Conserved telomere maintenance component 1 interacts with STN1 and maintains chromosome ends in higher eukaryotes

Abstract

Orthologs of the yeast telomere protein Stn1 are present in plants, but other components of the Cdc13/Stn1/Ten1 (CST) complex have only been found in fungi. Here we report the identification of conserved telomere maintenance component 1 (CTC1) in plants and vertebrates. CTC1 encodes an approximately 140 kDa telomere-associated protein predicted to contain multiple OB-fold domains. Arabidopsis mutants null for CTC1 display a severe telomere deprotection phenotype accompanied by a rapid onset of developmental defects and sterility. Telomeric and subtelomeric tracts are dramatically eroded, and chromosome ends exhibit increased G overhangs, recombination, and end-to-end fusions. AtCTC1 both physically and genetically interacts with AtSTN1. Depletion of human CTC1 by RNAi triggers a DNA damage response, chromatin bridges, increased G overhangs, and sporadic telomere loss. These data indicate that CTC1 participates in telomere maintenance in diverse species and that a CST-like complex is required for telomere integrity in multicellular organisms.

Figure 1

Identification of CTC1 in Arabidopsis thaliana. (A) Top, schematic of the AtCTC1 gene locus. Rectangles represent exons; horizontal black lines are introns. The positions of the point mutation (ctc1-1) and T-DNA insertions (ctc1-2 and ctc1-3) are shown. (B) Co-localization of AtCTC1 and telomeres at the nucleolus periphery of leaf nuclei from seedlings. (i) CFP-AtCTC1 localization detected with anti-GFP antibody; (ii) telomere FISH using probe made from DIG-UTP labeled T₃AG₃-C₃TA₃; (iii) CFP-AtCTC1– telomere merge; (iv) image from panel (iii) is combined with DAPI stained nucleus. The nucleolus appears as a ring where DAPI staining is excluded, arrows in (i)-(iv) indicate internal stretches of telomeric DNA sequence (Armstrong et al., 2001). Scale bar = 2.5 μm. (C) Morphological defects in ctc1 mutants. Left panel, wild type; middle and right panels, first generation ctc1-1 and ctc1-3 mutants of similar age. Fasciated stems and fused organs in ctc1 mutants are shown. The severity of morphological defects varies among ctc1 mutants.

Figure 2

Telomere length deregulation and increased G-overhangs in AtCTC1 mutants. (A) TRF analysis of ctc1-1. Results are shown for progeny segregated from a parent heterozygous for ctc1. (B) Subtelomeric TRF analysis of DNA from ctc1-1 mutant. DNA blots were hybridized with a probe corresponding to subtelomeric regions on the right arm of chromosome 5 (5R). (C) PETRA analysis of DNA from ctc1-1 mutants. Results for the 1L and 2R telomeres are shown. (D) In-gel hybridization of (C₃TA₃)₄ probe to telomeric restriction fragments under native and denaturing conditions (left). Quantification of ctc1-1 signal relative to wild type is shown in the middle panel. Data are the average of 8 independent experiments ±SD, (P=1.3E-5 Student's t-test). Right panel, in-gel hybridization of ctc1-1 DNA in the absence (-) or presence (+) of 3′→5′ exonuclease (T4 DNA polymerase). In panels A and C, blots were hybridized with a radiolabeled telomeric DNA probe (T₃AG₃)₄. Molecular weight markers are indicated.

Figure 3

ctc1-1 mutants display elevated telomere recombination and end-to-end fusions. (A) T-circle amplification with ctc1-1 DNA. Reactions were performed in the presence or absence of phi29 polymerase. ku70 DNA was used as a positive control. (B) Bubble trapping results for ctc1-1 and ku70 mutants. All blots were hybridized with a radiolabeled telomeric probe. In panels A and B, the probe hybridized to both circular and linear telomeric DNA products. Arrows mark TCA product/circles, smears correspond to TRFs and the asterisk indicates an interstitial telomeric repeat signal. (C) Cytogenetic analysis of ctc1-1 mutants showing DAPI-stained chromosome spreads with anaphase figures. (D) Telomere fusion PCR analysis of ctc1-1 mutants. Primers were specific for 4R and 5R (left) or 4R and 3L (right). The table shows types of fusion junctions found after sequencing PCR products.

