Differential phosphorylation of DNA-PKcs regulates the interplay between end-processing and end-ligation during nonhomologous end-joining

Abstract

Nonhomologous end-joining (NHEJ) is a major DNA double-strand break repair pathway that is conserved in eukaryotes. In vertebrates, NHEJ further acquires end-processing capacities (e.g., hairpin opening) in addition to direct end-ligation. The catalytic subunit of DNA-PK (DNA-PKcs) is a vertebrate-specific NHEJ factor that can be autophosphorylated or transphosphorylated by ATM kinase. Using a mouse model expressing a kinase-dead (KD) DNA-PKcs protein, we show that ATM-mediated transphosphorylation of DNA-PKcs regulates end-processing at the level of Artemis recruitment, while strict autophosphorylation of DNA-PKcs is necessary to relieve the physical blockage on end-ligation imposed by the DNA-PKcs protein itself. Accordingly, DNA-PKcs(KD/KD) mice and cells show severe end-ligation defects and p53- and Ku-dependent embryonic lethality, but open hairpin-sealed ends normally in the presence of ATM kinase activity. Together, our findings identify DNA-PKcs as the molecular switch that coordinates end-processing and end-ligation at the DNA ends through differential phosphorylations.

Figure 1. Homozygous kinase dead (KD) mutation of DNA-PKcs leads to severe genomic instability and embryonic lethality with extensive neuronal apoptosis

(A) DNA-PKcs^+/+ and DNA-PKcs^KD/KD embryos at E15.5. The targeting scheme and basic characterization of the DNA-PKcs KD allele can be found in Fig. S1. (B) Upper panel: Genotypes of embryos at different ages obtained by inter-crossing DNA-PKcs^+/KD mice. * indicates post-mortem embryos. The p-values were calculated using the chi-squared test. Lower panel: The number of live birth mice obtained from intercrossing between DNA-PKcs^+/− and DNA-PKcs^+/KD mice. The p-value was calculated with the chi-square test. (C) H&E staining of E14.5 embryonic brain. Cortical plate (CP) and intermediate zone (IZ) contain post-mitotic neurons and ventricular zone (VZ) contains the proliferating cells. Black arrowheads denote apoptotic inclusions. (D) The frequency of apoptotic inclusions per 40× field in E14.5 brain. (E) The frequency of chromosomal (black box) or chromatid (white box) breaks per metaphase in ES cells. The panel on the right shows the examples of intact chromosome, chromosomal or chromatid breaks. The raw counts can be found in Fig.S2A. (F) Left panel: Frequency of metaphases with cytogenetic abnormalities among P3 primary DNA-PKcs^+/+, DNA-PKcs^−/− and DNA-PKcs^KD/KD MEF cells. At least three independently derived lines were assayed for each genotype. Right panel: The frequency of chromatid (white box) and chromosomal (black box) breaks measured by T-FISH analyses in WT, DNA-PKcs^−/− and DNA-PKcs^KD/KD MEF cells. (G) IR sensitivity of WT, DNA-PKcs^−/−, DNA-PKcs^KD/KD and XRCC4^−/− ES cells measured by colony formation assay. (H) Proliferation of P2 primary MEFs with different genotypes. One of two independent repeats is shown. The y-axis is the relative cell number measured by the fluorescence-nucleotide dye (CyQuant Cell Proliferation Assay, Invitrogen, CA).

Figure 2. Cell autonomous and p53-indepndent developmental defects of DNA-PKcs^KD/KD lymphocytes

(A) Genotype distribution from DNA-PKcs^+/KDp53^+/− intercrossing. (B) Representative picture of p53^+/−DNA-PKcs^KD/KD and p53^+/−DNA-PKcs^+/+ littermates at 21 days of age. Spleen and thymus size are shown on the right. (C) Representative flow cytometry analyses of 4-week DNA-PKcs ^+/+, DNA-PKcs^+/KD, DNA-PKcs^KD/KDp53^+/− DNA-PKcs^−/− and p53 ^+/− mice. (D) Representative FACs analyses of day 10 fetal liver culture. Accumulation of naïve B cells (B220⁺IgM⁺) implies successful V(D)J recombination of both IgH and IgK loci. (E) The summary of IgM⁺% out of total B220⁺ B cells after 10 days of fetal liver culture as described before (Frank et al., 2000). Each dot represents an individual E14.5 embryo of the indicated genotypes. The dash lines represent the average of at least 3 independent embryos for each genotype.

