Eight types of short-chain lysine (Lys) acylations have recently been identified on histones: propionylation, butyrylation, 2-hydroxyisobutyrylation, succinylation, malonylation, glutarylation, crotonylation and β-hydroxybutyrylation. Emerging evidence suggest that these histone modifications affect gene expression and are structurally and functionally different from the widely studied histone Lys acetylation. In this review, we discuss the regulation of non-acetyl histone acylation by enzymatic and metabolic mechanisms, acylation “reader” proteins that mediate the effects of different acylations, and their physiological functions, including in signal-dependent gene activation, spermatogenesis, tissue injury and metabolic-induced stress. We propose a model to explain our present understanding of how differential histone acylation is regulated by metabolism of the different acyl-CoA forms, which in turn modulate the regulation of gene expression.