Human diseases, such as cancer and cardiovascular diseases, are associated with alterations of epigenetic regulation, including aberrant histone lysine acetylation. In eukaryotic cells, histone acetylation is catalyzed by lysine acetyltransferases (KATs); for example, Rtt109 and Piccolo NuA4, which are both essential for cell viability of yeast. Histone complexes, chaperones, and pre-existing histone modifications can individually alter the specificity of KATs for histone acetylation. However, how the specificity of a KAT is modulated by these biological factors is not well investigated. In this study, we utilized a high throughput, quantitative mass spectrometry-based method to determine the steady-state kinetic parameters of site-specific acetylation mediated by Rtt109-Vps75 and Piccolo NuA4 for different histone complexes. We found that Rtt109-Vps75 prefers to acetylate H3 monomer (less steric hindrance), while Piccolo NuA4 favors nucleosome (more complex). Additionally, Piccolo NuA4 primarily targets H4K5 and H4K12 in the nucleosome, and the favorable sites changes with different histone complexes. However, Rtt109-Vps75 primarily targets H3K9 and H3K23 across different histone complexes. Interestingly, we also found that the acetylation preference of Rtt109-Vps75 could be directed to H3K56 on histones purified from chicken erythrocytes, suggesting the pre-existing histone marks also play an important role in controlling the specificity of Rtt109-Vps75. Together, these results provide insight into how histone complexes, histone chaperones, and pre-existing histone marks influence KAT specificity and how modulating these biological factors may impact epigenetic regulation.

Chromatin structure and dynamics alter lysine acetyltransferase specificity

252nd National Meeting (2016)

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