Search

The invention relates to a diagnostic comprising a polynucleotide and to therapeutic agent comprising a polyribonucleotide capable of inhibiting and/or reducing the activity of a telomerase for use in medicine. The invention further provides a method of diagnosing a proliferative disorder. Also provided are therapeutic agent and methods of using the same

Target therapy; Telomeres; Triple-negative breast cancer Terapia dirigida; Telómeros; Cáncer de mama triple negativo Teràpia dirigida; Telòmers; Càncer de mama triple negatiu The telomeric repeat-binding factor 2 (TRF2) is a telomere-capping protein that plays a key role in the maintenance of telomere structure and function. It is highly expressed in different cancer types, and it contributes to cancer progression. To date, anti-cancer strategies to target TRF2 remain a challenge. Here, we developed a miRNA-based approach to reduce TRF2 expression. By performing a high-throughput luciferase screening of 54 candidate miRNAs, we identified miR-182-3p as a specific and efficient post-transcriptional regulator of TRF2. Ectopic expression of miR-182-3p drastically reduced TRF2 protein levels in a panel of telomerase- or alternative lengthening of telomeres (ALT)-positive cancer cell lines. Moreover, miR-182-3p induced DNA damage at telomeric and pericentromeric sites, eventually leading to strong apoptosis activation. We also observed that treatment with lipid nanoparticles (LNPs) containing miR-182-3p impaired tumor growth in triple-negative breast cancer (TNBC) models, including patient-derived tumor xenografts (PDTXs), without affecting mouse survival or tissue function. Finally, LNPs-miR-182-3p were able to cross the blood–brain barrier and reduce intracranial tumors representing a possible therapeutic option for metastatic brain lesions. The research leading to these results has been funded by Italian Association for Cancer Research (AIRC # 21579) and Ministry of Health (CO-2019-12369662) to AB. This work was financially supported by Ministry of Health Ricerca Corrente 2022 and intramural grant-in-aid to EP. RD, LP and EP were supported by AIRC fellowships.

Pathways that direct the selection of the telomerase-dependent or recombination-based, alternative lengthening of telomere (ALT) maintenance pathway in cancer cells are poorly understood. Using human lung cancer cells and tumor organoids we show that formation of the 2,2,7-trimethylguanosine (TMG) cap structure at the human telomerase RNA 5′ end by the Trimethylguanosine Synthase 1 (TGS1) is central for recruiting telomerase to telomeres and engaging Cajal bodies in telomere maintenance. TGS1 depletion or inhibition by the natural nucleoside sinefungin impairs telomerase recruitment to telomeres leading to Exonuclease 1 mediated generation of telomere 3′ end protrusions that engage in RAD51-dependent, homology directed recombination and the activation of key features of the ALT pathway. This indicates a critical role for 2,2,7-TMG capping of the RNA component of human telomerase (hTR) in enforcing telomerase-dependent telomere maintenance to restrict the formation of telomeric substrates conductive to ALT. Our work introduces a targetable pathway of telomere maintenance that holds relevance for telomere-related diseases such as cancer and aging.

SUMMARY Biogenesis of the human telomerase RNA (hTR) involves a complex series of posttranscriptional modifications, including hypermethylation of the 5′ mono-methylguanosine cap to a tri-methylguanosine cap (TMG). How the TMG cap affects hTR maturation is unknown. Here, we show that depletion of trimethylguanosine synthase 1 (TGS1), the enzyme responsible for cap hypermethylation, increases levels of hTR and telomerase. Diminished trimethylation increases hTR association with the cap-binding complex (CBC) and with Sm chaperone proteins. Loss of TGS1 causes an increase in accumulation of mature hTR in both the nucleus and the cytoplasm compared with controls. In TGS1 mutant cells, increased hTR assembles with telomerase reverse transcriptase (TERT) protein to yield elevated active telomerase complexes and increased telomerase activity, resulting in telomere elongation in cultured human cells. Our results show that TGS1-mediated hypermethylation of the hTR cap inhibits hTR accumulation, restrains levels of assembled telomerase, and limits telomere elongation., Graphical Abstract, In Brief hTR, the RNA component of telomerase, acquires a trimethylguanosine cap synthesized by Trimethylguanosine synthase 1 (TGS1). Chen et al. show that TGS1 and cap hypermethylation control hTR abundance and intracellular distribution. Loss of TGS1 results in elevated hTR levels, increased telomerase activity and telomere elongation.

