In contrast to two ended exogenously

In contrast to two-ended exogenously induced DSBs, which can be repaired by HR and c-NHEJ, one-ended DSBs arising at the replication fork are predominantly repaired by HR (Moynahan and Jasin, 2010). Such DSBs occur endogenously when replication forks encounter spontaneous Free Fatty Acid Quantification Colorimetric/Fluorometric Kit damage and/or single-strand breaks but also arise from agents inducing such single-stranded lesions (Ensminger et al., 2014). Additionally, HR factors are important for protecting stalled replication forks and their absence leads to degradation of newly synthesized DNA (Zeman and Cimprich, 2014). In order for DNA repair to take place, chromatin undergoes extensive reorganization and modification, allowing access to DNA and regulating subsequent repair (Smeenk and van Attikum, 2013, Gursoy-Yuzugullu et al., 2016). A key aspect of chromatin modification is the exchange of canonical histones for variants that serve specific functions in physiological conditions and in response to DNA damage. One main histone variant shown to be involved in DNA repair is the histone H3.3. Unlike the canonical histone H3.1, whose expression peaks in S phase, H3.3 is constitutively expressed throughout the cell cycle, and its incorporation is replication independent (Ahmad and Henikoff, 2002). H3.3 is rapidly deposited at sites of UV damage and facilitates recovery of transcription and replication fork progression after repair (Adam et al., 2013, Frey et al., 2014). Additionally, it is exchanged into chromatin at DSBs to promote NHEJ and is involved in post-repair chromatin assembly (Li and Tyler, 2016, Luijsterburg et al., 2016). Two distinct chaperon complexes mediate H3.3 deposition. The histone regulator A (HIRA) directs H3.3 incorporation in promoters of actively transcribed genes and gene bodies, and the chromatin remodeler alpha-thalassemia mental retardation X-linked protein (ATRX) interacts with the death-domain-associated protein (DAXX) to deposit H3.3 in telomeric and pericentric heterochromatin (Drané et al., 2010, Goldberg et al., 2010). ATRX belongs to the switch/sucrose non-fermenting (SWI/SNF) chromatin remodeling family, mutations in which cause syndromal mental retardation and downregulation of α-globin expression (Gibbons et al., 1995). Most of these mutations are located in two highly conserved regions of the ATRX protein: a C-terminal ATP-dependent motor domain and an N-terminal chromatin-binding ATRX-DNMT3-DNMT3L (ADD) domain that includes a plant homeodomain (PHD) zinc finger (Gibbons et al., 2008). The alternative lengthening of telomeres (ALT) pathway is a HR-associated process that is activated in 10%–15% of all cancer cells to maintain telomere length independently of telomerase activity (Dilley and Greenberg, 2015). Mutations in the ATRX-DAXX-H3.3 complex have been found in a variety of cell lines and tumors with the ALT phenotype, leading to the suggestion that this complex functions to suppress the ALT pathway (Lovejoy et al., 2012, Maciejowski and de Lange, 2017). ATRX also functions during replication, as ATRX knockdown cells show hypersensitivity to agents inducing replication stress, exhibit perturbed S-phase progression, and fail to properly handle stalled replication forks (Leung et al., 2013). Collectively, this suggests that ATRX regulates recombination processes although it is currently unclear how this is achieved.