Cell Culture Conditions and Treatments

T24 and HEK293 cells were grown in DMEM medium, and RT112 cells were grown in RPMI-1640 medium. DR-GFP U2OS cells were provided by Dr. Sovan Sarkar, University of Oxford, and grown in DMEM medium supplemented with 3 μg/mL puromycin. SA-GFP U2OS cells were provided by Dr. Pavel Janscak, University of Zurich, and grown in DMEM supplemented with 3 μg/mL puromycin. Stable HEK293 Flp-In T-REx (p97-E578Q-cSSH) cells for p97 SILAC-MS were used as previously described (Meerang et al., 2011 (link)). RT112 cells with stable shRNA knockdown of MRE11 were kept in RPMI-1640 medium supplemented with G418 (500 μg/mL), and provided by Dr. Juri Na, University of Oxford. Cells were treated as follows: 10 μM BrdU (#B5002; Sigma) and 10 μM Edu (#C1042; Sigma) for 24 hours and in the last 20 minutes of the 24 hours, respectively; 10 μM CB-5083 (#HY-12861; MCE) for 2 hours; 500 μM hydroxyurea (#H8627; Sigma) for 1 hour; MRE11 inhibitors used were 100 μM Mirin (#M9948; Sigma), 100 μM PFM01 (#6222; Tocris), 100 μM PFM39 (#SML1839; Sigma) for 3 hours. Concentrations of PFM01 and PFM39 were chosen according to a previous publication (Shibata et al., 2014 (link)). For clonogenic survival assays, appropriate concentrations of CB-5083 and Mirin were applied for 6 hours and 24 hours, respectively.