In vertebrates, the UUAGGG telomere repeat containing long non-coding RNA TERRA is prone to form RNA:DNA hybrids at telomeres resulting the formation of R-loop structures, replicative stress and telomere instability. RNA:DNA hybrids represent a threat to genomic stability, but also contribute to recombination based alternative lengthening of telomeres (ALT). My PhD thesis aimed to identifie novel TERRA interactors involved in regulation of RNA:DNA hybrids (project 1) and to obtain new insights into the molecular function of TERRA interactrors in telomere regulation by identifying novel proteins (project 2). Here, we identify the TERRA binding proteins SFPQ as novel regulators of RNA:DNA hybrid related telomere instability. NONO and SFPQ locate at telomeres and have a common role in suppressing RNA:DNA hybrids and replication defects at telomeres. SFPQ acts as a barrier for homologous recombination at telomeres, thereby impacting on telomere length homeostasis. Our data identifies the RNA binding proteins SFPQ as novel regulators at telomeres that collaborate to ensure telomere integrity by suppressing telomere fragility and homologous recombination triggered by RNA:DNA hybrids. Because of lack of enzymatic activity in SFPQ, we performed a mass spectrometry analysis and we found DAXX as novel SFPQ interacting protein. After the identification od SFPQ interacting domain with DAXX, we carried out preliminary experiment to evaluate the role od DAXX in DNA damage activation, in induction of replication defects and telomere dysfunction.

Pseudogenes are defined as non-functional genomic sequences originally derived from functional genes to which they are similar but with important defects, such as mutations, insertions and deletions, that make them unable to produce a functional protein. For a long time, pseudogenes have been considered as non-functional RNA relics, however, recently, some pseudogenes-derived lncRNA have been shown to be functional and play an important role in various physiological and pathological conditions. We recently discovered a murine Oct4 pseudogene (mOct4P4) which encodes a nuclear restricted lncRNA able to silence the transcription of the ancestral Oct4 gene. mOct4P4 is upregulated during mESC differentiation and recruits SUV39H1 to the Oct4 promoter to impose repressive heterochromatin in trans, leading to Oct4 gene silencing to promote cell differentiation. In this study, we obtained novel insights into the molecular mechanism of mOct4P4 pseudogene-dependent gene silencing and its conservation in human cells. CRISPR/Cas9 mediated mOct4P4 loss-of-function experiments showed an essential role for mOct4P4 in orchestrating an effective mESC differentiation. In addition, mOct4P4 deletion analysis identified the minimal functional region in mOct4P4 lncRNA (base pairs 984-1183) required for SUV39H1 binding and Oct4 ancestral gene targeting. Moreover, mass spectrometry analysis on mOct4P4 lncRNA pull-down identified a novel mOct4P4 interactor, the RNA binding protein FUS, which is required for mOct4P4 dependent silencing of Oct4 expression, suggesting that a mOct4P4 lncRNA/FUS/SUV39H1 complex has an important role in the silencing of Oct4 during mESC differentiation. Finally, we characterized the human homolog of mOct4P4 (hOCT4P3) and demonstrated the functional conservation between the two pseudogene-derived lncRNAs. In fact, we show that hOCT4P3 is able to form a complex with SUV39H1 and FUS that is able to impose repressive heterochromatin marks on ancestral gene promoter leading to silencing of OCT4 expression in ovarian cancer cells. In conclusion, we provided novel insights into the epigenetic mechanism that the murine Oct4P4 lncRNA uses to control ancestral Oct4 expression in trans to regulate self-renewal and differentiation and further demonstrated that this mechanism is also conserved in humans. Pseudogenes are defined as non-functional genomic sequences originally derived from functional genes to which they are similar but with important defects, such as mutations, insertions and deletions, that make them unable to produce a functional protein. For a long time, pseudogenes have been considered as non-functional RNA relics, however, recently, some pseudogenes-derived lncRNA have been shown to be functional and play an important role in various physiological and pathological conditions. We recently discovered a murine Oct4 pseudogene (mOct4P4) which encodes a nuclear restricted lncRNA able to silence the transcription of the ancestral Oct4 gene. mOct4P4 is upregulated during mESC differentiation and recruits SUV39H1 to the Oct4 promoter to impose repressive heterochromatin in trans, leading to Oct4 gene silencing to promote cell differentiation. In this study, we obtained novel insights into the molecular mechanism of mOct4P4 pseudogene-dependent gene silencing and its conservation in human cells. CRISPR/Cas9 mediated mOct4P4 loss-of-function experiments showed an essential role for mOct4P4 in orchestrating an effective mESC differentiation. In addition, mOct4P4 deletion analysis identified the minimal functional region in mOct4P4 lncRNA (base pairs 984-1183) required for SUV39H1 binding and Oct4 ancestral gene targeting. Moreover, mass spectrometry analysis on mOct4P4 lncRNA pull-down identified a novel mOct4P4 interactor, the RNA binding protein FUS, which is required for mOct4P4 dependent silencing of Oct4 expression, suggesting that a mOct4P4 lncRNA/FUS/SUV39H1 complex has an important role in the silencing of Oct4 during mESC differentiation. Finally, we characterized the human homolog of mOct4P4 (hOCT4P3) and demonstrated the functional conservation between the two pseudogene-derived lncRNAs. In fact, we show that hOCT4P3 is able to form a complex with SUV39H1 and FUS that is able to impose repressive heterochromatin marks on ancestral gene promoter leading to silencing of OCT4 expression in ovarian cancer cells. In conclusion, we provided novel insights into the epigenetic mechanism that the murine Oct4P4 lncRNA uses to control ancestral Oct4 expression in trans to regulate self-renewal and differentiation and further demonstrated that this mechanism is also conserved in humans.

