Yeast telomere capping protein Stn1 overrides DNA replication control through the S phase checkpoint

Telomere integrity is maintained through end-protection proteins that block nuclease degradation and prevent telomeres from being recognized as DNA breaks. Although less well understood, end protection proteins may also play a role in facilitating telomere replication. Here, we show that overproduction (OP) of the yeast telomere capping protein Stn1 makes cells highly sensitive to the replication inhibitors hydroxyurea (HU) and methyl-methane sulfonate (MMS). Unexpectedly, this sensitivity corresponds with Stn1 OP blocking most, if not all, aspects of the S phase checkpoint. The checkpoint kinase Rad53 is phosphorylated with normal timing in Stn1 OP cells, indicating Stn1 does not interfere with signaling steps involved in activating the checkpoint. Part of the role of Stn1 in telomere integrity is mediated through the Pol12 subunit of DNA polymerase α (Polα). We show that overproduced Stn1 generally associates with chromosomes in HU treated and untreated cells, and, remarkably, Stn1 chromosome binding and OP checkpoint defects are rescued in pol12 mutants. We propose Stn1 normally promotes Polα activity at telomeres but can be recruited through Pol12 to nontelomeric sites when overproduced. During replication stress, the mislocalized Stn1 may inappropriately promote Polα in a manner that interferes with Rad53 effector mechanisms controlling replication fork integrity.     

Lack of positional requirements for autonomously replicating sequence elements on artificial yeast chromosomes.

In the yeast Saccharomyces cerevisiae, origins of replication (autonomously replicating sequences; ARSs), centromeres, and telomeres have been isolated and characterized. The identification of these structures allows the construction of artificial chromosomes in which the architecture of eukaryotic chromosomes may be studied. A common feature of most, and possibly all, natural yeast chromosomes is that they have an ARS within 2 kilobases of their physical ends. To study the effects of such telomeric ARSs on chromosome maintenance, we introduced artificial chromosomes of approximately 15 and 60 kilobases into yeast cells and analyzed the requirements for telomeric ARSs and the effects of ARS-free chromosomal arms on the stability of these molecules. We find that terminal blocks of telomeric repeats are sufficient to be recognized as telomeres. Moreover, artificial chromosomes containing telomere-associated Y' sequences and telomeric ARSs were no more stable during both mitosis and meiosis than artificial chromosomes lacking terminal ARSs, indicating that yeast-specific blocks of telomeric sequences are the only cis-acting requirement for a functional telomere during both mitotic growth and meiosis. The results also show that there is no requirement for an origin of replication on each arm of the artificial chromosomes, indicating that a replication fork may efficiently move through a functional centromere region.     

Ataxia telangiectasia mutated (Atm) is not required for telomerase-mediated elongation of short telomeres

Telomerase-mediated telomere addition counteracts telomere shortening due to incomplete DNA replication. Short telomeres are the preferred substrate for telomere addition by telomerase; however, the mechanism by which telomerase recognizes short telomeres is unclear. In yeast, the Ataxia telangiectasia mutated (Atm) homolog, Tel1, is necessary for normal telomere length regulation likely by altering telomere structure, allowing telomerase recruitment to short telomeres. To examine the role of Atm in establishing preference for elongation of short telomeres in mice, we examined telomerase-mediated elongation of short dysfunctional telomeres in the presence or absence of Atm. Here we show that Atm is dispensable for elongation of short telomeres by telomerase, suggesting that telomerase recruitment in mammalian cells and in yeast may be regulated differently.     

