Chromosome End Fusions Research Articles

The non-telomeric evolutionary trajectory of TRF2 in zebrafish reveals its specific roles in neurodevelopment and aging.

The shelterin protein complex is required for telomere protection in various eukaryotic organisms. In mammals, the shelterin subunit TRF2 is specialized in preventing ATM activation at telomeres and chromosome end fusion in somatic cells. Here, we demonstrate that the zebrafish ortholog of TRF2 (encoded by the terfa gene) is protecting against unwanted ATM activation genome-wide. The terfa-compromised fish develop a prominent and specific embryonic neurodevelopmental failure. The heterozygous fish survive to adulthood but exhibit a premature aging phenotype. The recovery from embryonic neurodevelopmental failure requires both ATM inhibition and transcriptional complementation of neural genes. Furthermore, restoring the expression of TRF2 in glial cells rescues the embryonic neurodevelopment phenotype. These results indicate that the shelterin subunit TRF2 evolved in zebrafish as a general factor of genome maintenance and transcriptional regulation that is required for proper neurodevelopment and normal aging. These findings uncover how TRF2 links development to aging by separate functions in gene expression regulation and genome stability control.

Compartmentalization of telomeres through DNA-scaffolded phase separation

Telomeres form unique nuclear compartments that prevent degradation and fusion of chromosome ends by recruiting shelterin proteins and excluding DNA damage repair factors. To understand how these dynamic components protect chromosome ends, we reconstitute human shelterin in vitro and show that shelterin components form multicomponent liquid condensates with selective biomolecular partitioning on telomeric DNA. TRF1 and TRF2 subunits of shelterin drive phase separation, and their N-terminal domains specify interactions with telomeric DNA in vitro.

Compartmentalization of telomeres through DNA-scaffolded phase separation.

SummaryTelomeres form unique nuclear compartments that prevent degradation and fusion of chromosome ends by recruiting shelterin proteins and regulating access of DNA damage repair factors. To understand how these dynamic components protect chromosome ends, we combine in vivo biophysical interrogation and in vitro reconstitution of human shelterin. We show that shelterin components form multicomponent liquid condensates with selective biomolecular partitioning on telomeric DNA. Tethering and anomalous diffusion prevent multiple telomeres from coalescing into a single condensate in mammalian cells. However, telomeres coalesce when brought into contact via an optogenetic approach. TRF1 and TRF2 subunits of shelterin drive phase separation, and their N-terminal domains specify interactions with telomeric DNA in vitro. Telomeric condensates selectively recruit telomere-associated factors and regulate access of DNA damage repair factors. We propose that shelterin mediates phase separation of telomeric chromatin, which underlies the dynamic yet persistent nature of the end-protection mechanism.

Corrigendum: Hepatocytes with extensive telomere deprotection and fusion remain viable and regenerate liver mass through endoreduplication.

We report that mouse liver cells are highly resistant to extensive telomere dysfunction. In proliferating cells, telomere dysfunction results in chromosome end fusions, a DNA damage signal, and apoptosis or senescence. To determine the consequences of telomere dysfunction in noncycling cells, we used conditional deletion of the telomeric protein TRF2 in hepatocytes. TRF2 loss resulted in telomeric accumulation of gamma-H2AX and frequent telomere fusions, indicating telomere deprotection. However, there was no induction of p53 or apoptosis, and liver function appeared unaffected. Furthermore, the loss of TRF2 did not compromise liver regeneration after partial hepatectomy. Remarkably, liver regeneration occurred without cell division involving endoreduplication and cell growth, thereby circumventing the chromosome segregation problems associated with telomere fusions. We conclude that nondividing hepatocytes can maintain and regenerate liver function despite substantial loss of telomere integrity.

Cdc13 is predominant over Stn1 and Ten1 in preventing chromosome end fusions.

