Extensive SUMO modification of chromatin factors distinguishes pluripotent from somatic cells

The post-translational modification of proteins by SUMO acts as a key gatekeeper of cell identity. In mouse embryonic fibroblast (MEFs), SUMO impedes reprogramming to pluripotency, while in embryonic stem cells (ESCs), it represses the emergence of totipotent-like cells, suggesting that SUMO targets distinct sets of substrates to preserve the somatic and pluripotent states. Using MS-based proteomics, we show here that the composition of the endogenous SUMOylomes differs dramatically between MEFs and ESCs. In MEFs, SUMOylated proteins organize in a rather diffuse functional network enriched in nuclear factors with general cellular functions. In contrast, in ESCs, SUMOylated proteins form a tightly interconnected network mainly composed of repressive chromatin complexes. We also characterized several SUMOylated pluripotency factors and show that SUMO modification of Dppa2 and Dppa4 hampers their ability to induce a totipotent-like state. Altogether, we propose that rewiring the repertoire of SUMO target networks is a major driver of cell fate transition during embryonic development. MERVL:tdTomato Dppa2/4 knock out embryonic stem cells were transfected with Dppa2 and Dppa4 WT-GFP plasmids or SUMO deficient Dppa2 and Dppa4 GFP plasmids using lipofectamine. GFP+ cells were selected by flow cytometry and total RNA was prepared by TRIzol extraction (Invitrogen).