The DNA damage signaling pathways mediated by the ataxia-telangiectasia mutated (ATM) and the ATM and Rad3-related (ATR) kinases play crucial roles in the maintenance of genomic integrity and may function as an anti-cancer barrier during early tumorigenesis. Although the ATM and ATR pathways share some of their downstream functions, the DNA damage that evoke these two pathways are distinct. While ATM plays a primary role in the response to double-stranded DNA breaks (DSBs), ATR controls the response to a much broader spectrum of DNA damage, including many that interfere with DNA replication. And, unlike ATM, ATR is crucial for maintaining genomic integrity during S phase of the cell cycle, and is indispensable for cell survival. Clearly, revealing the DNA structure that elicits the ATR pathway would be a critical step toward understanding the essential function of ATR and the genomic instability that it counters. The versatility of the ATR pathway in DNA damage response suggests that this pathway is likely able to sense a common signal generated by different types of DNA damage and genomic instability. Two simple structures commonly generated at sites of DNA repair and stressed DNA replication forks are single-stranded DNA coated with replication protein A (RPA-ssDNA) and junctions of single-and doublestranded DNA. Both of these structures have been implicated in the activation of ATR checkpoint by a number of studies using different model organisms. In this issue of Genes & Development, Cimprich and colleagues (MacDougall et al. 2007) report that circular singlestranded DNA (ssDNA) annealed with primers specifically triggers the ATR-mediated checkpoint responses in Xenopus egg extracts, revealing the first defined DNA structure sufficient to activate the ATR checkpoint pathway.
Hints from yeast, Xenopus, and humanStudies using budding and fission yeast (Saccharomyces cerevisiae and Schizosaccharomyces pombe, respectively) have provided important clues to the DNA structures that activate the ATR checkpoint. Mec1, the S. cerevisiae homolog of ATR, is activated by DNA replication inhibitor hydroxyurea (HU), DNA-alkylating agent methyl methanesulfonate (MMS), ultraviolet light (UV), telomeric defects in the cdc13 mutant, and DSBs induced by the HO endonuclease. At both the telomeres in the cdc13 mutant and the HO-induced DSBs, ssDNA is generated through the action of 5Ј-to-3Ј exonucleases (Garvik et al. 1995;Lee et al. 1998). Accompanying the formation of ssDNA, 3Ј ssDNA ends and 5Ј double/ single-stranded DNA (ds/ssDNA) junctions are also generated. It is not clear whether additional DNA structures are formed at these DNA damage sites. The ability of these two specific types of DNA damage to elicit the Mec1-mediated checkpoint indicates that ssDNA and/or ds/ssDNA junctions may be part of the checkpointactivating DNA structure.DNA replication interference is also a major stimulus of the ATR checkpoint. In budding yeast, electron microscopy studies of stressed replication forks have revealed some of the DNA structur...