1
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Rivosecchi J, Jurikova K, Cusanelli E. Telomere-specific regulation of TERRA and its impact on telomere stability. Semin Cell Dev Biol 2024; 157:3-23. [PMID: 38088000 DOI: 10.1016/j.semcdb.2023.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/02/2023] [Indexed: 01/08/2024]
Abstract
TERRA is a class of telomeric repeat-containing RNAs that are expressed from telomeres in multiple organisms. TERRA transcripts play key roles in telomere maintenance and their physiological levels are essential to maintain the integrity of telomeric DNA. Indeed, deregulated TERRA expression or its altered localization can impact telomere stability by multiple mechanisms including fueling transcription-replication conflicts, promoting resection of chromosome ends, altering the telomeric chromatin, and supporting homologous recombination. Therefore, a fine-tuned control of TERRA is important to maintain the integrity of the genome. Several studies have reported that different cell lines express substantially different levels of TERRA. Most importantly, TERRA levels markedly vary among telomeres of a given cell type, indicating the existence of telomere-specific regulatory mechanisms which may help coordinate TERRA functions. TERRA molecules contain distinct subtelomeric sequences, depending on their telomere of origin, which may instruct specific post-transcriptional modifications or mediate distinct functions. In addition, all TERRA transcripts share a repetitive G-rich sequence at their 3' end which can form DNA:RNA hybrids and fold into G-quadruplex structures. Both structures are involved in TERRA functions and can critically affect telomere stability. In this review, we examine the mechanisms controlling TERRA levels and the impact of their telomere-specific regulation on telomere stability. We compare evidence obtained in different model organisms, discussing recent advances as well as controversies in the field. Furthermore, we discuss the importance of DNA:RNA hybrids and G-quadruplex structures in the context of TERRA biology and telomere maintenance.
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Affiliation(s)
- Julieta Rivosecchi
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Katarina Jurikova
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy; Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Emilio Cusanelli
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy.
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2
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Liu Q, Sheng N, Zhang Z, He C, Zhao Y, Sun H, Chen J, Yang X, Tang C. Initial nutrient condition determines the recovery speed of quiescent cells in fission yeast. Heliyon 2024; 10:e26558. [PMID: 38455543 PMCID: PMC10918017 DOI: 10.1016/j.heliyon.2024.e26558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/10/2024] [Accepted: 02/15/2024] [Indexed: 03/09/2024] Open
Abstract
Most of microbe cells spend the majority of their times in quiescence due to unfavorable environmental conditions. The study of this dominant state is crucial for understanding the basic cell physiology. Retained recovery ability is a critical property of quiescent cells, which consists of two features: how long the cells can survive (the survivability) and how fast they can recover (the recovery activity). While the survivability has been extensively studied under the background of chronological aging, how the recovery activity depends on the quiescent time and what factors influence its dynamics have not been addressed quantitatively. In this work, we systematically quantified both the survivability and the recovery activity of long-lived quiescent fission yeast cells at the single cell level under various nutrient conditions. It provides the most profound evolutionary dynamics of quiescent cell regeneration ability described to date. We found that the single cell recovery time linearly increased with the starvation time before the survivability significantly declined. This linearity was robust under various nutrient conditions and the recovery speed was predetermined by the initial nutrient condition. Transcriptome profiling further revealed that quiescence states under different nutrient conditions evolve in a common trajectory but with different speed. Our results demonstrated that cellular quiescence has a continuous spectrum of depths and its physiology is greatly influenced by environmental conditions.
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Affiliation(s)
- Qi Liu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
- The Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Nan Sheng
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Zhiwen Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Chenjun He
- College of Life Science and Technology, Huazhong Agriculture University, Wuhan, 430070, China
| | - Yao Zhao
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Haoyuan Sun
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Jianguo Chen
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
- The Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiaojing Yang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Chao Tang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
- School of Physics, Peking University, Beijing, 100871, China
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3
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Chaux F, Agier N, Garrido C, Fischer G, Eberhard S, Xu Z. Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii. Genome Res 2023; 33:1582-1598. [PMID: 37580131 PMCID: PMC10620057 DOI: 10.1101/gr.278043.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/09/2023] [Indexed: 08/16/2023]
Abstract
Telomeres and subtelomeres, the genomic regions located at chromosome extremities, are essential for genome stability in eukaryotes. In the absence of the canonical maintenance mechanism provided by telomerase, telomere shortening induces genome instability. The landscape of the ensuing genome rearrangements is not accessible by short-read sequencing. Here, we leverage Oxford Nanopore Technologies long-read sequencing to survey the extensive repertoire of genome rearrangements in telomerase mutants of the model green microalga Chlamydomonas reinhardtii In telomerase-mutant strains grown for hundreds of generations, most chromosome extremities were capped by short telomere sequences that were either recruited de novo from other loci or maintained in a telomerase-independent manner. Other extremities did not end with telomeres but only with repeated subtelomeric sequences. The subtelomeric elements, including rDNA, were massively rearranged and involved in breakage-fusion-bridge cycles, translocations, recombinations, and chromosome circularization. These events were established progressively over time and displayed heterogeneity at the subpopulation level. New telomere-capped extremities composed of sequences originating from more internal genomic regions were associated with high DNA methylation, suggesting that de novo heterochromatin formation contributes to the restoration of chromosome end stability in C. reinhardtii The diversity of alternative strategies present in the same organism to maintain chromosome integrity and the variety of rearrangements found in telomerase mutants are remarkable, and illustrate genome plasticity at short timescales.
