Ratcheted transport and sequential assembly of the yeast telomerase RNP

The telomerase ribonucleoprotein particle (RNP) replenishes telomeric DNA and minimally requires an RNA component and a catalytic protein subunit. However, telomerase RNP maturation is an intricate process occurring in several subcellular compartments and is incompletely understood. Here, we report how the co-transcriptional association of key telomerase components and nuclear export factors leads to an export-competent, but inactive, RNP. Export is dependent on the 5' cap, the 3' extension of unprocessed telomerase RNA, and protein associations. When the RNP reaches the cytoplasm, an extensive protein swap occurs, the RNA is trimmed to its mature length, and the essential catalytic Est2 protein joins the RNP. This mature and active complex is then reimported into the nucleus as its final destination and last processing steps. The irreversible processing events on the RNA thus support a ratchet-type model of telomerase maturation, with only a single nucleo-cytoplasmic cycle that is essential for the assembly of mature telomerase.

Telomere Replication: Solving Multiple End Replication Problems

Eukaryotic genomes are highly complex and divided into linear chromosomes that require end protection from unwarranted fusions, recombination, and degradation in order to maintain genomic stability. This is accomplished through the conserved specialized nucleoprotein structure of telomeres. Due to the repetitive nature of telomeric DNA, and the unusual terminal structure, namely a protruding single stranded 3′ DNA end, completing telomeric DNA replication in a timely and efficient manner is a challenge. For example, the end replication problem causes a progressive shortening of telomeric DNA at each round of DNA replication, thus telomeres eventually lose their protective capacity. This phenomenon is counteracted by the recruitment and the activation at telomeres of the specialized reverse transcriptase telomerase. Despite the importance of telomerase in providing a mechanism for complete replication of telomeric ends, the majority of telomere replication is in fact carried out by the conventional DNA replication machinery. There is significant evidence demonstrating that progression of replication forks is hampered at chromosomal ends due to telomeric sequences prone to form secondary structures, tightly DNA-bound proteins, and the heterochromatic nature of telomeres. The telomeric loop (t-loop) formed by invasion of the 3′-end into telomeric duplex sequences may also impede the passage of replication fork. Replication fork stalling can lead to fork collapse and DNA breaks, a major cause of genomic instability triggered notably by unwanted repair events. Moreover, at chromosomal ends, unreplicated DNA distal to a stalled fork cannot be rescued by a fork coming from the opposite direction. This highlights the importance of the multiple mechanisms involved in overcoming fork progression obstacles at telomeres. Consequently, numerous factors participate in efficient telomeric DNA duplication by preventing replication fork stalling or promoting the restart of a stalled replication fork at telomeres. In this review, we will discuss difficulties associated with the passage of the replication fork through telomeres in both fission and budding yeasts as well as mammals, highlighting conserved mechanisms implicated in maintaining telomere integrity during replication, thus preserving a stable genome.

Loss of Cdc13 causes genome instability by a deficiency in replication-dependent telomere capping

In budding yeast, Cdc13, Stn1, and Ten1 form the telomere-binding heterotrimer CST complex. Here we investigate the role of Cdc13/CST in maintaining genome stability by using a Chr VII disome system that can generate recombinants, chromosome loss, and enigmatic unstable chromosomes. In cells expressing a temperature sensitive CDC13 allele, cdc13^F684S, unstable chromosomes frequently arise from problems in or near a telomere. We found that, when Cdc13 is defective, passage through S phase causes Exo1-dependent ssDNA and unstable chromosomes that are then the source for additional chromosome instability events (e.g. recombinants, chromosome truncations, dicentrics, and/or chromosome loss). We observed that genome instability arises from a defect in Cdc13’s function during DNA replication, not Cdc13’s putative post-replication telomere capping function. The molecular nature of the initial unstable chromosomes formed by a Cdc13-defect involves ssDNA and does not involve homologous recombination nor non-homologous end joining; we speculate the original unstable chromosome may be a one-ended double strand break. This system defines a link between Cdc13’s function during DNA replication and genome stability in the form of unstable chromosomes, that then progress to form other chromosome changes.