Telomeres define the natural ends of eukaryotic chromosomes and are crucial for chromosomal stability. The budding yeast Cdc13, Stn1 and Ten1 proteins form a heterotrimeric complex, and the inactivation of any of its subunits leads to a uniformly lethal phenotype due to telomere deprotection. Although Cdc13, Stn1 and Ten1 seem to belong to an epistasis group, it remains unclear whether they function differently in telomere protection. Here, we employed the single-linear-chromosome yeast SY14, and surprisingly found that the deletion of CDC13 leads to telomere erosion and intrachromosome end-to-end fusion, which depends on Rad52 but not Yku. Interestingly, the emergence frequency of survivors in the SY14 cdc13Δ mutant was ~29 fold higher than that in either the stn1Δ or ten1Δ mutant, demonstrating a predominant role of Cdc13 in inhibiting telomere fusion. Chromosomal fusion readily occurred in the telomerase-null SY14 strain, further verifying the default role of intact telomeres in inhibiting chromosome fusion.

SMCHD1 promotes ATM-dependent DNA damage signaling and repair of uncapped telomeres.

Structural maintenance of chromosomes flexible hinge domain-containing protein 1 (SMCHD1) has been implicated in X-chromosome inactivation, imprinting, and DNA damage repair, and mutations in SMCHD1 can cause facioscapulohumeral muscular dystrophy. More recently, SMCHD1 has also been identified as a component of telomeric chromatin. Here, we report that SMCHD1 is required for DNA damage signaling and non-homologous end joining (NHEJ) at unprotected telomeres. Co-depletion of SMCHD1 and the shelterin subunit TRF2 reduced telomeric 3'-overhang removal in time-course experiments, as well as the number of chromosome end fusions. SMCHD1-deficient cells displayed reduced ATM S1981 phosphorylation and diminished formation of γH2AX foci and of 53BP1-containing telomere dysfunction-induced foci (TIFs), indicating defects in DNA damage checkpoint signaling. Removal of TPP1 and subsequent activation of ATR signaling rescued telomere fusion events in TRF2-depleted SMCHD1 knockout cells. Together, these data indicate that SMCHD1 depletion reduces telomere fusions in TRF2-depleted cells due to defects in ATM-dependent checkpoint signaling and that SMCHD1 mediates DNA damage response activation upstream of ATM phosphorylation at uncapped telomeres.

CSL controls telomere maintenance and genome stability in human dermal fibroblasts

Genomic instability is a hallmark of cancer. Whether it also occurs in Cancer Associated Fibroblasts (CAFs) remains to be carefully investigated. Loss of CSL/RBP-Jκ, the effector of canonical NOTCH signaling with intrinsic transcription repressive function, causes conversion of dermal fibroblasts into CAFs. Here, we find that CSL down-modulation triggers DNA damage, telomere loss and chromosome end fusions that also occur in skin Squamous Cell Carcinoma (SCC)-associated CAFs, in which CSL is decreased. Separately from its role in transcription, we show that CSL is part of a multiprotein telomere protective complex, binding directly and with high affinity to telomeric DNA as well as to UPF1 and Ku70/Ku80 proteins and being required for their telomere association. Taken together, the findings point to a central role of CSL in telomere homeostasis with important implications for genomic instability of cancer stromal cells and beyond.

Telomere Structure, Function, and Maintenance in Plants

Telomeres in eukaryotes comprise specific repetitive DNA sequences and binding proteins. Since their absence results in chromosomal end fusions and gene deletions, they are considered critical for genomic stability. In plants, as in yeasts and mammals, telomeres are essential for normal development and differentiation. Despite recent discoveries concerning plant telomeres, many questions remain about the mechanism of telomere homeostasis in plants. In this review, we summarize the roles of telomeres and telomerasebinding proteins in plant biology and explain how the length of a plant telomere is regulated.

CTCF prevents genomic instability by promoting homologous recombination-directed DNA double-strand break repair

CTCF is an essential epigenetic regulator mediating chromatin insulation, long-range regulatory interactions, and the organization of large topological domains in the nucleus. Phenotypes of CTCF haploinsufficient mutations in humans, knockout in mice, and depletion in cells are often consistent with impaired genome stability, but a role of CTCF in genome maintenance has not been fully investigated. Here, we report that CTCF maintains genome stability, is recruited to sites of DNA damage, and promotes homologous recombination repair of DNA double-strand breaks (DSBs). CTCF depletion increased chromosomal instability, marked by chromosome breakage and end fusions, elevated genotoxic stress-induced genomic DNA fragmentation, and activated the ataxia telangiectasia mutated (ATM) kinase. We show that CTCF could be recruited to drug-induced 53BP1 foci and known fragile sites, as well as to I-SceI endonuclease-induced DSBs. Laser irradiation analysis revealed that this recruitment depends on ATM, Nijmegen breakage syndrome (NBS), and the zinc finger DNA-binding domain of CTCF. We demonstrate that CTCF knockdown impaired homologous recombination (HR) repair of DSBs. Consistent with this, CTCF knockdown reduced the formation of γ-radiation-induced Rad51 foci, as well as the recruitment of Rad51 to laser-irradiated sites of DNA lesions and to I-SceI-induced DSBs. We further show that CTCF is associated with DNA HR repair factors MDC1 and AGO2, and directly interacts with Rad51 via its C terminus. These analyses establish a direct, functional role of CTCF in DNA repair and provide a potential link between genome organization and genome stability.

