(A) Targeting of the mouse Apollo locus. The structure of the genomic locus, the targeting construct, the floxed allele and the deleted allele are shown. loxP sites are represented as triangles; FRT sites surrounding the neo gene are shown as rectangles. Approximate positions of the PCR primers for genomic analysis (F and R1 and R2) and RT-PCR mRNA analysis (RTF and RTR) are shown. Restriction endonucleases and the probe used for analysis of genomic DNA: B, BamHI, N, NsiI, Nh, NheI, P, PacI, S, ScaI. (B) Genotyping PCR for Apollo using DNA from MEFs. (C) RT-PCR with two independent sets of primers for both Apollo and Ap4b1 using RNA purified from cells treated with or without Cre. GAPDH was used as a control. (D) Schematic of the mouse Apollo protein indicating regions that are altered in Apollo rescue alleles. Amino acids in red indicate important residues for nuclease activity and TRF2 interaction. (E) Immunoblotting analysis of Apollo^F/F MEFs expressing the indicated Apollo alleles in the absence of Cre and at 120h after Cre. Apollo is detected with the HA.11 antibody. (F) Immunofluorescence showing the localization of the indicated Apollo alleles (detected with HA.11 Ab) in Apollo^F/F MEFs at 72h after Cre infection. Telomeric loci are detected with Ab 644 to the shelterin component TRF1. DNA is stained with DAPI. See also Figure S1.

(A) TIF assay on Apollo^F/F MEFs expressing the indicated Apollo alleles to detect telomeric DNA damage signaling before (left) and after (right) deletion of the endogenous Apollo with Cre. Telomeres are detected using a FISH probe (green). DNA damage sites are marked with 53BP1 (red). DNA is counterstained with DAPI (blue). Circled TIFs in the enlarged images highlight the prevalence of TIF occurrence at two closely positioned telomeres or in cells with paired telomeres, indicative of DNA damage signaling during or after telomere replication. (B) Immunoblotting for the phosphorylation state of Chk2 at 6 days after Cre treatment. (C) Immunoblot showing depletion of ATM (Mat3-Sigma) 6 days after shRNA treatment and 3 days after the start of puromycin selection in Apollo^F/F MEFs expressing the indicated Apollo alleles. Apollo-ND* is identical to Apollo-ND, except without the mutation of H230. (D) Effect of ATM kinase knockdown on the TIF response in Apollo deficient cells. TIF analysis as in (A) but with cells expressing an shRNA to the ATM kinase. (E) Quantification of TIF responses as assayed in (A) and (D). TIFs were scored on the basis of co-localization of 53BP1 foci with 5 or more telomeres per cell. Values for alleles +Cre indicate the mean of 3 independent experiments (> 100 nuclei per experiment), and SDs. * indicates the use of the Apollo-ND* allele in the ATM shRNA experiment. See also Figure S2.

(A) Schematic of the FUCCI system to sort cells in G1 and S phase. SV40-LT Apollo^F/F MEFs were transduced with mKO2-hCdt1 (red) and mAG-hGeminin (green). Cells were selected by FACS for integration of both plasmids, replated, and infected with Hit&Run Cre. Cells were harvest at the desired time, sorted for Cdt1⁺Gem⁻ and Cdt1⁻Gem⁺ populations, and embedded in agarose for overhang analysis or plated on coverslips for immunofluorescence at desired timepoints. (B) Cell cycle profile and S phase index for different sorted populations at 1.5h or 6–8h after plating. Cells were pulsed for 30 min with BrdU before harvesting and fixing for cell cycle analysis. Cells were stained with FITC-anti-BrdU and propidium iodide (PI) for DNA content, and analyzed by flow cytometry. (C) TIF assay of G1, early/mid S, and late S/G2 Apollo^F/F MEFs at 72h post Cre. G1 and late S/G2 cells were obtained by sorting Cdt1⁺Gem⁻ and Cdt1⁻Gem⁺ populations and plating cells for 1.5h prior to fixation. Early/mid S phase cells were obtained by plating Cdt1⁺Gem⁻ sorted (G1) cells on coverslips for 6–8h prior to fixation. Telomeres are detected using a FISH probe (green). DNA damage sites are marked with 53BP1 (red). DNA is counterstained with DAPI (blue). (D) Quantification of the TIF response in G1, early/mid S, and late S phase as assayed in (C). Values are the mean of three independent experiments (>60 nuclei per experiment) and SDs. p-values were determined using paired student’s t-test. See also Figure S3.

