Abstract
Two kinases, ATM and DNA-PKcs, control rapid responses to DNA double-strand breaks (DSBs). The paradigm for ATM control is recruitment and activation by the Mre11−Rad50−NBS1 (MRN) sensor complex, whereas DNA-PKcs requires the sensor Ku (Ku70−Ku80). Using mouse cells containing targeted mutant alleles of Mre11 (Mre11a) and/or Ku70 (Xrcc6), together with pharmacologic kinase inhibition, we demonstrate that ATM can be activated by DSBs in the absence of MRN. When MRN is deficient, DNA-PKcs efficiently substitutes for ATM in facilitating local chromatin responses. In the absence of both MRN and Ku, ATM is recruited to chromatin, where it phosphorylates H2AX and triggers the G2-M cell-cycle checkpoint, but the DNA-repair functions of MRN are not restored. These results suggest that, in contrast to straightforward recruitment and activation by MRN, a complex interplay between sensors has a substantial role in ATM control.
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Acknowledgements
The authors thank X. Yu (University of Michigan) for reagents and for use of the laser microirradiation apparatus, M. Jasin (Memorial Sloan Kettering Cancer Center) for the DR-GFP reporter, F. Graham and P. Ng (McMaster University) for the AdNGUS24i I-SceI adenovirus and J. Sekiguchi for helpful discussions regarding the manuscript. Support for this work was provided by US National Institutes of Health (NIH) grant R01-HL079118 (D.O.F.), a Leukemia and Lymphoma Society Scholar Grant (D.O.F.) and University of Michigan Cancer Center Support Grant 5-P30-CA46592. A.J.H. was supported by NIH grant T32 CA009676 and M.J.M. by NIH grant T32 AI007413.
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A.J.H. planned and performed most experiments, analyzed and interpreted the data and participated in writing all portions of the manuscript. Y.W. performed and interpreted experiments in Figure 7d,e and Supplementary Figures 6 and 7e. M.J.M. performed and interpreted immunofluorescent foci experiments in Figure 5c and Supplementary Figures 3c,d and 4, and assisted A.J.H. with the laser microirradiation experiments in Figures 2a and 6. J.B. performed initial mouse breeding and analyses of Mendelian inheritance (Supplementary Table 1). D.O.F. participated in the design of all experiments as well as analyses and interpretation of data, and in writing of the manuscript.
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Integrated supplementary information
Supplementary Figure 1 Confirmation of Mre11 and Ku70 knockouts.
Immunoblots of Mre11 and Ku70 levels 30 minutes after IR (10 Gy). Genotypes are as shown. This confirms the genotypes shown and demonstrates that the levels of these proteins are not impacted by exposure to IR.
Supplementary Figure 2 Ku recruitment is unaltered in MRN-deficient cells.
(a,b) Quantitation of Ku fluorescence intensity at the site of laser microirradiation (example images shown in Figure 2b). Data shown are means and s.e.m. (n = 88 cells over 3 cell-culture replicates). p-values were calculated using an unpaired t-test.
Supplementary Figure 3 ATM target phosphorylations and ATM-dependent 53BP1 foci formation in the absence of MRN and Ku.
(a) Immunoblot of various protein levels 30 minutes after IR (10 Gy), with or without pretreatment with kinase inhibitors (ATMi, ATM inhibitor; PKi, DNA-PK inhibitor; AiPKi, ATM and DNA-PK inhibitors). Note that ATM-dependent phosphorylations are restored by Mre11 and Ku deficiency, but less efficiently than controls. (b) Quantification of pKap1S824 levels normalized to total Kap1 levels from immunoblots. Data shown are mean and s.e.m. (n = 3 cell-culture replicates). Results indicate a 60 to 70% reduction in pKap1S824 levels in the absence of MRN and Ku compared to controls. (c) 53BP1 immunofluorescent foci (green) 30 min after IR (3Gy), with or without pretreatment with kinase inhibitors (ATMi, PKi, and AiPKi). Nuclei are stained with 4’,6-diamidino-2-phenylindole (DAPI; blue). Genotypes are as shown. Scale bars, 10 μm. (d) Quantification of 53BP1 foci. Data shown are means and s.e.m. (n = 3 cell-culture replicates). Note that only a portion of 53BP1 foci formation is dependent on DNA damage kinases.