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Affiliation(s)
- Frédéric Chaux
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Nicolas Agier
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Clotilde Garrido
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Gilles Fischer
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Stephan Eberhard
- Sorbonne Université, CNRS, UMR7141, Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light-Sensing in Microalgae, 75005 Paris, France
| | - Zhou Xu
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France;
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4
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Vaurs M, Audry J, Runge KW, Géli V, Coulon S. A proto-telomere is elongated by telomerase in a shelterin-dependent manner in quiescent fission yeast cells. Nucleic Acids Res 2022; 50:11682-11695. [PMID: 36330920 PMCID: PMC9723628 DOI: 10.1093/nar/gkac986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/08/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Telomere elongation is coupled with genome replication, raising the question of the repair of short telomeres in post-mitotic cells. We investigated the fate of a telomere-repeat capped end that mimics a single short telomere in quiescent fission yeast cells. We show that telomerase is able to elongate this single short telomere during quiescence despite the binding of Ku to the proto-telomere. While Taz1 and Rap1 repress telomerase in vegetative cells, both shelterin proteins are required for efficient telomere extension in quiescent cells, underscoring a distinct mode of telomerase control. We further show that Rad3ATR and Tel1ATM are redundantly required for telomere elongation in quiescence through the phosphorylation of Ccq1 and that Rif1 and its associated-PP1 phosphatases negatively regulate telomerase activity by opposing Ccq1 phosphorylation. The distinct mode of telomerase regulation in quiescent fission yeast cells may be relevant to that in human stem and progenitor cells.
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Affiliation(s)
- Mélina Vaurs
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Equipe labellisée par la Ligue Nationale contre le Cancer, Marseille, F-13009, France
| | - Julien Audry
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Kurt W Runge
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Vincent Géli
- Correspondence may also be addressed to Vincent Géli.
| | - Stéphane Coulon
- To whom correspondence should be addressed. Tel: +33 4 86 97 74 07; Fax: +33 4 86 97 74 99;
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5
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Corda Y, Maestroni L, Luciano P, Najem MY, Géli V. Genome stability is guarded by yeast Rtt105 through multiple mechanisms. Genetics 2021; 217:6126811. [PMID: 33724421 DOI: 10.1093/genetics/iyaa035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 02/03/2021] [Indexed: 12/15/2022] Open
Abstract
Ty1 mobile DNA element is the most abundant and mutagenic retrotransposon present in the genome of the budding yeast Saccharomyces cerevisiae. Protein regulator of Ty1 transposition 105 (Rtt105) associates with large subunit of RPA and facilitates its loading onto a single-stranded DNA at replication forks. Here, we dissect the role of RTT105 in the maintenance of genome stability under normal conditions and upon various replication stresses through multiple genetic analyses. RTT105 is essential for viability in cells experiencing replication problems and in cells lacking functional S-phase checkpoints and DNA repair pathways involving homologous recombination. Our genetic analyses also indicate that RTT105 is crucial when cohesion is affected and is required for the establishment of normal heterochromatic structures. Moreover, RTT105 plays a role in telomere maintenance as its function is important for the telomere elongation phenotype resulting from the Est1 tethering to telomeres. Genetic analyses indicate that rtt105Δ affects the growth of several rfa1 mutants but does not aggravate their telomere length defects. Analysis of the phenotypes of rtt105Δ cells expressing NLS-Rfa1 fusion protein reveals that RTT105 safeguards genome stability through its role in RPA nuclear import but also by directly affecting RPA function in genome stability maintenance during replication.
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Affiliation(s)
- Yves Corda
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Laetitia Maestroni
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Pierre Luciano
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Maria Y Najem
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Vincent Géli
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
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6
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Polleys EJ, Freudenreich CH. Homologous recombination within repetitive DNA. Curr Opin Genet Dev 2021; 71:143-153. [PMID: 34464817 DOI: 10.1016/j.gde.2021.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 12/16/2022]
Abstract
Many microsatellite DNA sequences are able to form non-B form DNA secondary structures, such as hairpin loops, cruciforms, triplex DNA or G-quadruplexes. These DNA structures can form a significant impediment to DNA replication and repair, leading to DNA nicks, gaps, and breaks, which can be repaired by homologous recombination (HR). Recent work understanding HR at structure-forming repeats has focused on genetic requirements for replication fork restart, break induced replication (BIR) at broken forks, recombination during and after relocalization of breaks or stalled forks to the nuclear periphery, and how repair pathway choice and kinetics are navigated in the presence of a repeat tract. In this review, we summarize recent developments that illuminate the role of recombination in repairing DNA damage or causing tract length changes within repetitive DNA and its role in maintaining genome stability.
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Affiliation(s)
- Erica J Polleys
- Department of Biology, Tufts University, Medford MA 02155, United States
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford MA 02155, United States; Program in Genetics, Tufts University, Boston MA 02111, United States.