Guarding chromosomes from oxidative DNA damage to the very end.

The ends of each chromosome are capped by the telomere assembly to protect chromosomal integrity from telomere attrition and DNA damage. In response to DNA damage, DNA repair factors are enriched at damage sites by a sophisticated signaling and recruitment cascade. However, DNA damage response at telomeres is different from non-telomeric region of genomic DNA due to specialized sequences and structures of the telomeres. In the course of normal DNA replication or DNA damage repair, both the telomere shelterin protein complex and the condensed telomeric chromatin structure in mammalian cells are modified to protect telomeres from exposing free DNA ends which are subject to both telemere shortening and chromosome end fusion. Initiation of either homologous recombination or non-homologous end joint repair at telomeres requires disassembling and/or post-translational modifications of the shelterin complex and telomeric chromatin. In addition, cancer cells utilize distinct mechanisms to maintain telomere length and cell survival upon damage. In this review, we summarize current studies that focus on telomere end protection and telomere DNA repair using different methodologies to model telomere DNA damage and disruption. These include genetic ablation of sheltering proteins, targeting endonuclease to telomeres, and delivering oxidative damage directly. These different approaches, when combined, offer better understanding of the mechanistic differences in DNA damage response between telomeric and genomic DNA, which will provide new hope to identify potential cancer therapeutic targets to curtail cancer cell proliferation via induction of telomere dysfunctions.

ERK1/2/MAPK pathway-dependent regulation of the telomeric factor TRF2.

Telomere stability is a hallmark of immortalized cells, including cancer cells. While the telomere length is maintained in most cases by the telomerase, the activity of a protein complex called Shelterin is required to protect telomeres against unsuitable activation of the DNA damage response pathway. Within this complex, telomeric repeat binding factor 2 (TRF2) plays an essential role by blocking the ataxia telangiectasia-mutated protein (ATM) signaling pathway at telomeres and preventing chromosome end fusion. We showed that TRF2 was phosphorylated in vitro and in vivo on serine 323 by extracellular signal-regulated kinase (ERK1/2) in both normal and cancer cells. Moreover, TRF2 and activated ERK1/2 unexpectedly interacted in the cytoplasm of tumor cells and human tumor tissues. The expression of non-phosphorylatable forms of TRF2 in melanoma cells induced the DNA damage response, leading to growth arrest and tumor reversion. These findings revealed that the telomere stability is under direct control of one of the major pro-oncogenic signaling pathways (RAS/RAF/MEK/ERK) via TRF2 phosphorylation.

Engineering of plant chromosomes.

Engineered minimal chromosomes with sufficient mitotic and meiotic stability have an enormous potential as vectors for stacking multiple genes required for complex traits in plant biotechnology. Proof of principle for essential steps in chromosome engineering such as truncation of chromosomes by T-DNA-mediated telomere seeding and de novo formation of centromeres by cenH3 fusion protein tethering has been recently obtained. In order to generate robust protocols for application in plant biotechnology, these steps need to be combined and supplemented with additional methods such as site-specific recombination for the directed transfer of multiple genes of interest on the minichromosomes. At the same time, the development of these methods allows new insight into basic aspects of plant chromosome functions such as how centromeres assure proper distribution of chromosomes to daughter cells or how telomeres serve to cap the chromosome ends to prevent shortening of ends over DNA replication cycles and chromosome end fusion.

Nucleoplasmic bridges and acrocentric chromosome associations as early markers of exposure to low levels of ionising radiation in occupationally exposed hospital workers.