Eukaryotic chromosomes are linear molecules with specialized end structures called telomeres. Telomeres contain both unique repetitive DNA sequences and specialized proteins that solve several biological problems by differentiating chromosomal ends from internal breaks, thus preventing chromosome instability. When telomeres are defective, the entire chromosome can become unstable and change, causing mutations and pathology (cancer, aging, etc.). Here we study how a defect in specific telomere proteins causes chromosomal rearrangements, using the model organism Saccharomyces cerevisiae (budding or brewer’s yeast). We find that when specific telomere proteins are defective, errors in DNA replication generate a type of damage that likely involves extensive single-stranded DNA that forms inherently unstable chromosomes, subject to many subsequent instances of instability (e.g. allelic recombinants, chromosome loss, truncations, dicentrics). The telomere protein Cdc13 is part of a protein complex called CST that is conserved in most organisms including mammalian cells. The technical capacity of studies in budding yeast allow a detailed, real-time examination of how telomere defects compromise chromosome stability in a single cell cycle, generating lessons likely relevant to how human telomeres keep human chromosomes stable.

Identification of telomerase RNAs in species of the Yarrowia clade provides insights into the co-evolution of telomerase, telomeric repeats and telomere-binding proteins

Telomeric repeats in fungi of the subphylum Saccharomycotina exhibit great inter- and intra-species variability in length and sequence. Such variations challenged telomeric DNA-binding proteins that co-evolved to maintain their functions at telomeres. Here, we compare the extent of co-variations in telomeric repeats, encoded in the telomerase RNAs (TERs), and the repeat-binding proteins from 13 species belonging to the Yarrowia clade. We identified putative TER loci, analyzed their sequence and secondary structure conservation, and predicted functional elements. Moreover, in vivo complementation assays with mutant TERs showed the functional importance of four novel TER substructures. The TER-derived telomeric repeat unit of all species, except for one, is 10 bp long and can be represented as 5′-TTNNNNAGGG-3′, with repeat sequence variations occuring primarily outside the vertebrate telomeric motif 5′-TTAGGG-3′. All species possess a homologue of the Yarrowia lipolytica Tay1 protein, YlTay1p. In vitro, YlTay1p displays comparable DNA-binding affinity to all repeat variants, suggesting a conserved role among these species. Taken together, these results add significant insights into the co-evolution of TERs, telomeric repeats and telomere-binding proteins in yeasts.

Nuclear import of Cdc13 limits chromosomal capping

Cdc13 is an essential protein involved in telomere maintenance and chromosome capping. Individual domain analyses on Cdc13 suggest the presence of four distinct OB-fold domains and one recruitment domain. However, it remained unclear how these sub-domains function in the context of the whole protein in vivo. Here, we use individual single domain deletions to address their roles in telomere capping. We find that the OB2 domain contains a nuclear localization signal that is essential for nuclear import of Cdc13 and therefore is required for chromosome capping. The karyopherin Msn5 is important for nuclear localization, and retention of Cdc13 in the nucleus also requires its binding to telomeres. Moreover, Cdc13 homodimerization occurs even if the protein is not bound to DNA and is in the cytoplasm. Hence, Cdc13 abundance in the nucleus and, in consequence, its capping function is strongly affected by nucleo-cytoplasmic transport as well as nuclear retention by DNA binding.

SETDB1-dependent heterochromatin stimulates alternative lengthening of telomeres

Alternative lengthening of telomeres, or ALT, is a recombination-based process that maintains telomeres to render some cancer cells immortal. The prevailing view is that ALT is inhibited by heterochromatin because heterochromatin prevents recombination. To test this model, we used telomere-specific quantitative proteomics on cells with heterochromatin deficiencies. In contrast to expectations, we found that ALT does not result from a lack of heterochromatin; rather, ALT is a consequence of heterochromatin formation at telomeres, which is seeded by the histone methyltransferase SETDB1. Heterochromatin stimulates transcriptional elongation at telomeres together with the recruitment of recombination factors, while disrupting heterochromatin had the opposite effect. Consistently, loss of SETDB1, disrupts telomeric heterochromatin and abrogates ALT. Thus, inhibiting telomeric heterochromatin formation in ALT cells might offer a new therapeutic approach to cancer treatment.