Probing PML body function in ALT cells reveals spatiotemporal requirements for telomere recombination

Promyelocytic leukemia (PML) bodies (also called ND10) are dynamic nuclear structures implicated in a wide variety of cellular processes. ALT-associated PML bodies (APBs) are specialized PML bodies found exclusively in telomerase-negative tumors in which telomeres are maintained by recombination-based alternative (ALT) mechanisms. Although it has been suggested that APBs are directly implicated in telomere metabolism of ALT cells, their precise role and structure have remained elusive. Here we show that PML bodies in ALT cells associate with chromosome ends forming small, spatially well-defined clusters, containing on average 2–5 telomeres. Using an innovative approach that gently enlarges PML bodies in living cells while retaining their overall organization, we show that this physical enlargement of APBs spatially resolves the single telomeres in the cluster, but does not perturb the potential of the APB to recruit chromosome extremities. We show that telomere clustering in PML bodies is cell-cycle regulated and that unique telomeres within a cluster associate with recombination proteins. Enlargement of APBs induced the accumulation of telomere-telomere recombination intermediates visible on metaphase spreads and connecting heterologous chromosomes. The strand composition of these recombination intermediates indicated that this recombination is constrained to a narrow time window in the cell cycle following replication. These data provide strong evidence that PML bodies are not only a marker for ALT cells but play a direct role in telomere recombination, both by bringing together chromosome ends and by promoting telomere-telomere interactions between heterologous chromosomes.     

Generation of telomere-length heterogeneity in Saccharomyces cerevisiae.

Chromosome ends in the lower eukaryotes terminate in variable numbers of tandem, simple DNA repeats. We tested predictions of a model in which these telomeric repeats provide a substrate for the addition of more repeats by a terminal transferase-like mechanism that, in concert with DNA polymerase and primase, effectively counterbalances the loss of DNA due to degradation or incomplete replication. For individual chromosome ends in yeast, the mean length of any given telomere was shown to vary between different clonal populations of the same strain and to be determined by the initial length of that telomere in the single cell giving rise to the clone. This type of variation was independent of the major yeast recombination pathway. The length heterogeneity at each telomeric end increased with additional rounds of cell division or DNA replication. Lengths of individual telomeres within a single clone varied independently of each other. Thus, this clonal variability is distinct from genetic regulation of chromosome length, which acts on all chromosome ends coordinately. These in vivo phenomena suggest that lengthening and shortening activities act on yeast telomeres during each round of replication.     

Simulated shortening of proliferation-restricting telomeres during clonal proliferation and senescence of human cells

In the absence of telomerase or other mechanisms to maintain their length, telomeres in human cells shorten at each round of cell division. This has been suggested to ultimately cause cell cycle exit when a critical telomere length is reached, leading to replicative senescence of the cell. At present, it is not clear whether the division potential of human cells is limited by the overall shortening of telomeres at all chromosomes or the shortening of specific telomeres on certain particular chromosomes. By computer simulations, my previous work has suggested that if the telomere theory is correct, the shortening of only a few, most likely two, telomeres might be preferentially involved in restricting the division of human cells. In this work, the length dynamics of individual telomeres in simulated cell clones were examined over their life span. It is shown that if the shortening of only two telomeres is responsible for restricting the proliferation of a cell, these two specific telomeres will shorten at different rates and have different length distributions from those of the rest telomeres. The unique pattern of length dynamics associated with the proliferation-restricting telomeres (PRT) provides a possibility of experimentally identifying these particular telomeres in human cells.     

端粒长度与心血管疾病危险因素关系的研究进展

端粒是位于染色体末端的DNA重复序列,其功能是阻止染色体末端不被断裂和降解,维持染色体结构稳定和遗传稳定性,且随着细胞分裂而不断缩短,所以端粒长度可以作为生物衰老过程中的一个重要标记物。与2型糖尿病、阿尔茨海默病和骨质疏松等疾病一样,冠心病（CHD）也是一种年龄相关性疾病。端粒长度和CHD与机体衰老、退化均有着密切联系,且已有相关研究证明,白细胞端粒长度与CHD患病风险之间可能存在相关性,提示端粒可能参与了CHD的发生、发展,但其因果关系尚不明确。因此我们猜测端粒是否通过影响CHD的传统危险因素,进而促进CHD的发生、发展。本文就白细胞端粒长度与CHD传统危险因素关系研究进展作一综述。     

Telomeres in the mouse have large inter-chromosomal variations in the number of T2AG3 repeats

The ultra-long telomeres that have been observed in mice are not in accordance with the concept that critical telomere shortening is related to aging and immortalization. Here, we have used quantitative fluorescence in situ hybridization to estimate (T₂AG₃)_n lengths of individual telomeres in various mouse strains. Telomere lengths were very heterogeneous, but specific chromosomes of bone marrow cells and skin fibroblasts from individual mice had similar telomere lengths. We estimate that the shortest telomeres are around 10 kb in length, indicating that each mouse cell has a few telomeres with (T₂AG₃)_n lengths within the range of human telomeres. These short telomeres may be critical in limiting the replicative potential of murine cells.     