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7
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Ellis DA, Reyes-Martín F, Rodríguez-López M, Cotobal C, Sun XM, Saintain Q, Jeffares DC, Marguerat S, Tallada VA, Bähler J. R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements. PLoS Genet 2021; 17:e1009784. [PMID: 34464389 PMCID: PMC8437301 DOI: 10.1371/journal.pgen.1009784] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 09/13/2021] [Accepted: 08/18/2021] [Indexed: 12/03/2022] Open
Abstract
Aberrant repair of DNA double-strand breaks can recombine distant chromosomal breakpoints. Chromosomal rearrangements compromise genome function and are a hallmark of ageing. Rearrangements are challenging to detect in non-dividing cell populations, because they reflect individually rare, heterogeneous events. The genomic distribution of de novo rearrangements in non-dividing cells, and their dynamics during ageing, remain therefore poorly characterized. Studies of genomic instability during ageing have focussed on mitochondrial DNA, small genetic variants, or proliferating cells. To characterize genome rearrangements during cellular ageing in non-dividing cells, we interrogated a single diagnostic measure, DNA breakpoint junctions, using Schizosaccharomyces pombe as a model system. Aberrant DNA junctions that accumulated with age were associated with microhomology sequences and R-loops. Global hotspots for age-associated breakpoint formation were evident near telomeric genes and linked to remote breakpoints elsewhere in the genome, including the mitochondrial chromosome. Formation of breakpoint junctions at global hotspots was inhibited by the Sir2 histone deacetylase and might be triggered by an age-dependent de-repression of chromatin silencing. An unexpected mechanism of genomic instability may cause more local hotspots: age-associated reduction in an RNA-binding protein triggering R-loops at target loci. This result suggests that biological processes other than transcription or replication can drive genome rearrangements. Notably, we detected similar signatures of genome rearrangements that accumulated in old brain cells of humans. These findings provide insights into the unique patterns and possible mechanisms of genome rearrangements in non-dividing cells, which can be promoted by ageing-related changes in gene-regulatory proteins.
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Affiliation(s)
- David A. Ellis
- Institute of Healthy Ageing, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Félix Reyes-Martín
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - María Rodríguez-López
- Institute of Healthy Ageing, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Cristina Cotobal
- Institute of Healthy Ageing, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Xi-Ming Sun
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Quentin Saintain
- Institute of Healthy Ageing, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Daniel C. Jeffares
- Institute of Healthy Ageing, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Samuel Marguerat
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Víctor A. Tallada
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Jürg Bähler
- Institute of Healthy Ageing, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
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8
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Pobiega S, Alibert O, Marcand S. A new assay capturing chromosome fusions shows a protection trade-off at telomeres and NHEJ vulnerability to low-density ionizing radiation. Nucleic Acids Res 2021; 49:6817-6831. [PMID: 34125900 PMCID: PMC8266670 DOI: 10.1093/nar/gkab502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/31/2021] [Accepted: 05/27/2021] [Indexed: 11/14/2022] Open
Abstract
Chromosome fusions threaten genome integrity and promote cancer by engaging catastrophic mutational processes, namely chromosome breakage-fusion-bridge cycles and chromothripsis. Chromosome fusions are frequent in cells incurring telomere dysfunctions or those exposed to DNA breakage. Their occurrence and therefore their contribution to genome instability in unchallenged cells is unknown. To address this issue, we constructed a genetic assay able to capture and quantify rare chromosome fusions in budding yeast. This chromosome fusion capture (CFC) assay relies on the controlled inactivation of one centromere to rescue unstable dicentric chromosome fusions. It is sensitive enough to quantify the basal rate of end-to-end chromosome fusions occurring in wild-type cells. These fusions depend on canonical nonhomologous end joining (NHEJ). Our results show that chromosome end protection results from a trade-off at telomeres between positive effectors (Rif2, Sir4, telomerase) and a negative effector partially antagonizing them (Rif1). The CFC assay also captures NHEJ-dependent chromosome fusions induced by ionizing radiation. It provides evidence for chromosomal rearrangements stemming from a single photon-matter interaction.
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Affiliation(s)
- Sabrina Pobiega
- Université de Paris and Université Paris-Saclay, Inserm, CEA IBFJ/iRCM, UMR Stabilité Génétique Cellules Souches et Radiations, 92265 Fontenay-au-Roses, France
| | | | - Stéphane Marcand
- To whom correspondence should be addressed. Tel: +33 1 46 54 82 33;
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9
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Vohhodina J, Goehring LJ, Liu B, Kong Q, Botchkarev VV, Huynh M, Liu Z, Abderazzaq FO, Clark AP, Ficarro SB, Marto JA, Hatchi E, Livingston DM. BRCA1 binds TERRA RNA and suppresses R-Loop-based telomeric DNA damage. Nat Commun 2021; 12:3542. [PMID: 34112789 PMCID: PMC8192922 DOI: 10.1038/s41467-021-23716-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 05/11/2021] [Indexed: 12/13/2022] Open
Abstract
R-loop structures act as modulators of physiological processes such as transcription termination, gene regulation, and DNA repair. However, they can cause transcription-replication conflicts and give rise to genomic instability, particularly at telomeres, which are prone to forming DNA secondary structures. Here, we demonstrate that BRCA1 binds TERRA RNA, directly and physically via its N-terminal nuclear localization sequence, as well as telomere-specific shelterin proteins in an R-loop-, and a cell cycle-dependent manner. R-loop-driven BRCA1 binding to CpG-rich TERRA promoters represses TERRA transcription, prevents TERRA R-loop-associated damage, and promotes its repair, likely in association with SETX and XRN2. BRCA1 depletion upregulates TERRA expression, leading to overly abundant TERRA R-loops, telomeric replication stress, and signs of telomeric aberrancy. Moreover, BRCA1 mutations within the TERRA-binding region lead to an excess of TERRA-associated R-loops and telomeric abnormalities. Thus, normal BRCA1/TERRA binding suppresses telomere-centered genome instability. BRCA1-mediated resolution of R-loops has previously been described. Here the authors reveal a functional association of BRCA1 with TERRA RNA at telomeres, which develops in an R-loop-, and a cell cycle-dependent manner.
