Embryonic Stem Cell Differentiation Is Regulated by SET through Interactions with p53 and β-Catenin

The multifunctional histone chaperone, SET, is essential for embryonic development in the mouse. Previously, we identified SET as a factor that is rapidly downregulated during embryonic stem cell (ESC) differentiation, suggesting a possible role in the maintenance of pluripotency. Here, we explore SET's function in early differentiation. Using immunoprecipitation coupled with protein quantitation by LC-MS/MS, we uncover factors and complexes, including P53 and β-catenin, by which SET regulates lineage specification. Knockdown for P53 in SET-knockout (KO) ESCs partially rescues lineage marker misregulation during differentiation. Paradoxically, SET-KO ESCs show increased expression of several Wnt target genes despite reduced levels of active β-catenin. Further analysis of RNA sequencing datasets hints at a co-regulatory relationship between SET and TCF proteins, terminal effectors of Wnt signaling. Overall, we discover a role for both P53 and β-catenin in SET-regulated early differentiation and raise a hypothesis for SET function at the β-catenin-TCF regulatory axis. •Loss of SET impairs proliferation of ESCs and disrupts the pluripotent state•SET directly interacts with P53 and β-catenin•P53 partially contributes to disturbed expression of lineage markers in SET-KO ESCs•Loss of SET transactivates β-catenin and enhances Wnt gene expression Previously, Meshorer and colleagues identified the rapid downregulation of SETα following ESC differentiation. This study reveals that interaction of SET with P53 contributes to defects in lineage marker expression observed in SET-KO ESCs. Paradoxically, although canonical Wnt signaling is activated in the absence of SET, lower levels of active β-catenin are observed, suggesting a SET-mediated redistribution of nuclear β-catenin.