DNA damage | DNA repair | chromatin | remodeling T he highly condensed nature of the chromatin assembly restricts the interaction of DNA with most nuclear factors. To create accessible DNA for various nuclear events, chromatin dynamics is regulated by the coordinated actions of two types of cellular mechanisms, posttranslational modifications of the core histones and ATP-dependent chromatin remodeling. Whereas covalent histone modifications, instigated mainly from regulation of yeast gene transcription, have been extensively studied, less is known about the chromatin remodeling process and how chromatin remodeling impacts various nuclear events.ATP-dependent chromatin remodeling is catalyzed by a distinct class of enzymes that comprises four families of structurally related ATP-dependent protein complexes (1). Biological activities of these complexes, defined by a variety of in vitro assays, include disruption of histone-DNA contact within nucleosomes, increased accessibility of nucleosomal DNA to transcription factors or restriction endonucleases, and cis and trans movement of histone octamers (2, 3). The INO80 chromatin remodeling complex was identified from the ino80-1 mutant defective in inositol/choline response (4-6). It contains the Ino80 ATPase, which belongs to the SNF/SWI2 superfamily (7). The Ino80 ATPase associates with 14 proteins to form a 1-MDa complex exhibiting 3′-5′ helicase activity (6,8). The INO80 complex also contains three actinrelated proteins (ARPs), of which ARP5 and ARP8 are specific to the INO80 complex. Deletion of either INO80-specific ARP compromises the ATPase activity of the remaining complex and gives rise to DNA-damage-sensitive phenotypes indistinguishable to the INO80 null mutant (9). Purification of human INO80 revealed a complex with virtually identical core components and a role in transcription (10, 11), indicating ...

Multiple modes of regulation of the human Ino80 SNF2 ATPase by subunits of the INO80 chromatin-remodeling complex

“…Our findings identify the Ies2 protein as a potent activator of Ino80 catalytic activity and bring to light an important role for the Ies6 and Arp5 proteins in nucleosome recognition and binding. These observations may provide a mechanistic basis for previous evidence that Ies2, Arp5, and Ies6 contribute to various Ino80-dependent nuclear transactions in fungi and in higher eukaryotes (4,10,(22)(23)(24)(25).…”

The mINO80 chromatin remodeling complex is required for efficient telomere replication and maintenance of genome stability

“…In contrast to these cells, CAG-CreER; mIno80 ∆/∆ MEFs retained strong CPD staining after 24 h ( Figure 3E, P = 0.0001). Similarly, repair of 6-4PP was also significantly impaired in CAG-CreER; mIno80 ∆/∆ MEFs when compared to WT cells ( Figure 3F, P = 0.0007 at 1 h and P = 0.0001 at 3 h), suggesting a significant reduction in the efficiency of UV repair in the absence of mIno80 [29]. Consistent with the delayed removal of UV-induced photo lesions, CAGCreER; mIno80 ∆/∆ MEFs displayed decreased cellular survival 48 h after UV exposure (Supplementary information, Figure S2D).…”

“…Cells were replenished with growth media every 2 days and monitored for anchorage-independent growth over 2 weeks. Analysis for UVinduced photo lesions was performed as described previously [29].…”

piRNA profiling during specific stages of mouse spermatogenesis

“…It was noted that the enriched FAT nucleotide binding contained the highest number of genes in Class A CDS-PRMRs, and most of these genes are not well studied. However, some of them such as ERCC3, INO80, CHD3, PMS2, BLM, MSH2, and LIG4 are reported to participate in chromatin remodeling, DNA repair, and genome maintenance (Kim et al 1999;Mills et al 2004;Chu et al 2010;Jiang et al 2010;Larocque and Jasin 2010;Rybanska et al 2010;van Oers et al 2010). For example, mice with a mutation in the ATP-binding domain of MLH1 were sterile due to its inability to interact with meiotic chromosomes of pachynema (Avdievich et al 2008).…”