(A) Immunoblot for TRF2 and Chk2 in TRF2^F/− p53^−/− MEFs expressing the indicated TRF2 alleles without Cre and at 144 hours after Hit&Run Cre. (B) IF showing localization of TRF2 alleles in TRF2^F/− p53^−/− MEFs at 72h after Cre. TRF2 alleles are detected with the myc antibody 9B11. Telomeres are detected with the TRF1 antibody #644. (C) Growth curve showing cumulative population doublings after infection with Cre. Filled squares: vector (no Cre). Open squares: vector +Cre. Open circles: TRF2 +Cre. Open triangles: TRF2-F120A +Cre. (D) TIF assay on TRF2^F/− p53^−/− MEFs expressing the indicated TRF2 alleles to detect telomeric DNA damage signaling before (left) and after (right) deletion of the endogenous TRF2 with Cre. Telomeres are detected using a FISH probe (green). DNA damage sites are marked with 53BP1 (red). DNA is counterstained with DAPI (blue). (E) Quantification of TIF response as assayed in (D). TIFs were scored on the basis of co-localization of 53BP1 foci with 5 or more telomeres per cell. Values indicate the mean of 3 independent experiments (>100 nuclei per experiment) and SDs. p-values were determined based on paired student’s t-test.

(A) Telomere fusions in metaphase spreads from Apollo-deficient cells. Metaphase spreads were obtained from Apollo^F/F MEFs before or after introduction of Cre and processed for telomeric FISH (FITC, green). DNA was stained with DAPI (false-colored in red). Arrowheads highlight chromatid-type fusion events. (B) Quantification of chromatid-type fusion events after deletion of Apollo. (C) CO-FISH analysis of leading and lagging end telomeres. Metaphases harvested from Apollo^F/F MEFs or TRF2^F/− p53^−/− MEFs expressing the indicated rescuing alleles were incubated with BrdU/BrdC and treated with ExoIII and UV to remove the newly-synthesized DNA strand. The undigested parental telomeric DNA strands were detected with TAMRA-(TTAGGG)₃ (red) and FITC-(CCCTAA)₃ (green). DNA is stained with DAPI (blue). The telomere replicated by leading-strand DNA synthesis is highlighted in red, and the telomere replicated by lagging-strand DNA synthesis is highlighted in green. (D) Quantification of leading-end telomere fusions from metaphase analyses shown in (C) at 120 hours post Cre. Values represent means of three or more experiments (chromosome number >1000 per experiment) and SDs. (E) Quantification of other telomere fusions events (lagging-to-lagging, lagging-to-leading chromatid-type fusions, and chromosome-type fusions). Values represent means of three or more experiments (>1000 chromosomes per experiment) and SDs. See also Figure S4.

(A) Representative telomeric overhang analysis of Apollo^F/F MEFs expressing the indicated rescuing alleles without Cre and at 120 h after pWzl-Cre infection. The single-stranded telomeric signal was determined by in-gel hybridization (left) of an end-labeled ³²P-(AACCCT)₄ telomeric oligonucleotide to native MboI-digested genomic DNA. After capture of the signal, the DNA was denatured in situ and the gel was rehybridized with the same probe to determine the total telomeric DNA signal (right). The single-stranded telomeric signal between ~9–100kb in each lane was normalized to the total telomeric DNA signal in the same region of that lane. The relative single-stranded signal was then determined with the lane containing vector only (no Cre) set to 100. (B) Quantification of relative single-stranded telomeric overhang signal with Apollo^F/F MEFs. Values represent means for five independent experiments with SDs. For each rescuing allele (or cells infected with the empty vector) the normalized value was set at 100 for cells not treated with Cre and the post-Cre values are given as a percentage of this value. p-values were determined using paired student t-test. (C) Representative telomeric overhang analysis of TRF2^F/− p53^−/− MEFs expressing the indicated alleles without Cre and at 120h post Cre-infection, assayed as in (A). (D) Quantification of relative single-stranded telomeric signal with TRF2^F/− p53^−/− MEFs. Values represent means for three independent experiments with SDs. For each rescuing allele (or cells infected with the empty vector) the normalized value was set at 100 for cells not treated with Cre and the post-Cre values are given as a percentage of this value. p-values were determined using paired student t-test. (E) Representative telomeric overhang analysis of G1 and late S/G2 Apollo^F/F MEFs without Cre and at 120 h after Cre. FUCCI-sorted cells were immediately embedded in agarose plugs for overhang analysis as in (A). The relative single-stranded signal was normalized to total TTAGGG signal and determined as a percentage of the signal in the lane containing G1 cells without Cre (set at 100). (F) Quantification of relative single-stranded telomeric signal in G1 and late S/G2 as assayed in (E). The single-stranded telomeric signal was normalized to total TTAGGG signal and determined as a percentage of the signal in G1 cells without Cre (set at 100). Values are the mean of three independent experiments and SDs. p-values were determined by paired student’s t-test. See also Figure S5.