Apoptotic cell death is accompanied by degradation of chromosomal DNA. Here, we established in Drosophila a null mutation in the gene for inhibitor of caspase-activated DNase (ICAD) by P-element insertion. We also identified a loss-of-function mutant in Drosophila for DNase II-like acid DNase. The flies deficient in the ICAD gene did not express CAD, and did not undergo apoptotic DNA fragmentation during embryogenesis and oogenesis. In contrast, the deficiency of DNase II enhanced the apoptotic DNA fragmentation in the embryos and ovary, but paradoxically, the mutant flies accumulated a large amount of DNA, particularly in the ovary. This accumulation of DNA in the DNase II mutants caused the constitutive expression of the antibacterial genes for diptericin and attacin, which are usually activated during bacterial infection. The expression of these genes was further enhanced in flies lacking both dICAD and DNase II. These results indicated that CAD and DNase II work independently to degrade chromosomal DNA during apoptosis, and if the DNA is left undigested, it can activate the innate immunity in Drosophila.[Keywords: apoptosis; DNA fragmentation; mutagenesis; antibacterial peptides; innate immunity] Apoptosis, or programmed cell death, is an evolutionarily conserved process that removes harmful or useless cells during development (Jacobson et al. 1997;Vaux and Korsmeyer 1999). The apoptotic process is accompanied by morphological changes, such as shrinkage and fragmentation of the cells and nuclei, and loss of microvilli from the plasma membranes . Genetic and biochemical studies revealed that caspases, a family of cysteine proteases, are activated during apoptosis (Thornberry and Lazebnik 1998;Earnshaw et al. 1999;Los et al. 1999). More than 100 cellular proteins have been identified in mammalian systems as caspase substrates, the cleavage of which brings about the morphological changes of the cells and nuclei, leading to the cell death (Stroh and Schulze-Osthoff 1998).In addition to the morphological changes of cell and nuclei, the apoptotic process is often accompanied by the degradation of chromosomal DNA (Wyllie 1980; Nagata 2000). We and others have identified a DNase (caspaseactivated DNase, CAD; also called DNA fragmentation factor, DFF40), that is activated in dying cells (Liu et al. 1997;Enari et al. 1998). CAD is complexed with its inhibitor (ICAD, inhibitor of CAD) in proliferating cells. When apoptosis is triggered, caspases-in particular caspase 3-cleave ICAD, and the CAD released from ICAD degrades the chromosomal DNA into nucleosomal units . Accordingly, cells that are deficient in the CAD system do not undergo apoptotic DNA fragmentation in vitro. However, DNA degradation is still observed in vivo in CAD-deficient mice. Because this DNA fragmentation is detected in apoptotic cells inside macrophages, we proposed that the DNA of apoptotic cells can be cleaved by lysosomal acid DNase (DNase II) after the cells are engulfed by macrophages (McIlroy et al. 2000).Programmed cell death plays an import...