In vertebrates, the telomere repeat containing long, non-coding RNA TERRA is prone to form RNA:DNA hybrids at telomeres. This results in the formation of R-loop structures, replication stress and telomere instability, but also contributes to alternative lengthening of telomeres (ALT). Here, we identify the TERRA binding proteins NONO and SFPQ as novel regulators of RNA:DNA hybrid related telomere instability. NONO and SFPQ locate at telomeres and have a common role in suppressing RNA:DNA hybrids and replication defects at telomeres. NONO and SFPQ act as heterodimers to suppress fragility and homologous recombination at telomeres, respectively. Combining increased telomere fragility with unleashing telomere recombination upon NONO/SFPQ loss of function causes massive recombination events, involving 35% of telomeres in ALT cells. Our data identify the RNA binding proteins SFPQ and NONO as novel regulators at telomeres that collaborate to ensure telomere integrity by suppressing telomere fragility and homologous recombination triggered by RNA:DNA hybrids., LncRNA TERRA forms RNA-DNA hybrids at telomere sites leading to telomere instability. Here the authors identify the RNA interacting factors NONO and SFPQ as proteins that interact with TERRA and telomere chromatin and reveal putative roles for these factors in telomere integry maintenance by interfering with RNA:DNA hybrid formation.

I telomeri sono le regioni terminali dei cromosomi ed hanno il ruolo fondamentale di proteggere l’estremità del cromosoma stesso. Per ragioni intrinseche al suo meccanismo di duplicazione, il DNA telomerico non viene completamente replicato, provocando un accorciamento delle estremità cromosomiche ad ogni ciclo di replicazione, che causa un blocco della proliferazione cellulare noto come senescenza. Per controbilanciare questo fenomeno, le cellule tumorali possono riattivare la telomerasi, un enzima che sintetizza nuove ripetizioni telomeriche, o attivare meccanismi alternativi che si basano sulla ricombinazione omologa (ALT). La telomerasi è una ribonucleoproteina costituita da due componenti essenziali: una molecola di RNA denominata hTR ed una subunità con attività enzimatica nota come hTERT. Nonostante sia noto che l’espressione della telomerasi è altamente regolata sia ad un livello trascrizionale che post-traduzionale, il ruolo degli RNA non codificanti in tale regolazione è stato scarsamente spiegato. L’obiettivo della mia tesi di Dottorato è stato scoprire nuove pathway regolate da RNA non codificanti che potessero avere un ruolo nella regolazione della telomerasi in cellule tumorali. In particolare, il mio lavoro ha avuto come obiettivo i) l’identificazione di microRNAs coinvolti nella regolazione dell’espressione della telomerasi nel tumore della mammella (progetto 1) e ii) l’elucidazione del ruolo che il processo maturativo di hTR ad opera dell’RNA metiltransferasi TGS1 riveste nel mantenimento dell’omeostasi telomerica (progetto 2). Progetto 1: Il silenziameno dei miR-296-5p e miR-512-5p assicura una protezione dall’apoptosi hTERT-dipendente e il mantenimento dell’omeostasi telomerica in cellule di tumore basale della mammella Utilizzando come modello il tumore della mammella, è stato possibile identificare numerosi miRNAs che hanno come bersaglio specifico il 3’ UTR di hTERT. Da una successiva analisi bioinformatica è emerso che, tra i miRNAs precedentemente identificati, i livelli dei miR-296-5p e miR-512-5p sono particolarmente bassi nei tumori della mammella e che, conseguentemente, l’aumentato livello di hTERT è strettamente correlato ad una prognosi peggiore. Con il nostro lavoro, abbiamo mostrato che i miR-296-5p e miR-512-5p sono in grado di regolare la proliferazione ed il mantenimento della lunghezza telomerica. Inoltre, dal momento che è stato possibile evidenziare un importante ruolo della regolazione epigenetica nel controllo dell’espressione dei suddetti miRNAs, è possibile concludere che l’utilizzo di composti che regolano l’espressione dei miR-296-5p e miR-512-5p potrebbe rappresentare una promettente strategia per controllare l’omeostasi telomerica nel tumore della mammella. Progetto 2: Regolazione dell’omeostasi telomerica ad opera della RNA metiltransferasi TGS1 hTR è un RNA non codificante trascritto dalla RNA polimerasi II e caratterizzato dalla presenza di un cap al 5’ di 2,2,7-trimetilguanosina, la cui completa maturazione avviene ad opera di TGS1. Il nostro lavoro ha mostrato che la riduzione della trimetilazione di hTR provoca un importante deficit dell’attività della telomerasi nell’allungamento dei telomeri, la