Fig. 4: SUMO-ID identifies SUMO-dependent interactors of PML.

a Volcano plot of LC-MS analysis comparing streptavidin pull-downs of U2OS double stable cell lines for TRIPZ-MYC-C-SUMO2nc together with FLAG-N-PML^WT or FLAG-N-PML^3MAS. Cells were treated with 1 μg/mL of doxycycline for 24 h and 50 μM of biotin for 2 h. 59 high-confidence SUMO-dependent PML interactors were defined. Asterisk (*) indicates that IRF2BP2 was detected with one peptide but further validated by Western blot and immunofluorescence. Statistical analyses were performed by two-sided Student’s t test. Data, including proteins identified with 1 peptide, are provided as Supplementary Data 1. b Western blot validations of PML SUMO-dependent interactors identified by SUMO-ID in a. Blots 1/2 represent two independent experiments. UBC9 was added as an expected positive control. Dots indicate endogenous carboxylases that are biotinylated constitutively by the cell. Black arrowheads point to specific PML SUMO-ID biotinylating activity. Dotted lines indicate different exposures of the same blot. IN: input; St PD: streptavidin pull-down. Molecular weight markers are shown to the left of the blots in kDa. Source data are provided in the Source Data file. c STRING network analysis of the 59 SUMO-dependent interactors of PML identified in a. A highly interconnected cluster related to protein SUMOylation/ubiquitylation, transcriptional regulation, DNA repair and RNA stability proteins is depicted. Color, transparency and size of the nodes were discretely mapped to the Log2 enrichment value as described. The border line type was discretely mapped to the p value as described. d Gene ontology analysis of the 59 SUMO-dependent interactors of PML identified in a. Biological processes and molecular functions related to SUMOylation/ubiquitylation, stress response, DNA repair, transcription and RNA stability were significantly enriched. Dotted line represents the threshold of the p value (0.05). Data are provided as Supplementary Data 2.