Alterations in the chromatin structure are preferentially involved in the regulation of cell functions, including gene expression, in eukaryotes. Three types of mechanisms, by which the alterations are caused have been reported: (i) variants of histone subtypes, (ii) chromatin remodeling, and (iii) post-translational modification. This review focuses mainly on the first and third mechanisms, especially on the acetylation of core histones, one of the third mechanisms. Using the gene targeting technique for the DT40 chicken B cell line, we systematically generated a number of mutants, respectively, devoid of particular genes encoding histones and histone deacetylase(s) (HDACs). Most of the H1 and core histone variants should be involved positively or negatively in the transcription regulation of particular genes. Of the chicken HDACs (chHDACs), chHDAC-2 controls the amount of the IgM H-chain at the steps of both transcription and alternative pre-mRNA processing, and chHDAC-3 is essential for cell viability, whereas chHDAC-1 merely affects gene expression in DT40 cells. These results indicate that HDAC family members should participate, in combination with one another, and/or histone acetyltransferase(s) (HATs), in the acetylation of core histones that regulates gene expression through alterations in the chromatin structure.