cui lunghezza viene invece mantenuta tramite meccanismi ALT. Questi dati suggeriscono che, l’innapropriata maturazione di hTR possa provocare una “riprogrammazione” del meccanismo di mantenimento della lunghezza dei telomeri. In particolare, con le evidenze emerse dal nostro lavoro, suggeriamo che TGS1 possa indirizzare la cellula tumorale verso la scelta del meccanismo di mantenimento della lunghezza telomerica. In conclusione, il mio lavoro di Dottorato dimostra che, a diversi livelli, gli RNA non codificanti hanno un ruolo cruciale nella regolazione della funzione della telomerasi, provocando un importante impatto sul mantenimento dell’omeostasi telomerica in differenti tipi di tumore umano. Vertebrate telomeres are the protective ends of linear chromosomes that consist of TTAGGG tandem repeats. The conventional DNA replication machinery is unable to fully replicate chromosome ends, thus telomeres shorten with every cell division, finally leading to telomere dysfunction and cellular senescence. The escape from cellular senescence can be achieved in tumor cells by two different mechanisms: the reactivation of the reverse transcriptase telomerase in 90% of human cancers or the alternative lengthening of telomeres (ALT) that relies on the homologous recombination. The minimal catalytic core of telomerase consists of the telomerase RNA component (hTR) and the reverse transcriptase subunit (hTERT). Telomerase can replenish telomere repeats, thus antagonizing the end replication problem and its expression is tightly regulated at transcriptional and post-translational level. However, the role of non-coding RNAs in telomere and telomerase regulation is poorly understood. The goal of my PhD thesis was to explore new non-coding RNA related pathways that regulate telomerase and telomere homeostasis in cancer cells. In particular, my work aimed to i) identify novel miRNAs that can regulate telomerase expression in breast cancer cells and demonstrate clinical relevance for these miRNAs (project 1) and ii) better elucidate the role of the post-transcriptional maturation of the non-coding RNA hTR by the RNA methyltransferase TGS1 in telomere homeostasiss (project 2). Project 1: Silencing of miR-296 and miR-512 ensures hTERT dependent apoptosis protection and telomere maintenance in basal-type breast cancer cells We performed a high-throughput luciferase reporter screening in HeLa cells and identified a panel of miRNAs that target the 3’UTR of hTERT. Among these miRNAs, we found that miR-296-5p and miR-512-5p can induce hTERT mRNA degradation, thus reducing telomerase activity. Clinical data revealed that miR-296-5p and miR-512-5p are downregulated in breast cancer tissues. Importantly, we found that increased hTERT and miR-296-5p or miR-512-5p target genes expression is linked to poor survival in basal breast cancer patients, thus highlighting the clinical relevance of miR-296-5p and miR-512-5p in this cancer subtype. We showed that miR-296-5p and miR-512-5p can regulate cell proliferation and telomere lengthening maintenance in basal breast cancer cells. We further found that epigenetic silencing of miR-296 and miR-512 genes in a basal breast cancer cells, thus ensuring hTERT expression. These evidences suggest that drugs that impinge on miR-296-5p or miR-512-5p expression might be a promising strategy to control telomere homeostasis in human breast cancer. Project 2: Regulation of telomere homeostasis by the RNA methyltransferase TGS1 The enzymatic activity of telomerase depends on a precise processing of the hTR and proper assembly with hTERT to form the telomerase RNP complex. The ncRNA component of telomerase hTR differs from other RNA Polymerase II transcripts by exhibiting a 2,2,7-trimethylguanosine cap at its 5’ end, generated by the RNA-methyltransferase TGS1. We found that loss of the trimethylguanosine cap of hTR results in an impairment of normal telomerase dependent telomere maintenance in cancer cells. This process is paralleled by the activation of features of the ALT pathwway. This evidence suggests a redirection from telomerase dependent to ALT maintenance in the absence of trimethylation. Our data suggest that the 2,2,7-trimethylguanosine cap of hTR is important for telomerase based elongation of telomeres and that TGS1 may act as a switch between telomerase and recombination based telomere maintenance by imposing a trimethylguanosine cap on hTR. Altogether, these evidences demonstrate that non-coding RNAs might represent new regulators of telomerase function, thus impacting on telomere homeostasis in human cancer.

