SummaryThe response to DNA double-strand breaks (DSBs) requires alterations in chromatin structure to promote the assembly of repair complexes on broken chromosomes. Non-homologous end-joining (NHEJ) is the dominant DSB repair pathway in human cells, but our understanding of how it operates in chromatin is limited. Here, we define a mechanism that plays a crucial role in regulating NHEJ in chromatin. This mechanism is initiated by DNA damage-associated poly(ADP-ribose) polymerase 1 (PARP1), which recruits the chromatin remodeler CHD2 through a poly(ADP-ribose)-binding domain. CHD2 in turn triggers rapid chromatin expansion and the deposition of histone variant H3.3 at sites of DNA damage. Importantly, we find that PARP1, CHD2, and H3.3 regulate the assembly of NHEJ complexes at broken chromosomes to promote efficient DNA repair. Together, these findings reveal a PARP1-dependent process that couples ATP-dependent chromatin remodeling with histone variant deposition at DSBs to facilitate NHEJ and safeguard genomic stability.

Among the earliest responses of mammalian cells to DNA damage is catalytic activation of a nuclear enzyme poly(ADP-ribose) polymerase-1 (PARP-1). Activated PARP-1 forms the polymers of ADPribose (pADPr or PAR) that posttranslationally modify its target proteins, such as PARP-1 and DNA repair-related proteins. Although this metabolism is known to be implicated in other repair pathways, here we show its role in the versatile nucleotide excision repair pathway (NER) that removes a variety of DNA damages including those induced by UV. We show that PARP inhibition or specific depletion of PARP-1 decreases the efficiency of removal of UV-induced DNA damage from human skin fibroblasts or mouse epidermis. Using NER-proficient and -deficient cells and in vitro PARP-1 assays, we show that damaged DNA-binding protein 2 (DDB2), a key lesion recognition protein of the global genomic subpathway of NER (GG-NER), associates with PARP-1 in the vicinity of UV-damaged chromatin, stimulates its catalytic activity, and is modified by pADPr. PARP inhibition abolishes UV-induced interaction of DDB2 with PARP-1 or xeroderma pigmentosum group C (XPC) and also decreases localization of XPC to UV-damaged DNA, which is a key step that leads to downstream events in GG-NER. Thus, PARP-1 collaborates with DDB2 to increase the efficiency of the lesion recognition step of GG-NER.M ammalian cells respond very rapidly to different types of DNA damage by activation of an abundant and ubiquitous nuclear enzyme poly(ADP-ribose) polymerase-1 (PARP-1). The activated PARP-1 uses NAD + to form polymers of ADP-ribose (pADPr or PAR) that modify PARP-1 itself and selected target proteins, such as histones and DNA repair proteins (1). This posttranslational modification, i.e., PARylation, has been implicated in cellular responses ranging from DNA repair to cell death. Among mammalian DNA repair pathways, PARP-1 has been implicated in base excision repair, homologous recombination, and nonhomologous end-joining pathways (2, 3), but we do not know its role in the most versatile nucleotide excision repair (NER) pathway that removes a wide variety of DNA lesions, including UV-induced thymine dimers (T-T) and other cyclobutane pyrimidine dimers (CPD), as well as 6-4 photoproducts (6-4PP) (4).The core mammalian NER pathway uses more than 30 proteins to recognize the damaged site on DNA, remove 24-to 32-nucleotide-long single-stranded DNA containing the lesion, fill the gap using the nondamaged strand as a template, and finally ligate the nick (4). There are two subpathways of NER: the transcription-coupled NER (TC-NER) removes lesions from the actively transcribed strands of the genes and the global genomic NER (GG-NER) repairs lesions from the entire genome. These two pathways differ in the initial step of lesion recognition: TC-NER is initiated when elongating RNA polymerase II stalls at the lesion, whereas GG-NER is initiated when the lesion is recognized in the chromatin context by DDB2 (XPE), which through its participation in the UV-DDB-E3 ligase complex ub...

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Poly(ADP-ribose) glycohydrolase (PARG) is responsible for the catabolism of poly(ADP-ribose) synthesized by poly(ADP-ribose) polymerase (PARP-1) and other PARP-1-like enzymes. In this work, we report that PARG is cleaved during etoposide-, staurosporine-, and Fasinduced apoptosis in human cells. This cleavage is concomitant with PARP-1 processing and generates two C-terminal fragments of 85 and 74 kDa. In vitro cleavage assays using apoptotic cell extracts showed that a protease of the caspase family is responsible for PARG processing. A complete inhibition of this cleavage was achieved at nanomolar concentrations of the caspase inhibitor acetyl-Asp-Glu-Val-Asp-aldehyde, suggesting the involvement of caspase-3-like proteases. Consistently, recombinant caspase-3 efficiently cleaved PARG in vitro, suggesting the involvement of this protease in PARG processing in vivo. Furthermore, caspase-3-deficient MCF-7 cells did not show any PARG cleavage in response to staurosporine treatment. The cleavage sites identified by site-directed mutagenesis are DEID 256 2 V and the unconventional site MDVD 307 2 N. Kinetic studies have shown similar maximal velocity (V max ) and affinity (K m ) for both full-length PARG and its apoptotic fragments, suggesting that caspase-3 may affect PARG function without altering its enzymatic activity. The early cleavage of both PARP-1 and PARG by caspases during apoptosis suggests an important function for poly(ADP-ribose) metabolism regulation during this cell death process.Poly(ADP-ribose) polymerase (PARP-1) 1 synthesizes poly-(ADP-ribose) (pADPr) in response to DNA strand breaks. This nuclear enzyme, present in most eukaryotic cells, is involved in the maintenance of the DNA integrity (1, 2). Recently, other pADPr synthesizing enzymes were identified, suggesting the presence within mammalian cells of a PARP-1-like enzyme family. A protein named tankyrase with homology to ankyrins and to the catalytic domain of PARP-1 was isolated from human tissue and shown to be associated with telomeres (3). Other proteins homologous to the catalytic domain of PARP-1 have also been reported (4 -8).Cells display a low basal level of pADPr, which can increase dramatically in response to DNA damaging agents (9 -11). This increase in pADPr synthesis is transient and is followed by a rapid degradation by poly(ADP-ribose) glycohydrolase (PARG) (10, 12, 13). Two forms of PARG (74 and 59 kDa) have previously been purified from various tissues (14 -19). However, the PARG cDNA recently isolated encodes an active protein of 111 kDa (20). Furthermore, we have recently reported the presence of only the 111-kDa form of PARG, which is localized mostly in the cytoplasm of the cells (21,22). These findings raise questions about the cellular mechanism of pADPr catabolism and the physiological significance of the 59-and 74-kDa forms of PARG.Programmed cell death, or apoptosis, is an essential mechanism for appropriate embryogenesis, normal cell turnover, and the selection of lymphocytes (23,24). Apoptosis is characterized b...