Histone acetyltransferases (HATs) are involved in the acetylation of core histones, which is an important event for transcription regulation through alterations in the chromatin structure in eukaryotes. To clarify participatory in vivo roles of two such enzymes known as GCN5 and PCAF, we generated homozygous DT40 mutants, DeltaGCN5 and DeltaPCAF, devoid of two alleles of each of the GCN5 and PCAF genes, respectively, with the help of gene targeting technique. While the PCAF-deficiency exhibited no effect on growth rate, the GCN5-deficiency caused delayed growth rate of DT40 cells. FACS analyses revealed not only that the number of cells in S phase decreased, but also that the cell cycle progression was suppressed at G1/S phase transition for DeltaGCN5. RT-PCR analyses revealed that the GCN5-deficiency exhibited opposite influences on transcriptions of G1/S phase transition-related genes, i.e. repressions for E2F-1, E2F-3, E2F-4, E2F-6, DP-2, cyclin A, cyclin D3, PCNA, cdc25B and p107; and activations for p27, c-myc, cyclin D2 and cyclin G1. Similarly, the deficiency influenced oppositely transcriptions of apoptosis-related genes, i.e. decreased expression of bcl-xL and increased expression of bcl-2. Immunoblotting analyses using a number of anti-acetylated histone antisera revealed that the GCN5-deficiency led to decreased acetylation levels of K16/H2B and K9/H3, and increased those of K7/H2A, K18/H3, K23/H3, K27/H3, K8/H4 and K12/H4. These results indicate that GCN5 preferentially acts as a supervisor in the normal cell cycle progression having comprehensive control over expressions of these cell cycle-related genes, as well as apoptosis-related genes, probably via alterations in the chromatin structure, mimicked by changing acetylation status of core histones, surrounding these widely distributed genes.