Abrupt disruption of capping and a single source for recombinationally elongated telomeres in Kluyveromyces lactis

Eukaryotic cells, including some human cancers, that lack telomerase can sometimes maintain telomeres by using recombination. It was recently proposed that recombinational telomere elongation (RTE) in a telomerase-deletion mutant of the yeast Kluyveromyces lactis occurs through a roll-and-spread mechanism as described in our previous work. According to this model, a tiny circle of telomeric DNA is copied by a rolling-circle mechanism to generate one long telomere, the sequence of which is then spread to all other telomeres by gene-conversion events. In support of this model, we demonstrate here that RTE in K. lactis occurs by amplification of a sequence originating from a single telomere. When a mutationally tagged telomere is of normal length, its sequence is spread to all other telomeres at a frequency (≈10%) consistent with random selection among the 12 telomeres in the cell. However, when the mutationally tagged telomere is considerably longer than other telomeres, cellular senescence is partially suppressed, and the sequence of the tagged telomere is spread to all other telomeres in >90% of cells. Strikingly, the transition between a state resistant to recombination and a state capable of initiating recombination is abrupt, typically occurring when telomeres are ≈3–4 repeats long. Last, we show that mutant repeats that are defective at regulating telomerase are also defective at regulating telomere length during RTE.     

Transmembrane protein Sun2 is involved in tethering mammalian meiotic telomeres to the nuclear envelope

Dynamic repositioning of telomeres is a unique feature of meiotic prophase I that is highly conserved among eukaryotes. At least in fission yeast it was shown to be required for proper alignment and recombination of homologous chromosomes. On entry into meiosis telomeres attach to the nuclear envelope and transiently cluster at a limited area to form a chromosomal bouquet. Telomere clustering is thought to promote chromosome recognition and stable pairing of the homologs. However, the molecular basis of telomere attachment and movement is largely unknown. Here we report that mammalian SUN-domain protein Sun2 specifically localizes to the nuclear envelope attachment sites of meiotic telomeres. Sun2-telomere association is maintained throughout the dynamic movement of telomeres. This association does not require the assembly of chromosomal axial elements or the presence of A-type lamins. Detailed EM analysis revealed that Sun2 is part of a membrane-spanning fibrillar complex that interconnects attached telomeres with cytoplasmic structures. Together with recent findings in fission yeast, our study indicates that the molecular mechanisms required for tethering meiotic telomeres and their dynamic movements during bouquet formation are conserved among eukaryotes.     

Telomerase activity in human ovarian carcinoma.

Telomeres fulfill the dual function of protecting eukaryotic chromosomes from illegitimate recombination and degradation and may aid in chromosome attachment to the nuclear membrane. We have previously shown that telomerase, the enzyme which synthesizes telomeric DNA, is not detected in normal somatic cells and that telomeres shorten with replicative age. In cells immortalized in vitro, activation of telomerase apparently stabilizes telomere length, preventing a critical destabilization of chromosomes, and cell proliferation continues even when telomeres are short. In vivo, telomeres of most tumors are shorter than telomeres of control tissues, suggesting an analogous role for the enzyme. To assess the relevance of telomerase and telomere stability in the development and progression of tumors, we have measured enzyme activity and telomere length in metastatic cells of epithelial ovarian carcinoma. We report that extremely short telomeres are maintained in these cells and that tumor cells, but not isogenic nonmalignant cells, express telomerase. Our findings suggest that progression of malignancy is ultimately dependent upon activation of telomerase and that telomerase inhibitors may be effective antitumor drugs.     

Conserved nucleoprotein structure at the ends of vertebrate and invertebrate chromosomes.