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Affiliation(s)
- Jekaterina Vohhodina
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Liana J Goehring
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ben Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Qing Kong
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Vladimir V Botchkarev
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Mai Huynh
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zhiqi Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Fieda O Abderazzaq
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Allison P Clark
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Elodie Hatchi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - David M Livingston
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA.
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10
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Matmati S, Lambert S, Géli V, Coulon S. Telomerase Repairs Collapsed Replication Forks at Telomeres. Cell Rep 2021; 30:3312-3322.e3. [PMID: 32160539 DOI: 10.1016/j.celrep.2020.02.065] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/17/2020] [Accepted: 02/14/2020] [Indexed: 02/06/2023] Open
Abstract
Telomeres are difficult-to-replicate sites whereby replication itself may threaten telomere integrity. We investigate, in fission yeast, telomere replication dynamics in telomerase-negative cells to unmask problems associated with telomere replication. Two-dimensional gel analysis reveals that replication of telomeres is severely impaired and correlates with an accumulation of replication intermediates that arises from stalled and collapsed forks. In the absence of telomerase, Rad51, Mre11-Rad50-Nbs1 (MRN) complex, and its co-factor CtIPCtp1 become critical to maintain telomeres, indicating that homologous recombination processes these intermediates to facilitate fork restart. We further show that a catalytically dead mutant of telomerase prevents Ku recruitment to telomeres, suggesting that telomerase and Ku both compete for the binding of telomeric-free DNA ends that are likely to originate from a reversed fork. We infer that Ku removal at collapsed telomeric forks allows telomerase to repair broken telomeres, thereby shielding telomeres from homologous recombination.
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Affiliation(s)
- Samah Matmati
- Marseille Cancer Research Centre (CRCM), U1068 INSERM, UMR7258 CNRS, UM105 Aix-Marseille University, Institut Paoli-Calmettes, Ligue Nationale Contre le Cancer (équipe labellisée) Marseille, F-13009, France
| | - Sarah Lambert
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405 Orsay, France
| | - Vincent Géli
- Marseille Cancer Research Centre (CRCM), U1068 INSERM, UMR7258 CNRS, UM105 Aix-Marseille University, Institut Paoli-Calmettes, Ligue Nationale Contre le Cancer (équipe labellisée) Marseille, F-13009, France.
| | - Stéphane Coulon
- Marseille Cancer Research Centre (CRCM), U1068 INSERM, UMR7258 CNRS, UM105 Aix-Marseille University, Institut Paoli-Calmettes, Ligue Nationale Contre le Cancer (équipe labellisée) Marseille, F-13009, France.
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11
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Adishesh M, Alnafakh R, Baird DM, Jones RE, Simon S, Button L, Kamal AM, Kirwan J, DeCruze SB, Drury J, Saretzki G, Hapangama DK. Human Endometrial Carcinogenesis Is Associated with Significant Reduction in Long Non-Coding RNA, TERRA. Int J Mol Sci 2020; 21:E8686. [PMID: 33217925 PMCID: PMC7698627 DOI: 10.3390/ijms21228686] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 11/16/2020] [Indexed: 12/25/2022] Open
Abstract
Telomeres are transcribed as long non-coding RNAs called TERRAs (Telomeric repeat containing RNA) that participate in a variety of cellular regulatory functions. High telomerase activity (TA) is associated with endometrial cancer (EC). This study aimed to examine the levels of three TERRAs, transcribed at chromosomes 1q-2q-4q-10q-13q-22q, 16p and 20q in healthy (n = 23) and pathological (n = 24) human endometrium and to examine their association with cellular proliferation, TA and telomere lengths. EC samples demonstrated significantly reduced levels of TERRAs for Chromosome 16p (Ch-16p) (p < 0.002) and Chromosome 20q (Ch-20q) (p = 0.0006), when compared with the postmenopausal samples. No significant correlation was found between TERRA levels and TA but both Ch-16p and Ch-20q TERRA levels negatively correlated with the proliferative marker Ki67 (r = -0.35, p = 0.03 and r = -0.42, p = 0.01 respectively). Evaluation of single telomere length analysis (STELA) at XpYp telomeres demonstrated a significant shortening in EC samples when compared with healthy tissues (p = 0.002). We detected TERRAs in healthy human endometrium and observed altered individual TERRA-specific levels in malignant endometrium. The negative correlation of TERRAs with cellular proliferation along with their significant reduction in EC may suggest a role for TERRAs in carcinogenesis and thus future research should explore TERRAs as potential therapeutic targets in EC.
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Affiliation(s)
- Meera Adishesh
- Liverpool Women’s Hospital NHS Foundation Trust, Liverpool L8 7SS, UK; (M.A.); (J.K.); (S.B.D.)
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (S.S.); (L.B.); (A.M.K.); (J.D.)
| | - Rafah Alnafakh
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (S.S.); (L.B.); (A.M.K.); (J.D.)
| | - Duncan M. Baird
- Division of Cancer and Genetics, Cardiff University, Cardiff CF14 4XN, UK; (D.M.B.); (R.E.J.)
| | - Rhiannon E. Jones
- Division of Cancer and Genetics, Cardiff University, Cardiff CF14 4XN, UK; (D.M.B.); (R.E.J.)
| | - Shannon Simon
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (S.S.); (L.B.); (A.M.K.); (J.D.)
| | - Lucy Button
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (S.S.); (L.B.); (A.M.K.); (J.D.)
| | - Areege M. Kamal
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (S.S.); (L.B.); (A.M.K.); (J.D.)
