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TRF2 binds branched DNA to safeguard telomere integrity

Nature Structural & Molecular Biology volume 24, pages 734–742 (2017)Cite this article

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Abstract

Although t-loops protect telomeres, they are at risk of cleavage by Holliday junction (HJ) resolvases if branch migration converts the three-way t-loop junction into four-way HJs. T-loop cleavage is repressed by the TRF2 basic domain, which binds three- and four-way junctions and protects HJs in vitro. By replacing the basic domain with bacterial-protein domains binding three- and four-way junctions, we demonstrated the in vivo relevance of branched-DNA binding. Branched-DNA binding also repressed PARP1, presumably by masking the PARP1 site in the t-loop junction. Although PARP1 recruits HJ resolvases and promotes t-loop cleavage, PARP1 activation alone did not result in t-loop cleavage, thus suggesting that the basic domain also prevents formation of HJs. Concordantly, removal of HJs by BLM helicase mitigated t-loop cleavage in response to loss of the basic domain. We propose that TRF2 masks and stabilizes the t-loop three-way junction, thereby protecting telomeres from detrimental deletions and PARP1 activation.

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Figure 1: DNA binding and t-loop formation by the basic domain.
Figure 2: The basic domain functions as a branched DNA–binding domain in vivo.
Figure 3: PARP1 promotes t-loop cleavage and is repressed by branched-DNA binding by TRF2.
Figure 4: PARP1 activation is not sufficient to promote t-loop cleavage.
Figure 5: The role of branch migration in t-loop cleavage.
Figure 6: Repression of HR at telomeres by RuvC but not by the basic domain.

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Acknowledgements

We thank D. White for expert mouse husbandry and the members of the laboratory of T.d.L. for sharing cell lines, for discussion and for comments on the manuscript. I.S. was supported by funds from a Women & Science Irene Diamond Fellowship in Breast Cancer Research at the Rockefeller University and by Mobility fellowships from the Swiss National Science foundation (Early Mobility fellowships PBFRP3-137230 and PBFRP3_142824, and Advanced Mobility fellowship P300PA_161006). L.T. was supported by an Anderson Center for Cancer Research Graduate Fellowship (contract FA9550-11-C-0028, awarded by the Department of Defense, Air Force Office of Scientific Research, National Defense Science and Engineering Graduate (NDSEG) Fellowship 32 CFR 168a). This work was supported by grants from the NIH (AG016642) to T.d.L. and (GM104962) to D.J.P., and by a Memorial Sloan-Kettering Cancer Center NIH Core Grant (P30 CA008748). T.d.L. is supported as an American Cancer Society Rose Zarucki Trust Research Professor. SPR experiments were performed at the RU High-Throughput and Spectroscopy Resource Center with expert assistance from A. Alcaino. OMX-SI imaging experiments were supported by a grant (S10RR031855) from the National Center For Research Resources to the Bio-Imaging Center at RU. The content of this manuscript is solely the responsibility of the authors and does not necessarily represent the official views of the National Center For Research Resources or the National Institutes of Health. We thank G. Hannon (Cancer Research UK Cambridge Institute) for reagents.

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Authors and Affiliations

  1. Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York, USA

    Isabelle Schmutz, Leonid Timashev & Titia de Lange

  2. Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA

    Wei Xie & Dinshaw J Patel

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  1. Isabelle Schmutz
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  2. Leonid Timashev
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Contributions

I.S. and T.d.L. designed the experiments and wrote the manuscript. I.S. performed all in vivo experiments, except for the t-loop assays, which were performed by L.T. W.X. and D.J.P. performed the in vitro binding studies.

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Correspondence to Titia de Lange.

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Integrated supplementary information

Supplementary Figure 1 Functional analysis of TRF2 alleles.