Figure 4

AtCTC1 and AtSTN1 function in the same genetic pathway for chromosome end protection and physically interact in vitro. (A) PETRA analysis of telomere length with DNA from ctc1-1 stn1-1 double mutants, and their ctc1-1, stn1-1 and wild type siblings. (B) G-overhang analysis using in-gel hybridization. Native gel and quantification results (the average of 6 independent experiments ±SD) are shown. P≤0.005 for all mutant samples compared to wild type, and P≥0.4 for mutant samples compared to each other. In A and B, all progeny were segregated from a double heterozygous ctc1-1 stn1-1 parent. Blots were hybridized with a radiolabeled telomeric DNA probe. (C) Top, schematic of the full-length AtCTC1 protein and its truncation derivatives. AtCTC1 fragments that bind AtSTN1 are indicated. Bottom, co-immunoprecipitation experiments conducted with recombinant full length AtSTN1 and truncated AtCTC1 fragments A-D. Asterisks indicate ³⁵S-methionine labeled protein; the unlabeled protein was T7-tagged. S, supernatant; P, pellet. Ku70-Ku80 interaction was the positive control.

Figure 5

Depletion of human CTC1 causes genomic instability and sudden telomere loss. (A) Alignment of potential OB-folds in Arabidopsis and human CTC1 with OB-fold domains from POT1 and RPA. Dotted lines connect homologous domains. Dark shading, OB-fold homologies predicted by multiple approaches; light shading, homologies predicted by a single method. Dark rectangle within OB5 of HsCTC1 indicates putative Zn finger which is present in human and archaeal RPAs. MjRPA, archeal RPA from Methanococcus jannaschii; HsRPA1, human RPA70. (B) Knockdown of CTC1 mRNA in HeLa cells at indicated times after the second transfection. Values are the mean of five independent experiments ± SEM. The percent knockdown is relative to the mock transfection which was set at 100%. NC, non-silencing control; Mock, transfection reagent alone. (C & D) Chromatin bridges and γH2AX staining after CTC1 knockdown in HeLa cells. (C) DAPI staining (blue) shows bridges between interphase cells, γH2AX (red) shows DNA damage foci. (D) Frequency of chromatin bridges. Mean of three independent experiments ± SEM, stars indicate significance levels (*, p<0.05; **, p<0.01) from one-tailed Student's t-test. (E & F) Telomere FISH showing signal-free ends 48 hr after CTC1 knockdown in Hela cells. (E) Representative metaphase spreads hybridized with Cy3-OO-(TTAGGG)₃ PNA probe. The top panels show magnified view of selected chromosomes. (F) Percent of chromosome ends that lack a telomeric DNA signal after treatment with non-silencing control or CTC1 siRNA. Stars indicate significance of the increase in signal-free ends; significance levels are depicted as in (D).

Figure 6

Deregulation of the G-strand overhang after CTC1-knockdown in MCF7 cells. (A) In-gel hybridization of (CCCTAA)₄ probe to telomeric restriction fragments under native (upper panel) or denaturing (lower panel) conditions. +Exo I, DNA samples were treated with Exonuclease I prior to restriction digestion. (B and C) Quantification of G-strand signal (B) or CTC1 mRNA depletion (C) for experiment shown in A. Change in G-strand signal or CTC1 mRNA level is shown relative to the mock transfection. (D) Mean change in G-strand signal after CTC1 knockdown. Data are from three independent experiments ± SEM; p-values are from one-tailed Student's t-test. (E) Mean change in CTC1 mRNA level for experiments shown in (D). See caption to Figure 5B for details.