- The National Centre for Early Detection of Cancer, Oncology Teaching Hospital, Baghdad Medical City, Baghdad, Iraq
| | - John Kirwan
- Liverpool Women’s Hospital NHS Foundation Trust, Liverpool L8 7SS, UK; (M.A.); (J.K.); (S.B.D.)
| | - S. Bridget DeCruze
- Liverpool Women’s Hospital NHS Foundation Trust, Liverpool L8 7SS, UK; (M.A.); (J.K.); (S.B.D.)
| | - Josephine Drury
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (S.S.); (L.B.); (A.M.K.); (J.D.)
| | - Gabriele Saretzki
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE4 5PL, UK;
| | - Dharani K. Hapangama
- Liverpool Women’s Hospital NHS Foundation Trust, Liverpool L8 7SS, UK; (M.A.); (J.K.); (S.B.D.)
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (S.S.); (L.B.); (A.M.K.); (J.D.)
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12
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Coulon S, Vaurs M. Telomeric Transcription and Telomere Rearrangements in Quiescent Cells. J Mol Biol 2020; 432:4220-4231. [PMID: 32061930 DOI: 10.1016/j.jmb.2020.01.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 02/07/2023]
Abstract
Despite the condensed nature of terminal sequences, the telomeres are transcribed into a group of noncoding RNAs, including the TElomeric Repeat-containing RNA (TERRA). Since the discovery of TERRA, its evolutionary conserved function has been confirmed, and its involvement in telomere length regulation, heterochromatin establishment, and telomere recombination has been demonstrated. We previously reported that TERRA is upregulated in quiescent fission yeast cells, although the global transcription is highly reduced. Elevated telomeric transcription was also detected when telomeres detach from the nuclear periphery. These intriguing observations unveil unexpected facets of telomeric transcription in arrested cells. In this review, we present the different aspects of TERRA transcription during quiescence and discuss their implications for telomere maintenance and cell fate.
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Affiliation(s)
- Stéphane Coulon
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue contre le Cancer, Marseille, F-13009, France.
| | - Mélina Vaurs
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue contre le Cancer, Marseille, F-13009, France
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13
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Telomere replication-When the going gets tough. DNA Repair (Amst) 2020; 94:102875. [PMID: 32650286 DOI: 10.1016/j.dnarep.2020.102875] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/23/2020] [Accepted: 05/26/2020] [Indexed: 12/28/2022]
Abstract
Telomeres consist of repetitive tracts of DNA that shield a chromosome's contents from erosion and replicative attrition. However, telomeres are also late-replicating regions of the genome in which a myriad of replicative obstructions reside. The obstacles contained within telomeres, as well as their genomic location, drive replicative stalling and subsequent fork collapse in these regions. Consequently, large scale deletions, under-replicated DNA, translocations, and fusion events arise following telomere replication failure. Further, under-replicated DNA and telomere fusions that are permitted to enter mitosis will produce mitotic DNA bridges - known drivers of genetic loss and chromothripsis. Thus, aberrant telomere replication promotes genomic instability, which, in turn leads either to cellular death, senescence or oncogenic transformation. The importance of these issues for organismal well-being necessitates a need for resolute telomere maintenance. Here, we describe recent advances in identifying and understanding the molecular mechanisms that are in place in human cells to escort the replisome through the telomere's unwieldy structures and repetitive sequences. Finally, we review the pathways that combat the deleterious outcomes that occur when telomeric replication forks do collapse.
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14
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Long-lived post-mitotic cell aging: is a telomere clock at play? Mech Ageing Dev 2020; 189:111256. [PMID: 32380018 DOI: 10.1016/j.mad.2020.111256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/25/2020] [Accepted: 04/27/2020] [Indexed: 12/27/2022]
Abstract
Senescence is a cellular response to stress for both dividing and post-mitotic cells. Noteworthy, long-lived post-mitotic cells (collectively named LLPMCs), which can live for decades in the organism, can exhibit a distinct type of cellular aging characterized by a progressive functional decline not associated to an overt senescence phenotype. The age-related drivers of senescence and aging in LLPMCs remain largely unknown. There is evidence that an increased production of reactive oxygen species (ROS) due to dysfunctional mitochondria, coupled with an inherent inability of cellular-degradation mechanisms to remove damaged molecules, is responsible for senescence and aging in LLPMC. Although telomeric DNA shortening, by nature linked to cell division, is generally not considered as a driver of LLPMC aging and senescence, we discuss recent reports revealing the existence of age-related telomere changes in LLPMC. These findings reveal unexpected roles for telomeres in LLPMC function and invite us to consider the hypothesis of a complex telomere clock involved in both dividing and non-dividing cell aging.