(a) Schematic of RuvC-TRF2ΔB fusion proteins and the TRF2H31A construct. RuvCm contains mutations in the active site (D138N/D140N) and RuvCwt represents the wild type protein. The mutations in the active site abolish resolvase activity of RuvC but do not affect its binding to branched DNA structures29. (b) Immunoblot for TRF2 and γ-tubulin in NIH3T3 cells. (c) IF-FISH for TRF2 (red) and telomeres (green) in NIH3T3 cells expressing the indicated alleles. Blue, DAPI; Scale bar, 5 μm. (d) Telomeric ChIP analysis with TRF2 Ab in NIH3T3 cells expressing the different TRF2 alleles. (e) Quantification of telomeric DNA recovered with the TRF2 Ab (average % telomeric DNA recovered in two independent experiments). (f) IF-FISH for TRF1 (red) and telomeres (green) in NIH3T3 cells expressing the indicated alleles. Blue, DAPI; Scale bar, 5 μm. (g) Analysis of fragile telomeres, a proxy for TRF1 dysfunction, in the indicated NIH3T3 cells. Metaphase chromosomes were prepared five days after introduction of the TRF2 alleles. Data points represent individual metaphases from 3 independent experiments; bars show the median. Significance was calculated by One-way ANOVA with Tukey post-test, ns, not significant. (h) Immunoblot showing expression of TRF2 in SV40-LT TRF2F/F MEFs complemented with TRF2 alleles 96 h after Cre. Cre minus cells were harvested at the same time-point. (i) 53BP1 TIF analysis in cells as in (h); means±SDs from 3 independent experiments. (j) Quantification of telomere fusions in cells as in (h); median fusion frequency in one experiment (13-15 metaphases).

Supplementary Figure 2 RuvA and RuvC protect telomeres in place of the basic domain.

(a) Top: Illustration of the approach for measuring unequal sister telomeres. Middle: Representative image showing metaphase chromosomes of TRF2ΔB expressing NIH3T3 cells one day after introduction by retroviral infection. Scale bar, 10 μm. Green: Telomeric FISH; red, DAPI. Arrows: unequal sister telomere signals. Bottom: Enlarged examples of chromosomes with unequal sister telomeres. Right: a scatter plot of the raw sister telomere ratios from one representative experiment is shown. This experiment is part of the analysis of unequal sister telomeres shown in Fig. 2e. Data points represent individual sister ratios (from 330 chromosome ends on 10 metaphase spreads). The dotted line depicts the cut-off used in this experiment to calculate the % of ends with unequal sister telomeres. The cut-off represents the 80th percentile sister ratio in control cells (vec). The scatter plot shows more chromosome ends with a ratio above the threshold in cells expressing TRF2ΔB. The % of ratios above the threshold is indicated. All unequal sister ratios were determined as indicated in (a). (b) Scatter plot of raw telomere fluorescence units (TFU in arbitrary units) from Q-FISH analysis in NIH3T3 cells expressing the indicated TRF2 alleles as in Fig. 2f. Median TFU units from 3 independent experiments (medians±SEMs) are indicated (white bars). (c) Telomere blot of HindIII-digested DNA from NIH3T3 cells (day 5 post-infection). The membrane was hybridized with a chromosome-internal probe for normalization, stripped, and hybridized to the telomere-specific Sty11 probe to detect telomeric repeats. (d) Quantification of telomeric signal intensity, as determined in (c). Telomeric signals were normalized to the signal from the chromosome-internal probe and are shown relative to wt TRF2 (100%). Means±SDs from 6 independent experiments; p-values from One-way Anova with Dunnett’s test. (e) Quantification of chromosome ends with unequal sister telomeres in NIH3T3 cells. Scatter plots with medians are shown (≥25 metaphases from four independent experiments; p values from One-way ANOVA with Tukey post-test). The same data sets for vec, WT, and ΔB are shown Fig. 2l. (f) Q-FISH analysis of telomeric DNA signals in NIH3T3 cells expressing the indicated alleles (% telomeric DNA relative to empty vector; means±SDs from four independent experiments. The same data sets for vec, WT, and ΔB are shown in Fig. 2m. (g) Scatter plot of sister telomere ratios from one representative experiment as in Fig. 2l. Data points represent individual sister ratios. This experiment is part of the analysis of unequal sister telomeres shown in Fig. 2l. (h) Scatter plot of raw TFUs from Q-FISH analysis in NIH3T3 cells expressing the indicated TRF2 alleles as in Fig. 2m. Median TFU units from 5 independent experiments (medians±SEMs) are indicated (white bars).

