Zfp462 regulates the pluripotency of embryonic stem cells by cooperating with the core transcriptional network

Zfp462 is a vertebrate-specific C2H2-type transcription factor that has been found to play a crucial role in chromatin assembly and heterochromatin-mediated transcriptional silencing. However, its exact function in regulating the pluripotency of embryonic stem cells (ESCs) remains poorly understood. In this study, we observe that Zfp462 is highly expressed in undifferentiated ESCs, gradually decreases upon pluripotency exit, but then increases again during lineage differentiation. Knocking out of Zfp462 leads to reduced self-renewal of ESCs, abnormal pluripotency exit, and imbalance of lineage specification/differentiation. Multi-omics integrative analysis suggests that Zfp462 may function as a component of the ESC CORE module and collaborate with Oct4/Sox2/Nanog (OSN) to regulate the expression of pluripotency and developmental genes. Collectively, our research not only reveals the functions of Zfp462 in ESC self-renewal and differentiation but also proposes Zfp462 as a novel player in the pluripotency gene regulatory network (PGRN). To investigate the impact of Zfp462 knockout (KO) on the self-renewal and differentiation of embryonic stem cells (ESCs), we generated stable ESC lines with Zfp462 KO. Subsequently, we obtained Zfp462 KO ESCs and control (CTL) mESCs in the undifferentiated state (D0), as well as differentiated cells at embryoid body differentiation after 3 days (EB_D3), for RNA-seq analysis.