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15
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Nitrogen starvation reveals the mitotic potential of mutants in the S/MAPK pathways. Nat Commun 2020; 11:1973. [PMID: 32332728 PMCID: PMC7181643 DOI: 10.1038/s41467-020-15880-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 03/24/2020] [Indexed: 02/08/2023] Open
Abstract
The genetics of quiescence is an emerging field compared to that of growth, yet both states generate spontaneous mutations and genetic diversity fueling evolution. Reconciling mutation rates in dividing conditions and mutation accumulation as a function of time in non-dividing situations remains a challenge. Nitrogen-starved fission yeast cells reversibly arrest proliferation, are metabolically active and highly resistant to a variety of stresses. Here, we show that mutations in stress- and mitogen-activated protein kinase (S/MAPK) signaling pathways are enriched in aging cultures. Targeted resequencing and competition experiments indicate that these mutants arise in the first month of quiescence and expand clonally during the second month at the expense of the parental population. Reconstitution experiments show that S/MAPK modules mediate the sacrifice of many cells for the benefit of some mutants. These findings suggest that non-dividing conditions promote genetic diversity to generate a social cellular environment prone to kin selection. Nitrogen-starved fission yeast cells survive for weeks without dividing. Here, the authors show that some of these surviving cells accumulate mutations in the stress- and mitogen-activated protein kinase pathways and outcompete their parental cells, which provide nutrients for the mutant cells.
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16
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Maestroni L, Reyes C, Vaurs M, Gachet Y, Tournier S, Géli V, Coulon S. Nuclear envelope attachment of telomeres limits TERRA and telomeric rearrangements in quiescent fission yeast cells. Nucleic Acids Res 2020; 48:3029-3041. [PMID: 31980821 PMCID: PMC7102995 DOI: 10.1093/nar/gkaa043] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 11/12/2022] Open
Abstract
Telomere anchoring to nuclear envelope (NE) is a key feature of nuclear genome architecture. Peripheral localization of telomeres is important for chromatin silencing, telomere replication and for the control of inappropriate recombination. Here, we report that fission yeast quiescent cells harbor predominantly a single telomeric cluster anchored to the NE. Telomere cluster association to the NE relies on Rap1-Bqt4 interaction, which is impacted by the length of telomeric sequences. In quiescent cells, reducing telomere length or deleting bqt4, both result in an increase in transcription of the telomeric repeat-containing RNA (TERRA). In the absence of Bqt4, telomere shortening leads to deep increase in TERRA level and the concomitant formation of subtelomeric rearrangements (STEEx) that accumulate massively in quiescent cells. Taken together, our data demonstrate that Rap1-Bqt4-dependent telomere association to NE preserves telomere integrity in post-mitotic cells, preventing telomeric transcription and recombination. This defines the nuclear periphery as an area where recombination is restricted, creating a safe zone for telomeres of post-mitotic cells.
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Affiliation(s)
- Laetitia Maestroni
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe labellisée Ligue contre le Cancer, France
| | - Céline Reyes
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31062 Toulouse Cedex, France
| | - Mélina Vaurs
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe labellisée Ligue contre le Cancer, France
| | - Yannick Gachet
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31062 Toulouse Cedex, France
| | - Sylvie Tournier
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31062 Toulouse Cedex, France
| | - Vincent Géli
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe labellisée Ligue contre le Cancer, France
| | - Stéphane Coulon
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe labellisée Ligue contre le Cancer, France
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17
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Kim C, Sung S, Kim J, Lee J. Repair and Reconstruction of Telomeric and Subtelomeric Regions and Genesis of New Telomeres: Implications for Chromosome Evolution. Bioessays 2020; 42:e1900177. [PMID: 32236965 DOI: 10.1002/bies.201900177] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 02/20/2020] [Indexed: 12/12/2022]
Abstract
DNA damage repair within telomeres are suppressed to maintain the integrity of linear chromosomes, but the accidental activation of repairs can lead to genome instability. This review develops the concept that mechanisms to repair DNA damage in telomeres contribute to genetic variability and karyotype evolution, rather than catastrophe. Spontaneous breaks in telomeres can be repaired by telomerase, but in some cases DNA repair pathways are activated, and can cause chromosomal rearrangements or fusions. The resultant changes can also affect subtelomeric regions that are adjacent to telomeres. Subtelomeres are actively involved in such chromosomal changes, and are therefore the most variable regions in the genome. The case of Caenorhabditis elegans in the context of changes of subtelomeric structures revealed by long-read sequencing is also discussed. Theoretical and methodological issues covered in this review will help to explore the mechanism of chromosome evolution by reconstruction of chromosomal ends in nature.
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Affiliation(s)
- Chuna Kim
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08827, Korea.,Aging Research Institute, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro 125, Daejeon, 34141, Korea
| | - Sanghyun Sung
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08827, Korea
| | - Jun Kim
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08827, Korea
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08827, Korea
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18
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Henninger E, Teixeira MT. Telomere-driven mutational processes in yeast. Curr Opin Genet Dev 2020; 60:99-106. [DOI: 10.1016/j.gde.2020.02.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/18/2022]
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19
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Hu Y, Bennett HW, Liu N, Moravec M, Williams JF, Azzalin CM, King MC. RNA-DNA Hybrids Support Recombination-Based Telomere Maintenance in Fission Yeast. Genetics 2019; 213:431-447. [PMID: 31405990 PMCID: PMC6781888 DOI: 10.1534/genetics.119.302606] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/09/2019] [Indexed: 11/18/2022] Open
Abstract
A subset of cancers rely on telomerase-independent mechanisms to maintain their chromosome ends. The predominant "alternative lengthening of telomeres" pathway appears dependent on homology-directed repair (HDR) to maintain telomeric DNA. However, the molecular changes needed for cells to productively engage in telomeric HDR are poorly understood. To gain new insights into this transition, we monitored the state of telomeres during serial culture of fission yeast (Schizosaccharomyces pombe) lacking the telomerase recruitment factor Ccq1. Rad52 is loaded onto critically short telomeres shortly after germination despite continued telomere erosion, suggesting that recruitment of recombination factors is not sufficient to maintain telomeres in the absence of telomerase function. Instead, survivor formation coincides with the derepression of telomeric repeat-containing RNA (TERRA). In this context, degradation of TERRA associated with the telomere in the form of R-loops drives a severe growth crisis, ultimately leading to a novel type of survivor with linear chromosomes and altered cytological telomere characteristics, including the loss of the shelterin component Rap1 (but not the TRF1/TRF2 ortholog, Taz1) from the telomere. We demonstrate that deletion of Rap1 is protective in this context, preventing the growth crisis that is otherwise triggered by degradation of telomeric R-loops in survivors with linear chromosomes. These findings suggest that upregulation of telomere-engaged TERRA, or altered recruitment of shelterin components, can support telomerase-independent telomere maintenance.
