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

Abstract

Summary 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 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.

Epigenetic control of transcriptional regulation in pluripotency and early differentiation

“…In ESCs, it is largely dispensable for transcriptional activation and appears rather to repress developmental genes (Chen et al, 2013;Fazzio et al, 2008). A recent paper described KAT/ATPase-dependent and -independent functions of TIP60-P400 in ESCs (Acharya et al, 2017). Specifically, although TIP60-P400 proteins are essential for selfrenewal, their catalytic activities appear to be surprisingly dispensable.…”

Histone Lysine and Genomic Targets of Histone Acetyltransferases in Mammals

“…Null mutation of Kat6a gene in mice causes a complete lack of definitive hematopoietic stem cells. [51] The results suggest that the HAT activity is critical for embryo growth and timely expression of developmental genes, and that apart from these roles, TIP60 has another function that is critical for general cell survival. [49] Although the reduction in hematopoietic stem cell number and function is substantial, the data suggest that KAT6A may have roles in addition to lysine acetylation.…”

“…Growth restriction at day 6.5, ESCs can proliferate, minimal alterations in gene expression, chromatin accessibility, impaired differentiation into mesoderm and endoderm [51] MOF Null Embryonic death at E3.5. [38] MOF Null Embryonic death at E3.5.…”

TIP55, a splice isoform of the KAT5 acetyltransferase, is essential for developmental gene regulation and organogenesis

“…The KAT5 acetyltransferase activity is also necessary for the cellular response to DNA damage, in part by remodeling chromatin structure near sites of DNA damage 7 , 8 , 10 – 12 . Interestingly, KAT5 also has an essential non-catalytic role in regulation of chromatin accessibility and gene expression in embryonic stem cells and pre-implantation embryos 13 . KAT5 is a component of the 17-subunit TIP60-P400 complex, which remodels chromatin architecture not only through acetylation of histone tails, but also through incorporation of the H2A.Z histone variant into nucleosomes.…”

“…Black boxes: coding regions within exons; white boxes: non-coding sequences within exons; black lines: spliced introns; gray boxes: in frame intronic regions retained in specific Kat5 isoforms; gradient filled box: exon 5, which is spliced out in the Tip60β isoform. ( B ) Targeting construct used to generate both catalytic inactive Kat5 mutant mice 13 and Tip55 knockout mice (described herein). The Tip55 allele was made by removing the intronic regions retained selectively in Tip55 and fusing the remaining exons (which are all included in all other Kat5 isoforms).…”