Supplementary Figure 3 Control experiments on HeLa cells.

(a) IF-FISH to detect TRF2 (red) and telomeres (green) in HeLa1.2.11 cells (Day 8 post-infection). Blue, DAPI; Scale bar, 5 μm. (b) IF-FISH to detect TRF1 (red) and telomeres (green) in HeLa1.2.11 cells as in (a). TRF1 localization to telomeres is not affected by overexpression of TRF2 alleles. Blue, DAPI; Scale bar, 5 μm. (c) Quantification of chromosome ends with fragile telomeres, a proxy for TRF1 function in HeLa1.2.11 cells as in (a). The analysis shows that similar to mouse telomeres, expression of TRF2 alleles does not induce fragile telomeres. Data points represent individual metaphases from 3 independent experiments and significance is based on One-way ANOVA with Tukey post-test as in Fig. 1. Bars represent the median.

Supplementary Figure 4 TRF2ΔB-induced telomere loss depends on PARP1.

(a) Detection of PARP1 and telomeres in TRF1F/FTRF2F/FKu80-/-p53-/- MEFs with and without Cre (96 h). Red, IF for PARP1; green, telomeric FISH; blue, DAPI. Scale bar, 5 μm. (b) Quantification of PARP1 signals co-localizing with telomeres as assessed by IF-FISH in TRF1F/FTRF2F/FKu80-/-p53-/- MEFs with and without Cre treatment as in (a) (means±SDs from 3 independent experiments; Colocalization was assessed in 40-50 nuclei per experiment and experimental condition; p values from One-way ANOVA with Tukey post test). (c) Immunoblot showing TRF2 and TRF1 loss, and induction of PARsylation upon Cre treatment of TRF1F/FTRF2F/FKu80-/-p53-/- cells. Treatment with 5 μM Olaparib (PARPi) verifies PARP1 dependent PARsylation. (d) IF for PAR (green) in TRF1F/FTRF2F/FKu80-/-p53-/- cells. Dysfunctional telomeres are visualized by 53BP1 IF (red). Blue, DAPI; Scale bar, 5 μm. (e) Immunoblot showing TRF2 in control and TRF2ΔB-expressing NIH3T3 cells that were mock treated (DMSO) or treated with 2 μM Olaparib (PARPi). (f) Immunoblot showing TRF2ΔB expression in PARP1-proficient and -deficient MEFs infected with empty vector or TRF2ΔB. Control cell lines were PARP1wt/- (ctrl1) and PARP1wt/wt (ctrl2). (g) Scatter plot of telomere fluorescence units (TFU) from Q-FISH analysis in PARP1-proficient and -deficient MEFs infected with vec or TRF2ΔB as in (f). TFU units from 2 independent experiments (medians±SEMs) are shown (white bars).

Supplementary Figure 5 TRF2 and TIN2 independently repress telomeric PARP1 signaling.

(a) Quantification of cells with ≥5 53BP1 TIFs in the indicated conditional KO MEFs (Cre minus and plus; means±SDs from ≥3 independent experiments). 53BP1 TIF analysis serves as a control for efficient deletion of shelterin components in the survey of MEF cell lines for PARP1 activation. Note that deletion of Rap1 does not induce TIFs in Ku-proficient cells and only to a minor level in Ku-deficient cells. Efficient deletion was also verified by immunoblot analysis using specific antibodies for the individual shelterin subunits. (b) Quantification of cells with ≥5 53BP1 TIFs in cells as in Fig. 4b (Cre minus and plus; means±SDs from 3 independent experiments). 53BP1 TIF analysis was used to control for efficient deletion of shelterin components. Efficient deletion was also verified by immunoblot analysis using specific antibodies for the individual shelterin subunits (c) Immunoblot showing PAR and TRF2 in TIN2F/FKu70-/- MEFs. Note that PARsylation was rescued by expression of TIN2, but not expression of TRF2. (d) Immunoblot showing TRF2 overexpression in TIN2F/FKu70-/- MEFs. (e) Telomeric ChIP for TRF2 and TIN2 in TIN2F/FKu70-/- MEFs. The quantification shows that TRF2 overexpression re-establishes the telomeric TRF2 levels in TIN2/Ku70 DKO cells. (f) IF-FISH for PARP1 (red) and telomeres (green) in cells as in (d); DAPI (blue); Scale bar, 5 μm. (g) Quantification of PARP1 co-localization with telomeres as in (f) (means±SDs from 3 independent experiments). All experiments were performed at 96 h after Cre. For all experiments, P values are as in Fig. 1 based on One-way ANOVA with Tukey post-test.