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Affiliation(s)
- Yan Hu
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520-8002
| | - Henrietta W Bennett
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520-8002
| | - Na Liu
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520-8002
| | - Martin Moravec
- Institute of Biochemistry (IBC), Eidgenössische Technische Hochschule Zürich (ETHZ), 8093, Switzerland
| | - Jessica F Williams
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520-8002
| | - Claus M Azzalin
- Instituto de Medicina Molecular João Lobo Antunes (iMM), Faculdade de Medicina da Universidade de Lisboa, 1649-028, Portugal
| | - Megan C King
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520-8002
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20
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Bell WR, Meeker AK, Rizzo A, Rajpara S, Rosenthal IM, Flores Bellver M, Aparicio Domingo S, Zhong X, Barber JR, Joshu CE, Canto-Soler MV, Eberhart CG, Heaphy CM. A unique telomere DNA expansion phenotype in human retinal rod photoreceptors associated with aging and disease. Brain Pathol 2018; 29:45-52. [PMID: 29668072 DOI: 10.1111/bpa.12618] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 04/11/2018] [Indexed: 01/06/2023] Open
Abstract
We have identified a discrete, focal telomere DNA expansion phenotype in the photoreceptor cell layer of normal, non-neoplastic human retinas. This phenotype is similar to that observed in a subset of human cancers, including a large fraction of tumors of the central nervous system, which maintain their telomeres via the non-telomerase-mediated alternative lengthening of telomeres (ALT) mechanism. We observed that these large, ultra-bright telomere DNA foci are restricted to the rod photoreceptors and are not observed in other cell types. Additionally, focus-positive rod cells are dispersed homogeneously throughout the posterior retinal photoreceptor cell layer and appear to be human-specific. We examined 108 normal human retinas obtained at autopsy from a wide range of ages. These large, ultra-bright telomere DNA foci were not observed in infants before 6 months of age; however, the prevalence of focus-positive rod cells dramatically increased throughout life. To investigate associations between this phenotype and retinal pathology, we assessed adult glaucoma (N = 29) and diabetic retinopathy (N = 38) cases. Focus-positive rod cells were prominent in these diseases. When compared to the normal group, after adjusting for age, logistic regression modeling revealed significantly increased odds of falling in the high category of focus-positive rod cells for glaucoma and diabetic retinopathy. In summary, we have identified a dramatic telomere alteration associated with aging and diseases affecting the retina.
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Affiliation(s)
- W Robert Bell
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alan K Meeker
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD.,Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Anthony Rizzo
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Sumit Rajpara
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ian M Rosenthal
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Miguel Flores Bellver
- Departments of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Xiufeng Zhong
- Departments of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - John R Barber
- Departments of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Corinne E Joshu
- Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD.,Departments of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - M Valeria Canto-Soler
- Departments of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Charles G Eberhart
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD.,Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD.,Departments of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christopher M Heaphy
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD.,Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
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21
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Begnis M, Apte MS, Masuda H, Jain D, Wheeler DL, Cooper JP. RNAi drives nonreciprocal translocations at eroding chromosome ends to establish telomere-free linear chromosomes. Genes Dev 2018; 32:537-554. [PMID: 29654060 PMCID: PMC5959237 DOI: 10.1101/gad.311712.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/29/2018] [Indexed: 12/19/2022]
Abstract
In this study, Begnis et al. show that HAATI, which is a mode of telomerase-minus survival in which canonical telomeres are superseded by blocks of nontelomeric rDNA heterochromatin that have spread to all chromosome ends, is formed and maintained. Their findings demonstrate that HAATI arises when telomere loss triggers a newly recognized illegitimate recombination pathway that requires RNAi factors, uncovering novel roles for ncRNAs in assembling a telomere-free chromosome end protection device. The identification of telomerase-negative HAATI (heterochromatin amplification-mediated and telomerase-independent) cells, in which telomeres are superseded by nontelomeric heterochromatin tracts, challenged the idea that canonical telomeres are essential for chromosome linearity and raised crucial questions as to how such tracts translocate to eroding chromosome ends and confer end protection. Here we show that HAATI arises when telomere loss triggers a newly recognized illegitimate translocation pathway that requires RNAi factors. While RNAi is necessary for the translocation events that mobilize ribosomal DNA (rDNA) tracts to all chromosome ends (forming “HAATIrDNA” chromosomes), it is dispensable for HAATIrDNA maintenance. Surprisingly, Dicer (Dcr1) plays a separate, RNAi-independent role in preventing formation of the rare HAATI subtype in which a different repetitive element (the subtelomeric element) replaces telomeres. Using genetics and fusions between shelterin components and rDNA-binding proteins, we mapped the mechanism by which rDNA loci engage crucial end protection factors—despite the absence of telomere repeats—and secure end protection. Sequence analysis of HAATIrDNA genomes allowed us to propose RNA and DNA polymerase template-switching models for the mechanism of RNAi-triggered rDNA translocations. Collectively, our results reveal unforeseen roles for noncoding RNAs (ncRNAs) in assembling a telomere-free chromosome end protection device.
