br Acknowledgements br Introduction Double

Acknowledgements
Introduction Double-stranded DNA breaks (DSBs) are among the most deleterious DNA lesions that threaten genomic integrity. DSBs are generated not only by exogenous DNA-damaging agents but also by normal cellular processes such as V(D)J recombination, meiosis, and DNA replication. Furthermore, increased amounts of DSBs are induced by oncogenic stresses during the early stage of tumorigenesis (Bartkova et al., 2005). In response to DSBs, the ATM kinase phosphorylates and regulates a large number of substrates involved in DNA repair, DNA replication, and other cellular processes important for genomic stability (Matsuoka et al., 2007). In addition to DSBs, ATM also responds to other cellular stresses such as hypoxia and GDC-0068 alterations (Bakkenist and Kastan, 2003, Bencokova et al., 2008, Gibson et al., 2005). Mutations of ATM in humans result in ataxia-telangiectasia (AT), a genetic disorder associated with radiation sensitivity, neuron degeneration, immune deficiencies, premature aging, and predisposition to cancers (Shiloh and Kastan, 2001). ATM is also one of the most frequently mutated kinases in human cancers (Greenman et al., 2007). All evidence indicates that ATM is a crucial guardian of genomic integrity. The mechanisms by which ATM is activated have been under intensive investigation (Harper and Elledge, 2007). The activation of ATM coincides with the autophosphorylation of ATM at Ser1981 and the conversion of ATM oligomers to monomers (Bakkenist and Kastan, 2003). The Mre11-Rad50-Nbs1 (MRN) complex is a sensor of DSBs and a direct activator of the ATM kinase (Lee and Paull, 2005). While ATM is not solely regulated by MRN in vivo (Kanu and Behrens, 2007), its activation at DSBs is primarily mediated by MRN (Berkovich et al., 2007, Falck et al., 2005, Kitagawa et al., 2004, You et al., 2005). After the initial ATM activation by DSBs, ATM executes specific functions around the breaks through a chromatin-mediated mechanism involving H2AX, Mdc1, and other proteins (Lou et al., 2006, Stewart et al., 2003, Stucki et al., 2005). Direct tethering of a large number of ATM molecules or its regulators to an array of binding sites activates ATM even in the absence of DSBs (Soutoglou and Misteli, 2008), indicating that a critical function of DSBs in ATM activation is to nucleate ATM and its regulators at sites of DNA damage. The activation of ATM at and around actual DSBs is a stepwise process initiated by the breaks. Despite the clear involvement of DSBs in ATM activation, the exact DNA structural determinants for ATM activation have not been clearly defined. Furthermore, how the structures of DNA at DSBs contribute to ATM activation is not well understood. In addition to ATM, DSBs also activate ATR, another master checkpoint kinase that has overlapping substrate specificity with ATM. Like ATM, ATR is critical for the full checkpoint response to DSBs (Brown and Baltimore, 2003, Cortez et al., 2001), indicating that ATM and ATR have nonredundant functions in this process. Unlike ATM, however, ATR also responds to a broad spectrum of DNA damage besides DSBs, especially the damage interfering with DNA replication. The recruitment of ATR to DSBs requires RPA-coated single-stranded DNA (RPA-ssDNA), a structure generated by the nuclease-mediated resection of DSBs (Zou and Elledge, 2003). The junctions between single- and double-stranded DNA, another structure associated with resected DSBs, are also important for ATR activation (MacDougall et al., 2007, Zou, 2007). Several nucleases and helicases, including MRN, CtIP, Exo1, and BLM, have been implicated in the resection of DSBs (Gravel et al., 2008, Lengsfeld et al., 2007, Limbo et al., 2007, Mimitou and Symington, 2008, Sartori et al., 2007, Schaetzlein et al., 2007, Zhu et al., 2008). Interestingly, ATM is required for the efficient resection of DSBs and the activation of ATR by DSBs (Jazayeri et al., 2006, Myers and Cortez, 2006, Yoo et al., 2007).