Packaging of DNA into chromatin is essential for appropriate gene expression and the distribution of genetic material during cell division. Throughout the cell cycle, chromatin structure is maintained by balanced DNA replication and histone synthesis during S phase. DNA replication and histone synthesis are coupled and ongoing DNA replication is required to maintain histone gene expression. Cell cycle checkpoints control the timing and order of cell cycle events following genomic insult. Activation of checkpoint pathways by replicational stress or DNA damage inhibits the progression of the cell division cycle, by inactivating the cell cycle machinery. ATR, ATM, Chk1, and Chk2 are checkpoint kinases involved in cell cycle arrest in mammalian cells. ATM and ATR belong to the phosphatidylinositol 3-kinase-like kinase (PIKK) family. ATM activation is mainly triggered by the formation of DNA double-strand breaks, whereas ATR is activated by aberrant DNA structures induced by UV light, DNA synthesis inhibitors or chemotherapeutics. A further member of the PIKK family is DNA-activated protein kinase (DNA-PK). DNA-PK is primarily required for DNA double-strand break repair by non-homologous end joining. Here we investigate the role of check point kinases in coupling DNA replication with histone synthesis, which occurs mainly via the control of histone mRNA stability. Exposure of aphidicolin- or hydroxyurea-treated cells to kinase inhibitors, caffeine and LY294002, uncouples DNA replication from histone mRNA stability, by altering the efficiency of histone mRNA decay triggered by replicational stress. Specific interference with caffeine-sensitive checkpoint kinases alone has no effect on the efficiency of histone mRNA decay, indicating that ATR/ATM signalling alone cannot account for the linkage between replication and histone mRNA stability. LY294002 potentiates the ability of caffeine to uncouple histone mRNA stability from DNA replication, but only in cells containing functional DNA-PK, indicating that DNA-PK is the target of LY294002 in this process. DNA-PK is activated during replicational stress, and signalling through DNA-PK is enhanced when ATR/ATM signalling is abrogated, suggesting strongly that DNA-PK plays a role in this process. Our data show for the first time a role for DNA-PK in an intra S-phase checkpoint pathway coordinating DNA replication with histone protein synthesis. This role of DNA-PK was revealed when caffeine sensitive checkpoint kinases were inhibited, indicating that several signalling pathways link these two important processes.