Significance Single-cell approaches have shown that many mammalian genes are transcribed stochastically in bursts of specific sizes and frequencies; however, molecular mechanisms controlling these bursting parameters have remained largely undetermined. By studying transcriptional bursting of a luciferase reporter controlled by a circadian gene promoter, we found that the gene integration site mainly influenced the burst size, while the circadian time primarily modulated the burst frequency. These daily variations in burst frequency correlated with histone acetylation levels, and CRISPR-Cas9–mediated acetylation of the promoter was sufficient to change the burst frequency. Since this correlation was also observed in other genes and in several cell types, we conclude that the impact of histone acetylation on gene expression is achieved mainly through modulation of burst frequency.