SILAC-labelled nuclear extracts were prepared from HeLa S3 cells as previously described39 (link). For each pull-down, nucleosomes corresponding to 12.5 μg of octamer were immobilized on 10 μl Streptavidin Sepharose HP beads (GE Healthcare) in the final reconstitution buffer (10 mM Tris [pH 7.5], 250 mM KCl, 1 mM EDTA and 1 mM DTT; supplemented with 0.1% NP40) and then rotated with 0.5 mg HeLa S3 SILAC-labelled nuclear extract in 1 ml of SNAP buffer (20 mM HEPES [pH 7.9], 150 mM NaCl, 0.2 mM EDTA, 10% Glycerol) supplemented with 0.1% NP40, 1 mM DTT and protease inhibitors cocktail (Roche) for 4 hr at 4°C. After two washes with 1 ml SNAP buffer +0.1% NP40 followed by two washes with 1 ml SNAP buffer without NP40, the beads from both SILAC pull-downs were pooled. The supernatant was completely removed, and bound proteins were eluted by on-bead digestion.