Objective <p>This study aims to investigate the epigenetic regulation of TIPE3 in nasopharyngeal carcinoma (NPC) and its role in tumor progression, with a focus on enhancer elements and associated histone modifications, as well as the involvement of the Hedgehog signaling pathway.</p> Methods <p>The regulation of TIPE3 was explored through chromatin immunoprecipitation (ChIP) assays to identify histone modifications, specifically H3K27ac and H3K4me3, associated with enhancer elements upstream of the TIPE3 promoter. CRISPR-Cas9 technology was employed to delete these enhancer regions in NPC cell lines. The effects on TIPE3 expression, cell proliferation, and metastasis were assessed both in vitro and in vivo. Additionally, the roles of the histone-modifying enzymes KAT2A and SETD7 in modulating these enhancer marks were examined. The activation of the Hedgehog signaling pathway by TIPE3 was also investigated.</p> Results <p>TIPE3 was found to be regulated by enhancer elements marked by H3K27ac and H3K4me3. Deletion of these enhancers resulted in significant downregulation of TIPE3, leading to reduced proliferation and metastasis of NPC cells. KAT2A and SETD7 were identified as critical regulators of TIPE3 expression, acting through these enhancer-associated histone modifications. Moreover, TIPE3 was shown to activate the Hedgehog signaling pathway, contributing to NPC progression.</p> Conclusion <p>The study reveals that TIPE3 is epigenetically regulated by enhancer elements, which are modulated by KAT2A and SETD7, and that TIPE3 promotes NPC progression through activation of the Hedgehog signaling pathway. These findings suggest that targeting the enhancer-mediated regulation of TIPE3 and the associated signaling pathways could offer new therapeutic strategies for NPC.</p>