Figure 3. DNA-PKcs^KD/KD lymphocytes have end-ligation defects

(A) Schematic of pMX-INV V(D)J recombination substrates (Zha et al., 2011a). The un-rearranged substrate (UR), coding/signal end (CE/SE) intermediates and coding/signal joins (CJs/SJs) are diagramed. The recombination signal sequence (RSS, triangle), GFP probe (solid lines) and C4 probe (dash lines) are indicated. Positions of EcoRV (RV) sites and NcoI (N) sites are shown. The red box shows the isolated SE-CE fragments resulting from complete end-ligation defects. The blue box shows the SJ-CE fragments resulting from isolated CJ formation defects. (B) Southern blot analyses of inversional V(D)J rearrangements of representative DNA-PKcs^+/+, XRCC4^−/−, DNA-PKcs^−/− and DNA-PKcs^KD/KD cells with indicated digestion and probe. The red and blue boxes mark the SE-CE fragments and SJ-CE fragments, respectively. Flowcytometry analyses can be found in Fig. S4A. Additional clones can be found in Fig.S4B. (C) Western blot for DNA-PKcs, ATM, phosphorylated H2AX, total H2AX, phosphorylated KAP-1, total KAP-1, and α-tubulin in irradiated (10 Gy) MEFs with or without pre-incubation with 15 µM ATM kinase inhibitor (KU55933, Tocris Bioscience) or 5µM DNA-PKcs kinase inhibitor (NU7441, Tocris Bioscience) or both. Cell lysates were collected 2 hours after irradiation. Primary antibodies were used at the following dilutions: anti-DNA-PKcs (1:1000, Thermo), anti-ATM (1:500, MAT3, Sigma), anti-γH2AX (1:1,000, Millipore), anti-H2AX (1:1,000, Millipore), anti-KAP-1 (1:1,000, Cell Signaling), anti-phospho-KAP-1(S824) (1:1,000, Bethyl Laboratories) and anti-tubulin (1:1,000, Calbiochem). Additional experiments in v-abl kinse transformed pro-B cells can be found in Fig. S5A. (D) Extra-chromosomal V(D)J recombination efficiency. Each box represents the average and standard deviation of 4 independent repeats on two independent v-abl kinase transformed B cell lines of each genotype (see details in Fig.S5B). (E) Western blot for Lig4 and XRCC4 in DNA-PKcs^+/+, DNA-PKcs^−/−, DNA-PKcs^KD/KD, Lig4^−/−, and XRCC4^−/− v-abl transformed B cell lines. Primary antibodies were used at the following dilutions: anti-XRCC4 (1:500, Santa Cruz), anti-Lig4 antibody (1:500, a generous gift from Dr. David Schatz) and anti-β-actin (1:10,000, Sigma). (F) Laser induced recruitment of GFP-Lig4 in immortalized MEFs.