Eukaryotic chromosomes terminate with telomeres, nucleoprotein structures that are essential for chromosome stability. Vertebrate telomeres consist of terminal DNA tracts of sequence (TTAGGG)n, which in rat are predominantly organized into nucleosomes regularly spaced by 157 bp. To test the hypothesis that telomeres of other animals have nucleosomes, we compared telomeres from eight vertebrate tissues and cell cultures, as well as two tissues from an invertebrate. All telomeres have substantial tracts of (TTAGGG)n comprising 0.01-0.2% of the genome. All telomeres are long (20-100 kb), except for those of sea urchin, human, and some chicken chromosomes, which are 3-10 kb in length. All of the animal telomeres contained nucleosome arrays, consistent with the original hypothesis. The telomere repeat lengths vary from 151 to 205 bp, seemingly uncorrelated with telomere size, regularity of nucleosome spacing, species, or state of differentiation but surprisingly correlated with the repeat of bulk chromatin within the same cells. The telomere nucleosomes were consistently approximately 40 bp smaller than bulk nucleosomes. Thus, animal telomeres have highly conserved sequences and unusually short nucleosomes with cell-specific structure.     

Structural variation of the pseudoautosomal region between and within inbred mouse strains.

The pseudoautosomal region (PAR) is a segment of shared homology between the sex chromosomes. Here we report additional probes for this region of the mouse genome. Genetic and fluorescence in situ hybridization analyses indicate that one probe, PAR-4, hybridizes to the pseudoautosomal telomere and a minor locus at the telomere of chromosome 9 and that a PCR assay based on the PAR-4 sequence amplifies only the pseudoautosomal locus (DXYHgu1). The region detected by PAR-4 is structurally unstable; it shows polymorphism both between mouse strains and between animals of the same inbred strain, which implies an unusually high mutation rate. Variation occurs in the region adjacent to a (TTAGGG)n array. Two pseudoautosomal probes can also hybridize to the distal telomeres of chromosomes 9 and 13, and all three telomeres contain DXYMov15. The similarity between these telomeres may reflect ancestral telomere-telomere exchange.     

Bone marrow failure and the new telomere diseases: practice and research

The telomeropathies are a newly described group of human diseases based on the genetics and molecular biology of the telomeres, the ends of chromosomes. Telomeres are repeated hexanucleotides and their associated proteins; the protect chromosomes from recognition as damaged DNA, and their inevitable gradual loss with DNA replication is harmless as they are noncoding. However, when telomeres become critically short in a cell, senescence, apoptosis, or, rarely malignant transformation results. In individuals with mutations in genes involved in telomere repair, especially the enzymatic telomerase complex, telomere attrition is accelerated. Severe deficiencies result in dyskeratosis congenita, a congenital aplastic anemia with associated mucocutaneous abnormalities. Mutations in TERT, the catalytic component, and TERC, the RNA template, can behave as risk factors for the development of bone marrow failure, pulmonary fibrosis, and hepatic cirrhosis. Both penetrance and organ specificity are variable and not well understood. Chromosome instability is a result of critical shortening of telomeres and cancer. For example, short telomeres are the major prognostic risk factor for clonal evolution to myelodysplasia and acute leukemia. Practically, hematologists need to recognize the multisystem presentation of telomere disease, implications for outcomes, and options for therapy.     

Telomere length, telomeric proteins and genomic instability during the multistep carcinogenic process

Telomeres form specialized structures at the ends of eukaryotic chromosomes, preventing them from being wrongly recognized as DNA damage. The human telomere DNA sequence is a tandem repetition of the sequence TTAGGG. In normal cells, the DNA replication machinery is unable to completely duplicate the telomeric DNA; thus, telomeres are shortened after every cell division. Having reached a critical length, telomeres may be recognized as double strand break DNA lesions, and cells eventually enter senescence. Carcinogenesis is a multistep process involving multiple mutations and chromosomal aberrations. One of the most prevalent aberrations in pre-cancerous lesions is telomere shortening and telomerase activation. We discuss the role and homeostasis of telomeres in normal cells and their implication in the early steps of carcinogenesis. We also discuss various techniques used, and their limitations, in the study of telomeres and genome instability and their role in carcinogenesis and related genomic modifications.     

