dTAG-Mediated Protein Degradation Dissects Nanog Function During ESC Differentiation

Protein degradation systems, such as auxin-inducible degron (AID) and dTAG-mediated degradation, have become essential tools in molecular biology. Their primary advantage lies in the rapid and efficient elimination of proteins, which facilitates the study of short-term molecular perturbations. However, these techniques remain underutilized for investigating protein function during the dynamic process of embryonic stem cell (ESC) differentiation. Here, we employed these methods to unveil the role of Nanog during definitive endoderm specification. We demonstrate that dTAG-inducible degradation is significantly more efficient than the AID system for Nanog elimination. Using this approach, we show that Nanog is a context-dependent regulator; while it maintains pluripotency in undifferentiated ESCs, it promotes definitive endoderm maturation during spontaneous differentiation. Our results highlight the advantages of targeted protein degradation for studying developmental transitions and provide new insights into the multifaceted functions of Nanog.