The Suv39h1 and Suv39h2 H3K9 histone methyltransferases (HMTs) have a conserved role in the formation of constitutive heterochromatin and gene silencing. Using a transgenic mouse model system we demonstrate that elevated expression of Suv39h1 increases global H3K9me3 levels in vivo. More specifically, Suv39h1 overexpression enhances the imposition of H3K9me3 levels at constitutive heterochromatin at telomeric and major satellite repeats in primary mouse embryonic fibroblasts. Chromatin compaction is paralleled by telomere shortening, indicating that telomere length is controlled by H3K9me3 density at telomeres. We further show that increased Suv39h1 levels result in an impaired clonogenic potential of transgenic epidermal stem cells and Ras/E1A transduced transgenic primary mouse embryonic fibroblasts. Importantly, Suv39h1 overexpression in mice confers resistance to a DMBA/TPA induced skin carcinogenesis protocol that is characterized by the accumulation of activating H-ras mutations. Our results provide genetic evidence that Suv39h1 controls telomere homeostasis and mediates resistance to oncogenic stress in vivo. This identifies Suv39h1 as an interesting target to improve oncogene induced senescence in premalignant lesions.

OCT4 (Octamer-binding transcription factor 4) is essential for embryonic stem cell self-renewal. Here we show that OCT4 increases the aggressiveness of high-grade serous ovarian cancer (HG-SOC) by inactivating the Retinoblastoma tumor suppressor pathway and enhancing mitotic stability in cancer cells. OCT4 drives the expression of Nuclear Inhibitor of Protein Phosphatase type 1 (NIPP1) and Cyclin F (CCNF) that together inhibit Protein Phosphatase 1 (PP1). This results in pRB hyper-phosphorylation, accelerated cell proliferation and increased in vitro tumorigenicity of ovarian cancer cells. In parallel, OCT4 and NIPP1/CCNF drive the expression of the central Chromosomal Passenger Complex (CPC) components, Borealin, Survivin and the mitotic kinase Aurora B, promoting the clustering of supernumerary centrosomes to increase mitotic stability. Loss of OCT4 or NIPP1/CCNF results in severe mitotic defects, multipolar spindles and supernumerary centrosomes, finally leading to the induction of apoptosis. These phenotypes were recapitulated in different cancer models indicating general relevance for human cancer. Importantly, activation of these parallel pathways leads to dramatically reduced overall survival of HG-SOC patients. Altogether, our data highlights an unprecedented role for OCT4 as central regulator of mitotic fidelity and RB tumor suppressor pathway activity. Disrupting this pathway represents a promising strategy to target an aggressive subpopulation of HG-SOC cells.Oncogene advance online publication, 20 March 2017; doi:10.1038/onc.2017.20.

