Pull-down was carried out using 3 μg (30 μl) of Dynabeads M280 per condition. Beads were blocked overnight as described above. After three washes in 1× wash buffer, 100 pmol of nucleic acid was coupled to M280 beads according to the manufacturer’s instructions before equilibration in dialysis buffer [20 mM tris-HCl (pH 7.4), 0.5 mM EDTA, 150 mM NaCl, 10% glycerol, and 1.5 mM MgCl2]. Cytosolic extracts from HeLa S3 cells, prepared using the Dignam protocol, were diluted in dialysis buffer supplemented with 2% Tween, 1% Triton, 10 mM β-mercaptoethanol, and 0.5 mM PMSF and centrifuged at 13,000 rpm for 30 min at 4°C. One milliliter of diluted lysate was added to the beads and incubated at 4°C on a rocker for 4 hours in low-binding tubes (Axygen). Three consecutive washes were performed in 20 mM tris-HCl (pH 7.4), 0.5 mM EDTA, 0.05% Triton, 0.1% Tween, 150 mM NaCl, 10% glycerol, and 5 mM MgCl2. Tubes were changed at first and last washes. Bound material was eluted in 30 μl of Laemmli buffer.

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