INAUGURAL ARTICLE by a Recently Elected Academy Member:Circular permutation of a synthetic eukaryotic chromosome with the telomerator

Chromosome engineering is a major focus in the fields of systems biology, genetics, synthetic biology, and the functional analysis of genomes. Here, we describe the “telomerator,” a new synthetic biology device for use in Saccharomyces cerevisiae. The telomerator is designed to inducibly convert circular DNA molecules into mitotically stable, linear chromosomes replete with functional telomeres in vivo. The telomerator cassette encodes convergent yeast telomere seed sequences flanking the I-SceI homing endonuclease recognition site in the center of an intron artificially transplanted into the URA3 selectable/counterselectable auxotrophic marker. We show that inducible expression of the homing endonuclease efficiently generates linear molecules, identified by using a simple plate-based screening method. To showcase its functionality and utility, we use the telomerator to circularly permute a synthetic yeast chromosome originally constructed as a circular molecule, synIXR, to generate 51 linear variants. Many of the derived linear chromosomes confer unexpected phenotypic properties. This finding indicates that the telomerator offers a new way to study the effects of gene placement on chromosomes (i.e., telomere proximity). However, that the majority of synIXR linear derivatives support viability highlights inherent tolerance of S. cerevisiae to changes in gene order and overall chromosome structure. The telomerator serves as an important tool to construct artificial linear chromosomes in yeast; the concept can be extended to other eukaryotes.Chromosome engineering is the study of genetic modifications that affect large segments of chromosomes. Top-down approaches start with preexisting chromosomes and modify them in vivo by introducing, for instance, deletions, translocations, or duplications. Bottom-up approaches involve design and construction of chromosomes de novo. To facilitate successful chromosome engineering efforts, we need a strong understanding of chromosomal features that confer mitotic stability such as centromeres, telomeres, and replication origins. Moreover, it is important to appreciate the effects of the spatial relationships between such elements and other critical features such as genes.The Saccharomyces cerevisiae genome is an excellent platform to develop tools for eukaryotic chromosome engineering given its ease of genetic manipulation. The S. cerevisiae genome is composed of 12 Mb of DNA organized as 16 linear chromosomes ranging in size from 230 kb to more than 2 Mb (1). Three important cis elements are required to maintain chromosome stability through mitosis and meiosis: Compact point centromeres (∼125 bp) ensure faithful segregation of sister chromatids (2) and homologs in meiosis I, replication origins are necessary for genome duplication before cell division (3, 4), and conserved telomere sequences protect chromosome ends ensuring maintenance of chromosome length during replication (5, 6). With these elements intact, many lines of evidence indicate that budding yeast tolerate a high degree of chromosomal modification without affecting viability. For instance: (i) the largest yeast chromosome (IV) can be subdivided into 11 separate minichromosomes (7); (ii) more than 500 kb, including 247 nonessential genes, can be deleted in a single haploid strain (8); (iii) any of the 16 chromosomes can be individually destabilized in a diploid cell to generate a chromosomal complement of 2n−1 (9); (iv) synthetic chromosomes such as synIII (10) and synIXR (11), built to the designer specifications of the Sc2.0 Yeast Genome Project, power growth of budding yeast in the absence of the corresponding native chromosomes (10, 11).With the goal of systematically and specifically perturbing the order and orientation of genetic elements on chromosomes in S. cerevisiae, we developed the telomerator, a genetic tool that can linearize circular DNA molecules in vivo on demand. Importantly, the linear derivatives generated via the telomerator encode functional telomeres and are thus mitotically stable. We used the telomerator to circularly permute the synthetic yeast chromosome, synIXR, encoded in the form of a bacterial artificial chromosome (BAC; herein referred to as synIXR BAC). In 51 viable linear permutants, we discovered substantial phenotypic diversity that depends on changes in expression of genes required for growth, mediated by telomere position effects. Further, our results support the conclusion that telomerator-induced linearization generates linear chromosomes with functional telomeres on which heterochromatin is fully established.