Histone acetylation levels are regulated through the opposing activities of histone acetyltransferases (HATs) and deacetylases (HDACs). While much is known about gene-specific control of histone acetylation, little is understood about how total or cellular levels of histone acetylation are regulated. To identify regulators of cellular levels of histone acetylation, we developed an immunofluorescence-based approach to screen the single-gene deletion library of Saccharomyces cerevisiae for strains with significant reductions in cellular histone acetylation levels. Of the 4848 mutants screened, we identified 63 strains with considerable cellular hypoacetylation of N-terminal lysines in histones H3 and H4. The cellular hypoacetylation was validated for subsets of the identified strains through secondary screens including mass spectrometric analysis of individual lysines and chromatin immunoprecipitation of specific genomic loci. Among the identified mutants were several members of the Ccr4-Not complex, V-type ATPases, and vacuolar protein-sorting complexes as well as genes with unknown functions. We show that Gcn5, a major HAT in yeast, has diminished histone acetyltransferase activity in particular mutants, providing a plausible explanation for reduction of cellular acetylation levels in vivo. Our findings have revealed unexpected and novel links between histone acetylation, Gcn5 HAT activity, and diverse processes such as transcription, cellular ion homeostasis, and protein transport.
Histone modifications play important roles in essentially all DNA‐based processes such as transcription. Histones are modified through local, gene‐specific recruitment of histone modifiers by transcription factors and genomewide in a sequence‐independent manner. While the mechanism of targeted histone modification is understood, little is known about how global levels of histone acetylation are regulated. To identify potential regulators of global histone acetylation, using an immunofluorescence‐based approach, we have screened a single‐gene‐deletion library of S. cerevisiae (~5000 mutants) for genes whose deletions result in global reduction in acetylation levels. Sixty‐four mutants were identified, a subset of which has been confirmed through secondary screens including mass spectrometry. While some of the identified genes are unknown, others have been implicated previously in diverse cellular processes such as MAPK signaling, mitochondrial function and intracellular transport but, more importantly, have never been linked to histone acetylation. Our findings have revealed unexpected links between nuclear histone acetylation and seemingly disparate cellular processes in both the nucleus and cytoplasm. Since these processes are conserved among most eukaryotes, this study also provides novel targets for drug design and development for epigenetic therapy of diseases such as cancer.
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