Figure 4. DNA-PKcs regulates end-ligation at the DNA ends

(A) Genotype distribution from inter-crossing Ku70^+/− (or Ku80^+/−) DNA-PKcs^+/KD mice. Lymphocyte development of the Ku70−/−DNA-PKcs KD/KD mice and controls can be found in Fig. S5B. (B) The body weight (grams) of 15 day old mice of each genotype. The bar indicates the average and standard deviations. ***: p<0.01. *: p>0.5, using student t-test. (C) Western blot for Ku70 (1:1000, Abcam), Flag (M2, Sigma) and Actin (Sigma) in Ku80 deleted and reconstitute DNA-PKcs^KD/KD pro-B cell lines. (D) Southern blot analyses of pMX-INV rearrangement in DNA-PKcs ^KD/KDKU80^−/− cells with or without ectopic expression of full length (FL) or ΔCTD Ku80.The DNA was digested with EcoRV and probed with the GFP probe. The diagram can be found in Fig 3A. The summary and raw data of the SJ junctions can be found in Fig. S6 and Tab.S4 (E) Phosphorylation of S2056 and T2906 clusters in Hela cells after exposure to IR. The S2056 phosphorylation is selectively inhibited by DNA-PKcs kinase inhibitor, while the T2609 phosphorylation is abolished by ATM kinase inhibitor. The dose and the time after IR are listed in the table above. (F) Western blot for total DNA-PKcs protein in DNA-PKcs^KD/KD, DNA-PKcs^KDSD/KDSD and DNA-PKcs^SD/SD ES cells. All ES cells were targeted homozygously. (G) Telomere-FISH analyses of two independent clones of DNA-PKcs^KDSD/KDSD ES cells and their parental clone.

Figure 5. ATM-dependent hairpin opening in DNA-PKcs^KD/KD lymphocytes

Diagram (A) and results (B) from the TdT-mediated ligation PCR assay. Specifically, TdT adds a poly-A tail to open hairpins, which can be subsequently amplified with universal primers to poly T tails, and an internal primer within hCD4. The PCR product is then analyzed on a gel, transferred to a membrane and probed with P32 labeled oligo probes against hCD4. Two representative assays are shown in Fig 5B. PCR corresponding to the ROSA26 locus was used as loading control. Diagram (C) and results (D) of urea denaturing gel electrophoresis assay. DNA was digested with EcoRV. For denaturing gel electrophoresis, ½ of the DNA is subjected to 8M of Urea at 80°C to denature the double stranded DNA. RV=EcoRV. More detail of the experimental procedures can be found in (Zha et al., 2011a, Helmink et al., 2011).

Figure 6. Artemis, but not Artemis phosphorylation, is required for hairpin opening in DNA-PKcs^KD/KD lymphocytes

(A) Urea denaturing gel analyses of Artemis^+/+ and Artemis^−/− DNA-PKcs^KD/KD cells with or without pretreatment with ATM kinase inhibitor (KU55933, 15uM).The scheme of Crispr mediated deletion of Artemis can be found in Fig. S7. (B) Ectopic expression of Flag tagged Artemis (WT or 2A or 9A) in DNA-Pkcs^KD/KD cells. Flag antibody (M2, Sigma) was used at 1:1000. (C) TdT-mediated PCR of DNA-PKcs^KD/KDArtemis^−/− cells without or with ectopic expression of WT, 9A or 2A-Artemis. (D) Representative imaging of GFP-Artemis recruitment in immortalized MEFs. (E) Quantification of increased florescence intensity of GFP-Artemis at the laser damaged area. The data represents the average and standard deviation of 10 cells at each time point.

Figure 7. Distinct DNA-PKcs phosphorylations regulate end-ligation and end-processing

In this diagram, we illustrate the normal vertebrate NHEJ mechanism on the left and the NHEJ mechanism in the context of DNA-PKcs^−/− or DNA-PKcs^KD/KD backgrounds on the right. In this model, we highlight two kinds of DNA-PKcs phosphorylation: red, ATM-mediated phosphorylation of DNA-PKcs, and blue, strict auto-phosphorylation of DNA-PKcs. First, in red, we emphasize the role of ATM-mediated DNA-PKcs phosphorylation in Artemis endonuclease recruitment for end processing (e.g. hairpin opening). Notably, in the absence of ATM, DNA-PKcs can also phosphorylate Artemis at such sites (thinner red arrows). Second, in blue, we note the sites on DNA-PKcs where strict auto-phosphorylation occurs are required for end-ligation. For the illustration purposes, we have shown that DNA-PKcs opens up to allow end-ligation by the Lig4-XRCC4-XLF complex, but DNA-PKcs could also simply dissociate from the DNA to allow end-ligation.