Piccolo NuA4-Catalyzed Acetylation of Nucleosomal Histones: Critical Roles of an Esa1 Tudor/Chromo Barrel Loop and an Epl1 Enhancer of Polycomb A (EPcA) Basic Region

Abstract

Piccolo NuA4 is an essential yeast histone acetyltransferase (HAT) complex that targets histones H4 and H2A in nucleosome substrates. While Piccolo NuA4's catalytic subunit Esa1 alone is unable to acetylate nucleosomal histones, its accessory subunits, Yng2 and Epl1, enable Esa1 to bind to and to act on nucleosomes. We previously determined that the Tudor domain of Esa1 and the EPcA homology domain of Epl1 play critical roles in Piccolo NuA4's ability to act on the nucleosome. In this work, we pinpoint a loop within the Esa1 Tudor domain and a short basic region at the N terminus of the Epl1 EPcA domain as necessary for this nucleosomal HAT activity. We also show that this Esa1 Tudor domain loop region is positioned close to nucleosomal DNA and that the Epl1 EPcA basic region is in proximity to the N-terminal histone H2A tail, the globular region of histone H4, and also to nucleosomal DNA when Piccolo NuA4 interacts with the nucleosome. Since neither region identified is required for Piccolo NuA4 to bind to nucleosomes and yet both are needed to acetylate nucleosomes, these regions may function after the enzyme binds nucleosomes to disengage substrate histone tails from nucleosomal DNA.

Histone target selection within chromatin: an exemplary case of teamwork

“…Although this domain is proposed to recognize methyl marks in the homologous human enzyme (Tip60) (Sun et al 2009;Jeong et al 2011), its mutation cripples the activity of the yeast complex on recombinant nucleosomes lacking any PTMs and is lethal. This again supports the idea that the domain recognizes a histone-DNA interface in the nucleosome particle, which is corroborated by biochemical/structural data (Huang and Tan 2013). Similarities can be drawn to Drosophila MOF, also part of the MYST HAT family, which has a chromobarrel domain required for the acetylation of H4K16.…”

“…For example, incorporation of Esa1 into the core complex Piccolo NuA4 enhances its catalytic efficiency on nucleosome substrates by 3500-fold compared with Esa1 alone (Berndsen et al 2007), making it strikingly more active on chromatin than on free histones (Boudreault et al 2003). This significant difference can be explained by the presence of the Piccolo NuA4-associated factors Yng2 and Epl1 (Boudreault et al 2003;Selleck et al 2005;Chittuluru et al 2011;Huang and Tan 2013). Similarly, the presence of Ada2 and Ada3 is required for Gcn5-containing complexes to act on chromatin (Sendra et al 2000;Balasubramanian et al 2002;Carrozza et al 2003).…”

“…The small region mapped on JADE and BRPF proteins is related to a similar N-terminal region of the EPC1/Epl1 scaffold subunits of the TIP60 (humans) and NuA4 (yeast) H4/H2A-specific HAT complexes. It previously had been shown to be important for binding to nucleosomes and for acetylation and was found to interact with the histone H2A N-terminal tail within the nucleosome (Selleck et al 2005;Chittuluru et al 2011;Huang and Tan 2013). Further analysis demonstrated that this domain was essential for Tip60/NuA4 to acetylate the nucleosomal H4 tail, while acetylation of the nucleosomal H2A tail was still detected (Lalonde et al 2013).…”

“…The binding mechanism appears to occur through coordinated association of the PZP with histone H3 N-terminal tails and nucleosomal DNA (Saksouk et al 2009;Liu et al 2012;Lalonde et al 2013). Moreover, the Esa1 chromodomain, while not required for activity on free histones, is essential for acetylation of chromatin substrates by piccolo NuA4 (Selleck et al 2005;Huang and Tan 2013). Although this domain is proposed to recognize methyl marks in the homologous human enzyme (Tip60) (Sun et al 2009;Jeong et al 2011), its mutation cripples the activity of the yeast complex on recombinant nucleosomes lacking any PTMs and is lethal.…”

Exchange of associated factors directs a switch in HBO1 acetyltransferase histone tail specificity

“…Interestingly, truncation of this domain in human EPC1 and yeast Epl1 protein cripples Tip60/NuA4's ability to acetylate nucleosomal H4, but histone H2A acetylation persists. This basic region of Epl1 was recently shown in cross-linking experiments to bind the histone H2A N-terminal tail in nucleosomes (Huang and Tan 2013). Thus, it is tempting to speculate that this binding to H2A is orienting the NuA4 complex on the nucleosome to target the H4 tail for acetylation.…”