Western blotting analyses and dot-blot filter retardation assay

All protein fractions were assayed using the Bradford reagent (Bio-Rad) and then boiled in Laemmli sample buffer, resolved by SDS–PAGE, transferred onto a nitrocellulose membrane (GE Healthcare) and analysed by western blotting. Dot-blot filter retardation assays were performed in a 96-well BioDot microfiltration unit (Bio-Rad) using a 0.22 µm cellulose acetate membrane (Dutscher). After treatment, the samples were resuspended in 2% SDS, loaded onto the membrane, filtered and washed twice with 0.1% SDS. The list of primary antibodies is in Supplementary file 6. Secondary horseradish-peroxidase-conjugated antibodies (anti-mouse and anti-rabbit) were purchased from Jackson ImmunoResearch Laboratories; anti-rat antibodies were purchased from Bethyl Laboratories. The membranes were incubated with commercially available (Pierce) or homemade enhanced chemiluminescence substrate as described in (Bertolin et al., 2016). Chemiluminescence signals were captured on film (CP-BU new, Agfa Healthcare), developed using CURIX 60 developer (Agfa Healthcare) and quantified with ImageJ software (NIH). The relative abundance of specific bands of interest was calculated by normalising it towards the abundance of loading controls and indicated in each graph.