Studies in yeasts and mammals have identified many genes important for DNA damage-induced checkpoint activation, including Rad9, Hus1, and Rad1; however, the functions of these gene products are unknown. In this study we show by immunolocalization that human Rad9 (hRad9) is localized exclusively in the nucleus. However, hRad9 was readily released from the nucleus into the soluble extract upon biochemical fractionation of un-irradiated cells. In contrast, DNA damage promptly converted hRad9 to an extraction-resistant form that was retained at discrete sites within the nucleus. Conversion of hRad9 to the extraction-resistant nuclear form occurred in response to diverse DNA-damaging agents and the replication inhibitor hydroxyurea but not other cytotoxic stimuli. Additionally, extractionresistant hRad9 interacted with its binding partners, hHus1 and an inducibly phosphorylated form of hRad1.Thus, these studies demonstrate that hRad9 is a nuclear protein that becomes more firmly anchored to nuclear components after DNA damage, consistent with a proximal function in DNA damage-activated checkpoint signaling pathways.In eukaryotes, DNA damage activates complex cellular responses that initiate DNA repair and slow or block progression through the cell cycle (reviewed in Refs. 1-6). Activation of cell cycle arrest is mediated by the checkpoint signaling machinery. Many of the genes controlling checkpoint activation were identified by genetic studies in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. Recently, homologs of the yeast checkpoint genes were identified in higher eukaryotes, suggesting that much of the checkpoint machinery is highly conserved (7-23). Detailed biochemical and genetic studies in both mammals and yeasts provide a working model for checkpoint activation. Central to this model are the phosphatidylinositol 3-kinase-related kinases (PIKKs) 1 (1,3,4,24,25). Human cells lacking the PIKK ataxia telangiectasia mutated, the product of the ATM gene, have global checkpoint defects and are extremely sensitive to ionizing radiation (reviewed in Ref. 26). Likewise, S. pombe lacking the PIKK spRad3 and S. cerevisiae lacking scMec1 have similar phenotypes; they cannot block cell cycle progression after DNA damage and are exquisitely sensitive to diverse genotoxic agents (27,28). The PIKKs function as signal transducers that relay activating signals to downstream effector protein kinases, including spChk1 and spCds1 in S. pombe (18) and hChk1 and hChk2 (hCds1) in humans (20,22,23). Although hChk1 and hChk2 have different functions, one common downstream target is the cell-cycle phosphatase Cdc25 (22,23,29,30). Phosphorylation of Cdc25 inhibits its activity (21, 31), and phosphorylated Cdc25 is sequestered in the cytoplasm (32, 33), preventing it from activating cyclin B/Cdc2. Thus, the PIKKs function as signal transducers that relay activating signals to effector protein kinases, which then block the G 2 /M transition.The PIKKs are not the only components of the DNA damageactivated signaling pat...