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Cells were lysed in lysis buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 1% Triton X-100) with protease- and phosphatase inhibitors (Roche), except for the WABS fibroblasts (Fig. 3a, c), which were directly scraped in sample buffer. Proteins were separated by 3–8%, 4–15% or 8–16% SDS-PAGE (NU-PAGE or BioRad) and transferred to immobilon-P membranes (Millipore). Membranes were blocked in 5% dry milk in TBST-T (10 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.04% Tween-20), incubated with primary and peroxidase-conjugated secondary antibodies (DAKO Glostrup, Denmark; 1:10000) and bands were visualized by chemoluminescence (Amersham). Antibodies used for detection are mouse-anti-DDX11 (B01P, Abnova; 1:250–1:1000), goat-anti-β-actin (I-19, Santa Cruz; 1:1000), mouse-anti-α-tubulin (B-5-1-2, Santa Cruz #sc-23948; 1:2000), mouse-anti-CDC6 (Santa Cruz #sc-9964; 1:500), mouse-anti-p62 (D5L7G, cell signaling; 1:1000), mouse-anti-Flag (M2, Sigma; 1:10000), mouse-anti-p53 (DO-1, Santa Cruz #sc-126; 1:1000), mouse-anti-vinculin (H-10, Santa Cruz #sc-25336; 1:2000), guinea pig anti-ESCO2 (1:500^{83 (link)}). Uncropped western blots are provided in Supplementary Fig. 13.

Cells were lysed in lysis buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 1% Triton X-100) with protease- and phosphatase inhibitors (Roche). For DNA-bound protein fractions, cells were lysed in lysis buffer for 10 min and centrifuged at 1300 g for 10 min. The pellet was subsequently lysed in lysis buffer containing 5 units/μL benzonase nuclease (Sigma) for 1 h and centrifuged at maximum speed for 5 min. Proteins were separated by 3–8% or 8–16% SDS-PAGE (NU-PAGE or BioRad) and transferred to immobilon-P membranes (Millipore). Membranes were blocked in 5% dry milk in TBST-T (10 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.04% Tween-20), incubated with primary and peroxidase-conjugated secondary antibodies (DAKO Glostrup, Denmark) and bands were visualized by chemoluminescence (Amersham). Antibodies used for detection are mouse anti-DDX11 (B01P, Abnova), mouse anti-α-tubulin (B-5-1-2, Santa Cruz #sc-23948), mouse anti-vinculin (H-10, Santa Cruz sc-25336), guinea pig anti-ESCO2 [36 (link)], mouse anti-ESCO1 (gift from JM Peters), rabbit anti-PARP (9542, Cell signaling), AcSM3 (gift from K Shirahige), rabbit anti-SMC3 (A300-060A, Bethyl), rabbit anti-WAPL (A300-268, Bethyl), mouse anti-vinculin (H-10, sc-25336, Santa Cruz).

Material obtained from IP or ConA‐agarose concentration as described in the previous section was resolved either by SDS/PAGE or by nondenaturing PAGE on pre‐cast NuPAGE™ 4–12% w/v acrylamide Bis/Tris Protein Gels and NativePAGE™ 3–12% w/v acrylamide Bis/Tris Protein Gels (Bio‐Rad Laboratories Ltd), respectively. Samples were then transferred to LF‐PVDF membranes (Millipore Ltd, Hertfordshire, UK). Membranes were saturated in 5% w/v low‐fat milk (Cell Signaling Technology, Danvers, MA, USA) (New England Biolabs Ltd) in PBS‐0.1% v/v Tween, probed with the indicated primary antibodies and horseradish peroxidase (HRP)‐conjugated secondary antibodies (Santa Cruz Biotechnology, Dallas, USA) and revealed by ECL (Clarity; Bio‐Rad Laboratories Ltd). Western blot images were acquired with the Image Quant Las400 (GE Healthcare Life Sciences, CA, USA) and analysed with image studio lite software (LI‐COR Biosciences, Cambridge, UK). Statistical analysis was performed using the graphpad prism program.