Supplementary Figure 4 γH2AX foci are unaltered in MRN- and Ku-deficient cells.
Graph shows the quantification of γH2AX immunofluorescent foci (representative images shown in Fig. 5c) 30 min after IR, with or without pretreatment with kinase inhibitors (ATMi, ATM inhibitor; PKi, DNA-PK inhibitor; AiPKi, ATM and DNA-PK inhibitors). Genotypes are as shown. Data shown are means and s.e.m. (n = 3 cell-culture replicates). The majority of cells (65 to 80%) contained 10 or more γH2AX foci and the morphology of these foci (Fig. 5c) were similar amongst all genotypes.
Supplementary Figure 5 Sensor-independent ATM activation in diverse experimental conditions.
(a) Immunoblot of γH2AX levels 30 min after IR at doses ranging from 0.5 to 5 Gy. Genotypes are as shown. (b,c) Immunoblot as in (a) 30 min after IR at doses as indicated, with or without pretreatment with kinase inhibitors (ATMi, ATM inhibitor; PKi, DNA-PK inhibitor; AiPKi, ATM and DNA-PK inhibitors). Genotypes are as shown. Note that the pattern of kinase dependence does not change at lower or higher doses of IR in any genotype. (d) Immunoblot of γH2AX levels at various time points after IR. Genotypes are as shown. (e) Immunoblot of protein levels in cellular fractions (top) prepared 30 min after IR or with no IR. Genotypes are as shown. This demonstrates that ATM recruited to chromatin in MRN- and Ku-deficient cells is not phosphorylated on S1987.
Supplementary Figure 6 DNA-PKcs can fully substitute for ATM only when MRN is absent.
γH2AX immunofluorescent foci (green) 30 min after IR (3 Gy), with or without DNA-PK kinase inhibitor (PKi) pretreatment. Genotypes are as shown. Scale bars, 40 μm. In line with immunoblot data, DNA-PK inhibition has little impact on γH2AX focus formation in control (Mre11+/–) and Mre11 nuclease-deficient cells (Mre11H129N/–). γH2AX foci are noticeably dimmer in ATM-deficient cells compared to Mre11-deficient cells, demonstrating that loss of MRN (not loss of ATM activity), permits activation DNA-PKcs.
Supplementary Figure 7 Representative duplicates of key experiments.
(a) Immunoblot of various protein levels 30 minutes after IR, with or without pretreatment with kinase inhibitors (ATMi, ATM inhibitor; PKi, DNA-PK inhibitor; AiPKi, ATM and DNA-PK inhibitors). Genotypes are as shown. (b) Immunoblot of protein levels in cellular fractions (top) prepared 30 min after IR or with no IR. Genotypes are as shown. (c,d) Immunoblot of various protein levels as in (a). (e) Immunoblots of γH2AX levels at various time points after IR, with or without pretreatment with the DNA-PK inhibitor (PKi). Genotypes are as shown.
Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–7 and Supplementary Table 1 (PDF 1085 kb)
Supplementary Data Set 1
Uncropped images of immunoblots from key experiments (PDF 13602 kb)
Comparison of Ku recruitment in control versus MRN-deficient cells
GFP-tagged Ku70 and Ku80 were expressed in cells of the indicated genotypes and relocation kinetics were measured continuously via fluorescent microscopy video capture. The laser pulse is identified by a dark spot due to photo-bleaching of diffuse nuclear GFP-Ku. Time zero is defined as the first frame with an identifiable laser induced photo-bleached spot. Movies are shown side by side in real-time followed by one-tenth speed to allow closer comparison of protein recruitment. Initial video capture was at 3 frames per second. Movies were composited and labeled using Final Cut Pro X (Apple Inc.). (MOV 4534 kb)
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Hartlerode, A., Morgan, M., Wu, Y. et al. Recruitment and activation of the ATM kinase in the absence of DNA-damage sensors. Nat Struct Mol Biol 22, 736–743 (2015). https://doi.org/10.1038/nsmb.3072
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DOI: https://doi.org/10.1038/nsmb.3072
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