Summary Sox4 expression is restricted in mammals to embryonic structures and some adult tissues, such as lymphoid organs, pancreas, intestine, and skin. During embryogenesis, Sox4 regulates mesenchymal and neural progenitor survival, as well as lymphocyte and myeloid differentiation, and contributes to pancreas, bone, and heart development. Aberrant Sox4 expression is linked to malignant transformation and metastasis in several types of cancer. To understand the role of Sox4 in the adult organism, we first generated mice with reduced whole-body Sox4 expression. These mice display accelerated aging and reduced cancer incidence. To specifically address a role for Sox4 in adult stem cells, we conditionally deleted Sox4 (Sox4cKO) in stratified epithelia. Sox4cKO mice show increased skin stem cell quiescence and resistance to chemical carcinogenesis concomitantly with downregulation of cell cycle, DNA repair, and activated hair follicle stem cell pathways. Altogether, these findings highlight the importance of Sox4 in regulating adult tissue homeostasis and cancer.

The pluripotency of mouse embryonic stem cells (mESCs) is controlled by a network of transcription factors, mi-RNAs, and signaling pathways. Here, we present a new regulatory circuit that connects miR-335, Oct4, and the Retinoblastoma pathway to control mESC self-renewal and differentiation. Oct4 drives the expression of Nipp1 and Ccnf that inhibit the activity of the protein phosphatase 1 (PP1) complex to establish hyperphosphorylation of the retinoblastoma protein 1 (pRb) as a hallmark feature of self-renewing mESCs. The Oct4-Nipp1/Ccnf-PP1-pRb axis promoting mESC self-renewal is under control of miR-335 that regulates Oct4 and Rb expression. During mESC differentiation, miR-335 upregulation co-operates with the transcriptional repression of Oct4 to facilitate the collapse of the Oct4-Nipp1/Ccnf-PP1-pRb axis, pRb dephosphorylation, the exit from self-renewal, and the establishment of a pRb-regulated cell cycle program. Our results introduce Oct4-dependent control of the Rb pathway as novel regulatory circuit controlling mESC self-renewal and differentiation.

I telomeri sono strutture protettive localizzate all’estremità dei cromosomi. La struttura della cromatina telomerica svolge un ruolo principale nel mantenimento della lunghezza e della stabilità dei telomeri. L’eterocromatina telomerica è definita dall’attività delle istone metil trasferasi (HMT) Suv39h1 e Suv39h2 ed è associata ad un RNA non codificante chiamato TERRA. Abbiamo dimostrato che un nuovo complesso che interagisce con TERRA è formato da PSF e p54nrb, localizza al telomero e previene la fragilità e la ricombinazione telomerica sopprimendo la formazione di ibridi tra il DNA telomerico e l’RNA non codificante TERRA. Inoltre, utilizzando un modello murino transgenico abbiamo mostrato che Suv39h1 controlla l’omeostasi dei telomeri e media la resistenza allo stress oncogenico. Telomeres are protective nucleoprotein structures located at chromosomes ends. Telomeric chromatin structure plays a major role in the maintenance of telomere length homeostasis and stability. Telomeric heterochromatin is defined by the H3K9 specific histone methyltransferases (HMTs) Suv39h1 and Suv39h2 and is associated with a long non coding RNA named TERRA. We demonstrated that a novel TERRA interacting complex composed by PSF and p54nrb locates at telomeres and prevent telomere fragility and telomeric recombination by suppressing telomere-DNA/TERRA-RNA hybrid formation. In addition using a transgenic mouse model system we showed that Suv39h1 controls telomere homeostasis and mediates resistance to oncogenic stress.

Rap1 is a component of the shelterin complex at mammalian telomeres, but its in vivo role in telomere biology has remained largely unknown to date. Here we show that Rap1 deficiency is dispensable for telomere capping but leads to increased telomere recombination and fragility. We generated cells and mice deleted for Rap1; mice with Rap1 deletion in stratified epithelia were viable but had shorter telomeres and developed skin hyperpigmentation in adulthood. By performing chromatin immunoprecipitation coupled with ultrahigh-throughput sequencing, we found that Rap1 binds to both telomeres and to extratelomeric sites through the (TTAGGG)(2) consensus motif. Extratelomeric Rap1-binding sites were enriched at subtelomeric regions, in agreement with preferential deregulation of subtelomeric genes in Rap1-deficient cells. More than 70% of extratelomeric Rap1-binding sites were in the vicinity of genes, and 31% of the genes deregulated in Rap1-null cells contained Rap1-binding sites, suggesting a role for Rap1 in transcriptional control. These findings place a telomere protein at the interface between telomere function and transcriptional regulation.