Ionising radiation, with the contribution of telomere shortening, induces DNA double-strand breaks that result in chromosome end fusion, nucleoplasmic bridges (NPBs) and chromosome aberrations (ChAbs) as well as dicentric chromosomes. In order to investigate the chromosomal damage induced by occupational ionising radiation at low exposure levels, and to find early markers of health hazard, peripheral lymphocytes of occupationally exposed hospital workers were cytogenetically analysed. Results showed a significant difference in the frequency of ChAbs in exposed subjects relative to controls. A significant number of NPBs between nuclei of binucleated cultured lymphocytes from exposed subjects were also observed, as well as a consistent amount of acrocentric chromosomes with associations of their short arms. Excluding confounding factors, the frequencies of all these three biological endpoints differed significantly in exposed subjects from those in controls. Because the absence of telomeres and/or their short length could be a common root for both the findings, we utilised fluorescence in situ hybridisation technique with telomeric repeat as probe to demonstrate that, in exposed subjects, chromatin of short arms of involved acrocentric chromosomes did not exhibit a telomeric shortening but appeared strongly decondensed. This finding suggests that NPBs and telomeric acrocentric association should be regarded as early markers of exposure to low levels of ionising radiation and their increase should be seen as an early warning for the health of the involved workers.

A telomerase-independent component of telomere loss in chromatin assembly factor 1 mutants of Arabidopsis thaliana

Dysfunction of chromatin assembly factor 1 in FASCIATA mutants (fas) of Arabidopsis thaliana results in progressive loss of telomeric DNA. Although replicative telomere shortening is typically associated with incomplete resynthesis of their ends by telomerase, no change in telomerase activity could be detected in vitro in extracts from fas mutants. Besides a possible telomerase malfunction, the telomere shortening in fas mutants could presumably be due to problems with conventional replication of telomeres. To distinguish between the possible contribution of suboptimal function of telomerase in fas mutants under in vivo conditions and problems in conventional telomere replication, we crossed fas and tert (telomerase reverse transcriptase) knockout mutants and analyzed telomere shortening in segregated fas mutants, tert mutants, and double fas tert mutants in parallel. We demonstrate that fas tert knockouts show greater replicative telomere shortening than that observed even in the complete absence of telomerase (tert mutants). While the effect of tert and fas mutations on telomere lengths in double mutants is additive, manifestations of telomere dysfunction in double fas tert mutants (frequency of anaphase bridges, onset of chromosome end fusions, and common involvement of 45S rDNA in chromosome fusion sites) are similar to those in tert mutants. We conclude that in addition to possible impairment of telomerase action, a further mechanism contributes to telomere shortening in fas mutants.

Overexpression of hTERT in potentially malignant colorectal laterally spreading tumors

Human telomerase reverse transcriptase (hTERT) is the main subunit of the core enzyme telomerase, which consists of three subunits. Telomeres are essential for chromosomal stability and integrity, protecting the ends of chromosomes from degradation and preventing chromosomal end fusions and recombination. A loss of telomere function is a major mechanism for the generation of chromosomal abnormalities. Telomere shortening leads to mutations, chromosome rearrangements and translocations. Colorectal laterally spreading tumors (LSTs) are a special type of superficial colorectal tumor. They are considered to have a high malignancy potential. The aim of the present study was to characterize the expression of hTERT in an LST cell line and paraffin sections. Immunohistochemistry was utilized to examine the protein expression of hTERT in the LST cell line, 48resected LSTs, 48protruded-type colorectal adenomas (PAs) and 48normal mucosa samples. Statistical analyses were applied to test the associations between hTERT expression and clinicopathological parameters. The present study demonstrated that the positive expression levels of hTERT in LSTs, PAs and normal mucosa were 60.4, 22.9 and 10%, respectively. Compared with polypi and normal mucosa, the expression levels of hTERT were significantly increased in LSTs. The expression of hTERT was also observed in the LST cell line. The expression of hTERT was significantly higher in LSTs, which may indicate a potential for malignancy.

