Regulation of the protein stability of epigenetic regulators remains ill-defined despite its potential applicability in epigenetic therapies. The histone H3-lysine 4-methyltransferase MLL4 is an epigenetic transcriptional coactivator that directs overnutrition-induced obesity and fatty liver formation, and Mll4 mice are resistant to both. Here we show that the E3 ubiquitin ligase UBE3A targets MLL4 for degradation thereby suppressing high fat diet (HFD)-induced expression of the hepatic steatosis target genes of MLL4. In contrast to Mll4 mice, Ube3a mice are hypersensitive to HFD-induced obesity and fatty liver development. Ube3a ;Mll4 mice lose this hypersensitivity, supporting roles of increased MLL4 levels in both phenotypes of Ube3a mice. Correspondingly, our comparative studies with wild-type, Ube3a and Ube3a and UBE3A-overexpressing transgenic mouse livers demonstrate inverse-correlation of UBE3A protein levels with MLL4 protein levels, expression of the steatosis target genes of MLL4, and their decoration by H3-lysine 4-monomethylation, a surrogate marker for the epigenetic action of MLL4. Therefore, UBE3A indirectly exerts an epigenetic regulation of obesity and steatosis by degrading MLL4. This UBE3A-MLL4 regulatory axis provides a potential therapeutic venue for treating various MLL4-directed pathogeneses, including obesity and hepatic steatosis. This article is protected by copyright. All rights reserved.