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Affiliation(s)
- Martina Begnis
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.,Telomere Biology Laboratory, Cancer Research UK, London Research Institute, London WC2A 3LY, United Kingdom
| | - Manasi S Apte
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hirohisa Masuda
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Devanshi Jain
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - David Lee Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Julia Promisel Cooper
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.,Telomere Biology Laboratory, Cancer Research UK, London Research Institute, London WC2A 3LY, United Kingdom
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22
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Induction and relocalization of telomeric repeat-containing RNAs during diauxic shift in budding yeast. Curr Genet 2018; 64:1117-1127. [PMID: 29569051 DOI: 10.1007/s00294-018-0829-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/09/2018] [Accepted: 03/20/2018] [Indexed: 02/03/2023]
Abstract
Telomeres are maintained in a heterochromatic state that represses transcription of subtelomeric genes, a phenomenon known as telomere position effect. Nevertheless, telomeric DNA is actively transcribed, leading to the synthesis of telomeric repeat-containing noncoding RNA or TERRA. This nuclear noncoding RNA has been proposed to play important roles at telomeres, regulating their silencing, capping, repair and elongation by telomerase. In the budding yeast Saccharomyces cerevisiae, TERRA accumulation is repressed by telomeric silencing and the Rat1 exonuclease. On the other hand, telomere shortening promotes expression of TERRA. So far, little is known about the biological processes that induce TERRA expression in yeast. Understanding the dynamics of TERRA expression and localization is essential to define its function in telomere biology. Here, we aim to study the dynamics of TERRA expression during yeast cell growth. Using live-cell imaging, RNA-FISH and quantitative RT-PCR, we show that TERRA expression is induced as yeast cells undergo diauxic shift, a lag phase during which yeast cells switch their metabolism from anaerobic fermentation to oxidative respiration. This induction is transient as TERRA levels decrease during post-diauxic shift. The increased expression of TERRA is not due to the shortening of telomeres or increased stability of this transcript. Surprisingly, this induction is coincident with a cytoplasmic accumulation of TERRA molecules. Our results suggest that TERRA transcripts may play extranuclear functions with important implications in telomere biology and add a novel layer of complexity in the interplay between telomere biology, metabolism and stress response.
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23
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Maestroni L, Géli V, Coulon S. STEEx, a boundary between the world of quiescence and the vegetative cycle. Curr Genet 2018; 64:901-905. [PMID: 29392410 DOI: 10.1007/s00294-018-0808-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 01/24/2018] [Accepted: 01/27/2018] [Indexed: 12/20/2022]
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24
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Gangloff S, Achaz G, Francesconi S, Villain A, Miled S, Denis C, Arcangioli B. Quiescence unveils a novel mutational force in fission yeast. eLife 2017; 6. [PMID: 29252184 PMCID: PMC5734874 DOI: 10.7554/elife.27469] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 12/02/2017] [Indexed: 12/18/2022] Open
Abstract
To maintain life across a fluctuating environment, cells alternate between phases of cell division and quiescence. During cell division, the spontaneous mutation rate is expressed as the probability of mutations per generation (Luria and Delbrück, 1943; Lea and Coulson, 1949), whereas during quiescence it will be expressed per unit of time. In this study, we report that during quiescence, the unicellular haploid fission yeast accumulates mutations as a linear function of time. The novel mutational landscape of quiescence is characterized by insertion/deletion (indels) accumulating as fast as single nucleotide variants (SNVs), and elevated amounts of deletions. When we extended the study to 3 months of quiescence, we confirmed the replication-independent mutational spectrum at the whole-genome level of a clonally aged population and uncovered phenotypic variations that subject the cells to natural selection. Thus, our results support the idea that genomes continuously evolve under two alternating phases that will impact on their size and composition.
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Affiliation(s)
- Serge Gangloff
- Genomes and Genetics, Institut Pasteur, Paris, France.,UMR 3525, CNRS-Institut Pasteur, Paris, France
| | - Guillaume Achaz
- ISYEB UMR7505 CNRS MNHN UPMC EPHE CIRB UMR 7241 CNRS Collège de France INSERM, UPMC, Paris, France
| | - Stefania Francesconi
- Genomes and Genetics, Institut Pasteur, Paris, France.,UMR 3525, CNRS-Institut Pasteur, Paris, France
| | | | - Samia Miled
- Genomes and Genetics, Institut Pasteur, Paris, France.,UMR 3525, CNRS-Institut Pasteur, Paris, France
| | - Claire Denis
- Genomes and Genetics, Institut Pasteur, Paris, France.,UMR 3525, CNRS-Institut Pasteur, Paris, France
| | - Benoit Arcangioli
- Genomes and Genetics, Institut Pasteur, Paris, France.,UMR 3525, CNRS-Institut Pasteur, Paris, France
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