KAT-Independent Gene Regulation by Tip60 Promotes ESC Self-Renewal but Not Pluripotency

Although histone-modifying enzymes are generally assumed to function in a manner dependent on their enzymatic activities, this assumption remains untested for many factors. Here, we show that the Tip60 (Kat5) lysine acetyltransferase (KAT), which is essential for embryonic stem cell (ESC) self-renewal and pre-implantation development, performs these functions independently of its KAT activity. Unlike ESCs depleted of Tip60, KAT-deficient ESCs exhibited minimal alterations in gene expression, chromatin accessibility at Tip60 binding sites, and self-renewal, thus demonstrating a critical KAT-independent role of Tip60 in ESC maintenance. In contrast, KAT-deficient ESCs exhibited impaired differentiation into mesoderm and endoderm, demonstrating a KAT-dependent function in differentiation. Consistent with this phenotype, KAT-deficient mouse embryos exhibited post-implantation developmental defects. These findings establish separable KAT-dependent and KAT-independent functions of Tip60 in ESCs and during differentiation, revealing a complex repertoire of regulatory functions for this essential chromatin remodeling complex. [Display omitted] •The Tip60 acetylase (KAT) activity is dispensable for gene regulation in ESCs•Tip60-p400 complex limits chromatin accessibility independently of its KAT activity•The Tip60 KAT activity is necessary for induction of differentiation genes•Tip60 KAT mutant mice exhibit developmental defects later than null mutants Acharya et al. show that the Tip60 (Kat5) lysine acetyltransferase regulates gene expression and self-renewal independently of its KAT activity in mouse ES cells. The KAT activity is necessary for differentiation and post-implantation mouse development. Therefore, Tip60 has KAT-independent (early) and KAT-dependent (later) functions that are essential for development.