Misregulation of the level of RNA polymerase II carboxyl-terminal domain (CTD) phosphatase, Fcp1, in Drosophila results in high level of caspase-mediated apoptosis. Apoptosis induction by Fcp1 misregulation requires the presence of Drosophila melanogaster (Dm)p53, but occurs without the transcriptional activation of Dmp53 proapoptotic targets rpr, ark, and hid. Overproduction of a transcription activation-defective mutant Dmp53 protein increases, while Dmp53 null background decreases significantly the level of apoptosis in Fcp1-misregulated animals. Generating the apoptotic signal does not require the function of the ATM and Rad3-related kinase (ATR), and no significant level of nucleo-cytoplasmic translocation of Dmp53 is detectable in cells expressing Fcp1 at an abnormal level. Immunostaining of larval salivary gland polytene chromosomes with anti-Dmp53 antibodies indicates Dmp53 localization at several transcriptionally active chromosomal regions in wild-type cells, while in Fcp-misregulated cells the association of Dmp53 with specific chromosomal sites is decreased.