The siRNA transfections were performed with 50 nM siRNA duplexes using Lipofectamine RNAiMAX (Invitrogen). Samples were collected 60 h after transfection unless otherwise stated. The siRNA oligonucleotides were obtained from Eurofins Genomics (MWG). For annotations and sequences see Supplementary Table S1. The TCOF1 STTT, S1216A+S1199A and S1216A expression plasmids were previously described (28 (link),29 (link)) and primer sequences used for the generation of the ATM-null construct can be found in Supplementary Table S1. The shRNA against TCOF1 was generated by insertion of an oligonucleotide into the pSUPERIOR.puro vector (Oligoengine) (28 (link)). Cells were transfected in a 4:1 ratio of shTCOF1 and the rescue plasmid (either TCOF1 WT, TCOF1 STTT, TCOF1 ATM-null, TCOF1 S1216A+S1199A or TCOF1 S1216A) using Lipofectamine LTX with plus reagent (Invitrogen) according to the manufacturer's specifications. After 72 h cells were transfected with gRNAs and collected at indicated time points.