Telomere recombination and alternative telomere lengthening mechanisms

Telomeres are nucleoprotein structures at the ends of linear chromosomes that protect them from being recognized as DNA double stranded breaks. Telomeres shorten with every cell division and in the absence of the checkpoint mechanisms critical telomere shortening leads to chromosome end fusions and genomic instability. Cancer cells achieve immortality by engaging in one of the two known mechanisms for telomere maintenance: elongation by telomerase or through recombination. Recombination based elongation of telomeres, also known as alternative lengthening of telomeres or ALT, is prevalent among cancers of mesenchymal origin. However, the conditions favoring ALT emergence are not known. Here we will discuss possible players in ALT mechanisms, including recruitment of telomeres to recombination centers, alterations of telomere associated proteins and modifications at the level of chromatin that could generate recombination permissive conditions at telomeres.

Oligonucleotide Models of Telomeric DNA and RNA Form a Hybrid G-quadruplex Structure as a Potential Component of Telomeres

Telomeric repeat-containing RNA, a non-coding RNA molecule, has recently been found in mammalian cells. The detailed structural features and functions of the telomeric RNA at human chromosome ends remain unclear, although this RNA molecule may be a key component of the telomere machinery. In this study, using model human telomeric DNA and RNA sequences, we demonstrated that human telomeric RNA and DNA oligonucleotides form a DNA-RNA G-quadruplex. We next employed chemistry-based oligonucleotide probes to mimic the naturally formed telomeric DNA-RNA G-quadruplexes in living cells, suggesting that the process of DNA-RNA G-quadruplex formation with oligonucleotide models of telomeric DNA and RNA could occur in cells. Furthermore, we investigated the possible roles of this DNA-RNA G-quadruplex. The formation of the DNA-RNA G-quadruplex causes a significant increase in the clonogenic capacity of cells and has an effect on inhibition of cellular senescence. Here, we have used a model system to provide evidence about the formation of G-quadruplex structures involving telomeric DNA and RNA sequences that have the potential to provide a protective capping structure for telomere ends.

The Mph1 Helicase Can Promote Telomere Uncapping and Premature Senescence in Budding Yeast

Double strand breaks (DSBs) can be repaired via either Non-Homologous End Joining (NHEJ) or Homology directed Repair (HR). Telomeres, which resemble DSBs, are refractory to repair events in order to prevent chromosome end fusions and genomic instability. In some rare instances telomeres engage in Break-Induced Replication (BIR), a type of HR, in order to maintain telomere length in the absence of the enzyme telomerase. Here we have investigated how the yeast helicase, Mph1, affects DNA repair at both DSBs and telomeres. We have found that overexpressed Mph1 strongly inhibits BIR at internal DSBs however allows it to proceed at telomeres. Furthermore, while overexpressed Mph1 potently inhibits NHEJ at telomeres it has no effect on NHEJ at DSBs within the chromosome. At telomeres Mph1 is able to promote telomere uncapping and the accumulation of ssDNA, which results in premature senescence in the absence of telomerase. We propose that Mph1 is able to direct repair towards HR (thereby inhibiting NHEJ) at telomeres by remodeling them into a nuclease-sensitive structure, which promotes the accumulation of a recombinogenic ssDNA intermediate. We thus put forward that Mph1 is a double-edge sword at the telomere, it prevents NHEJ, but promotes senescence in cells with dysfunctional telomeres by increasing the levels of ssDNA.

CHIP Promotes Human Telomerase Reverse Transcriptase Degradation and Negatively Regulates Telomerase Activity

The maintenance of eukaryotic telomeres requires telomerase, which is minimally composed of a telomerase reverse transcriptase (TERT) and an associated RNA component. Telomerase activity is tightly regulated by expression of human (h) TERT at both the transcriptional and post-translational levels. The Hsp90 and p23 molecular chaperones have been shown to associate with hTERT for the assembly of active telomerase. Here, we show that CHIP (C terminus of Hsc70-interacting protein) physically associates with hTERT in the cytoplasm and regulates the cellular abundance of hTERT through a ubiquitin-mediated degradation. Overexpression of CHIP prevents nuclear translocation of hTERT and promotes hTERT degradation in the cytoplasm, thereby inhibiting telomerase activity. In contrast, knockdown of endogenous CHIP results in the stabilization of cytoplasmic hTERT. However, it does not affect the level of nuclear hTERT and has no effect on telomerase activity and telomere length. We further show that the binding of CHIP and Hsp70 to hTERT inhibits nuclear translocation of hTERT by dissociating p23. However, Hsp90 binding to hTERT was not affected by CHIP overexpression. These results suggest that CHIP can remodel the hTERT-chaperone complexes. Finally, the amount of hTERT associated with CHIP peaks in G(2)/M phases but decreases during S phase, suggesting a cell cycle-dependent regulation of hTERT. Our data suggest that CHIP represents a new pathway for modulating telomerase activity in cancer.

