Measurement of acetylation turnover at distinct lysines in human histones identifies long-lived acetylation sites

Histone acetylation has long been determined as a highly dynamic modification associated with open chromatin and transcriptional activation. Here we develop a metabolic labeling scheme using stable isotopes to study the kinetics of acetylation turnover at 19 distinct lysines on histones H3, H4, and H2A. Using human HeLa S3 cells, the analysis reveals 12 sites of histone acetylation with fast turnover and 7 sites stable over a 30 hour experiment. The sites showing fast turnover (anticipated from classical radioactive measurements of whole histones) have half-lives between ~1–2 hours. To support this finding, we use a broad-spectrum deacetylase inhibitor to verify that only fast turnover sites display 2–10 fold increases in acetylation whereas long-lived sites clearly do not. Most of these stable sites lack extensive functional studies or localization within global chromatin, and their role in non-genetic mechanisms of inheritance is as yet unknown.