Supplementary Figure 6 Rap1 deletion does not exacerbate phenotypes associated with telomeres containing TRF2ΔB.

(a) Immunoblot showing TRF2 alleles and Rap1 in Rap1F/F Ku70+/- p53-/- MEFs with and without Cre treatment. Cells were infected with TRF2 alleles and selected for integration of the TRF2 expression plasmid for 4-5 days. Then the cells were split, H&R Cre infected and harvested 120h post Cre treatment. This experimental setting allows the analysis of the effect of Rap1 deletion on TRF2ΔB-induced phenotypes in an isogenic background. (b) Quantification of PARP1 signals co-localizing with telomeres as assessed by IF-FISH in Rap1F/F Ku70+/- p53-/- MEFs as in (a) (means±SDs from 3 independent experiments, P values are based on One-way ANOVA with Tukey post-test). (c) Quantification of chromatids that do not have detectable telomere FISH signal in Rap1F/F Ku70+/- p53-/- MEFs as in (a). Scatter plots with medians are shown (≥40 metaphases from three independent experiments; p values from One-way ANOVA with Tukey post-test.) (d) Telomere blot analysis of MboI/AluI-digested DNA from Rap1F/F Ku70+/- p53-/- MEFs expressing the indicated TRF2 alleles with or without Cre treatment. Cells were harvested 120h (left panels) or 240h (right panels) post Cre treatment. The lower panels show the signal detected with the BamHI probe, which serves as loading control. The relative telomere abundance calculated from the telomere blot and normalized to the BamHI signal is indicated. The signal in Cre minus control cells was set to 100% for each time point. This panel shows a representative blot. The experiment was repeated 3 times. (e) Quantification of chromosome fusions that do not have detectable telomere signals at the fusion sites in Rap1F/F Ku70+/- p53-/- MEFs as in (a) (means±SDs from 3 independent experiments, ≥40 metaphase spreads, p-values from unpaired t-test). P value symbols are as in Fig.1.

Supplementary Figure 7 Generation of BLM-KO cells by CRISPR–Cas9 gene editing.

(a) Schematic of the BLM locus showing landmarks relevant to CRISPR/Cas9 gene editing. The guide RNA (gRNA) region and the PAM are indicated in the reference sequence and the changes in sequence are highlighted in the edited alleles of the two CRISPR clones. In clone BLM KO-2 only one allele variant (and no wt allele) was detected. The sequences were derived from TOPO-cloned PCR products amplified from the indicated primer pair. (b) Immunoblot showing BLM (arrow) in parental NIH3T3 cells but not in the KO clones. (c) SCE assay in parental NIH3T3 cells and the two BLM KO clones confirming BLM deficiency. (d) Quantification of chromosome fusions that do not have detectable telomere signals at the fusion sites in parental and BLM KO NIH3T3 cells on day 1 after infection. Dots represent the % of fused chromosomes in individual metaphase spreads and the mean is shown (40 metaphase spreads from 4 independent experiments. P values are as in Fig. 1 based on One-way ANOVA with Tukey post-test.

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Schmutz, I., Timashev, L., Xie, W. et al. TRF2 binds branched DNA to safeguard telomere integrity. Nat Struct Mol Biol 24, 734–742 (2017). https://doi.org/10.1038/nsmb.3451

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