Localization of αII Spectrin to Telomeres After DNA Interstrand Cross-Link Damage Is Deficient In Fanconi Anemia Group A Cells, Which May Lead to Telomere Dysfunction.

AbstractAbstract 1160A hallmark of the bone marrow failure disorder, Fanconi anemia (FA), is genomic instability which is characterized by both chromosome instability and defects in repair of DNA interstrand cross-links (ICLs). The chromosome instability in FA, in particular chromosome end fusions and breaks, suggests that there is telomere dysfunction. We have shown that the structural protein, nonerythroid a spectrin (aIISp), is present in the nucleus of normal human cells where it is critical in both repair of DNA ICLS and maintaining chromosome stability. aIISp is important in recruitment of the ICL repair protein, XPF, to sites of damage. We have shown that there is a deficiency in aIISp in FA cells lines, due to its increased breakdown, which correlates with reduced repair of DNA ICLs and increased chromosomal aberrations after ICL damage. The goal of the present study was to determine whether aIISp plays a role in telomere function after DNA ICL damage and whether telomere dysfunction in FA cells after damage can be corrected when levels of aIISp are restored to normal. Normal human and FA, complementation group A (FA-A) lymphoblastoid cells, which have telomerase, were used. Undamaged cells or cells treated with mitomycin C (MMC), a DNA ICL agent, were studied using immunofluorescence and in situ hybridization (IF-FISH). Cells were probed with anti-a-spectrin and either (C3TA2)3-Cy3 labeled peptide nucleic acid (PNA) telomeric probe or antibodies against two proteins, TRF1 or TRF2, which are components of the shelterin complex that is essential for protecting chromosome ends and preventing telomere dysfunction. The appropriate fluorescent secondary antibodies were used. The results showed that 47–50% of aIISp foci colocalized with the PNA probe, TRF1 or TRF2 in telomeres in MMC damaged but not undamaged normal cells. Levels of colocalization peaked at 16 hours and, by 24 hours, aIISp foci were no longer observed. This colocalization was specific for the S phase of the cell cycle. These results showed that in normal cells aIISp associates with telomeres in S phase after ICL damage and may play an important role in telomere function after damage. After ICLs are presumably unhooked/removed, aIISp dissociates from telomeres. The view that aIISp is involved in telomere function after ICL damage is strengthened by coimmunoprecipitation studies which show that aIISp has markedly enhanced binding for TRF1 and TFR2 after cells were damaged with MMC. IF-FISH also showed that the ICL repair protein, XPF, had enhanced association with telomeres after ICL damage, which further indicated that repair is taking place. In FA-A cells, in which aIISp levels are reduced, aIISp did not colocalize with the PNA probe, with TRF1 or with TRF2 after ICL damage; XPF also did not localize to telomeres after ICL formation. However, after aIISp levels were returned to normal in FA-A cells by siRNA knock down of m-calpain, a protease which cleaves aIISp and levels of which are elevated in FA cells, aIISp as well as XPF associated with telomeres after ICL damage. The chromosomal aberrations (i.e., breaks and end fusions) observed in FA-A cells after ICL damage were also corrected. ICLs can lead to stalled DNA replication forks in S phase. The present results suggest that, after damage, aIISp associates with telomeres in S phase at ICLs at stalled replication forks. Since aIISp is involved in ICL repair, this association could be of particular importance in repair of ICLs in replicating telomeres. In FA-A cells, failure of localization of aIISp and XPF to telomeres after ICL damage could have severe consequences. It could lead to unrepaired ICLs, which in replicating telomeres could lead to telomere dysfunction and to production of the chromosomal aberrations observed in these cells. These studies show that aIISp may play an important role in telomere function after DNA damage and during telomere replication. Correction of the deficiency in aIISp in FA cells by knocking down m-calpain could be significant in reversing telomere dysfunction and chromosomal aberrations after ICL damage and could potentially have important therapeutic relevance. Disclosures:No relevant conflicts of interest to declare.