Protocol for immuno-precipitation was followed as described previously12 (link). Briefly, the supernatants were pre-cleared by incubation with protein G beads. The pre-cleared cell lysates were incubated at 4°C for 1 h with either α-PARP-1, α-ATM, α-DNA-PKcs, α-TyrRS, α-Tip60 or non-immune IgG, at a concentration of 5 μg/ml followed by incubation with 30 μl Protein G-beads (pretreated with 10 mg/ml BSA) at 4°C for 1h with rotation. PARP-1 (AG14361) and PARG inhibitors (ADP-HPD, Millipore) were added to the cell lysis buffer to ensure unwanted PARylation and removal of PAR chains with PARG. Immuno-precipitates were washed three times, subjected to SDS-PAGE and immunoblotted with specific antibodies. Whenever mentioned, the ZZ domain allowed immuno-precipitation of ectopically expressed ZZ-PARP-1, using anti-IgG. Whenever Ni-NTA pull-down was performed, proteins with a 6X-His tag were overexpressed in E. coli. Cells were lysed and the supernatant fractions containing the soluble proteins were mixed with HeLa cell lysates. For Ni-NTA pull-downs, normal procedures for immunoprecipitation were followed with 15–20 mM imidazole in the washing buffer.