1
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Karimian K, Groot A, Huso V, Kahidi R, Tan KT, Sholes S, Keener R, McDyer JF, Alder JK, Li H, Rechtsteiner A, Greider CW. Human telomere length is chromosome end-specific and conserved across individuals. Science 2024; 384:533-539. [PMID: 38603523 DOI: 10.1126/science.ado0431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/30/2024] [Indexed: 04/13/2024]
Abstract
Short telomeres cause age-related disease, and long telomeres contribute to cancer; however, the mechanisms regulating telomere length are unclear. We developed a nanopore-based method, which we call Telomere Profiling, to determine telomere length at nearly single-nucleotide resolution. Mapping telomere reads to chromosome ends showed chromosome end-specific length distributions that could differ by more than six kilobases. Examination of telomere lengths in 147 individuals revealed that certain chromosome ends were consistently longer or shorter. The same rank order was found in newborn cord blood, suggesting that telomere length is determined at birth and that chromosome end-specific telomere length differences are maintained as telomeres shorten with age. Telomere Profiling makes precision investigation of telomere length widely accessible for laboratory, clinical, and drug discovery efforts and will allow deeper insights into telomere biology.
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Affiliation(s)
- Kayarash Karimian
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aljona Groot
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Vienna Huso
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ramin Kahidi
- Health Sciences Program, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Kar-Tong Tan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, The Broad Institute, Cambridge, MA, USA
| | - Samantha Sholes
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca Keener
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - John F McDyer
- Pulmonary, Allergy, Critical Care, and Sleep Medicine Division, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jonathan K Alder
- Pulmonary, Allergy, Critical Care, and Sleep Medicine Division, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Andreas Rechtsteiner
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Carol W Greider
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
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2
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Keller D, Stinus S, Umlauf D, Gourbeyre E, Biot E, Olivier N, Mahou P, Beaurepaire E, Andrey P, Crabbe L. Non-random spatial organization of telomeres varies during the cell cycle and requires LAP2 and BAF. iScience 2024; 27:109343. [PMID: 38510147 PMCID: PMC10951912 DOI: 10.1016/j.isci.2024.109343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/30/2023] [Accepted: 02/22/2024] [Indexed: 03/22/2024] Open
Abstract
Spatial genome organization within the nucleus influences major biological processes and is impacted by the configuration of linear chromosomes. Here, we applied 3D spatial statistics and modeling on high-resolution telomere and centromere 3D-structured illumination microscopy images in cancer cells. We found a multi-scale organization of telomeres that dynamically evolved from a mixed clustered-and-regular distribution in early G1 to a purely regular distribution as cells progressed through the cell cycle. In parallel, our analysis revealed two pools of peripheral and internal telomeres, the proportions of which were inverted during the cell cycle. We then conducted a targeted screen using MadID to identify the molecular pathways driving or maintaining telomere anchoring to the nuclear envelope observed in early G1. Lamina-associated polypeptide (LAP) proteins were found transiently localized to telomeres in anaphase, a stage where LAP2α initiates the reformation of the nuclear envelope, and impacted telomere redistribution in the next interphase together with their partner barrier-to-autointegration factor (BAF).
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Affiliation(s)
- Debora Keller
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
- Laboratory for Optics and Biosciences, École polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Sonia Stinus
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - David Umlauf
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Edith Gourbeyre
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Eric Biot
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Nicolas Olivier
- Laboratory for Optics and Biosciences, École polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Pierre Mahou
- Laboratory for Optics and Biosciences, École polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Emmanuel Beaurepaire
- Laboratory for Optics and Biosciences, École polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Philippe Andrey
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Laure Crabbe
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
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3
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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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4
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Rai R, Sodeinde T, Boston A, Chang S. Telomeres cooperate with the nuclear envelope to maintain genome stability. Bioessays 2024; 46:e2300184. [PMID: 38047499 DOI: 10.1002/bies.202300184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 12/05/2023]
Abstract
Mammalian telomeres have evolved safeguards to prevent their recognition as DNA double-stranded breaks by suppressing the activation of various DNA sensing and repair proteins. We have shown that the telomere-binding proteins TRF2 and RAP1 cooperate to prevent telomeres from undergoing aberrant homology-directed recombination by mediating t-loop protection. Our recent findings also suggest that mammalian telomere-binding proteins interact with the nuclear envelope to maintain chromosome stability. RAP1 interacts with nuclear lamins through KU70/KU80, and disruption of RAP1 and TRF2 function result in nuclear envelope rupture, promoting telomere-telomere recombination to form structures termed ultrabright telomeres. In this review, we discuss the importance of the interactions between shelterin components and the nuclear envelope to maintain telomere homeostasis and genome stability.
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Affiliation(s)
- Rekha Rai
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Tori Sodeinde
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ava Boston
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sandy Chang
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA
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5
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Bournaka S, Badra-Fajardo N, Arbi M, Taraviras S, Lygerou Z. The cell cycle revisited: DNA replication past S phase preserves genome integrity. Semin Cancer Biol 2024; 99:45-55. [PMID: 38346544 DOI: 10.1016/j.semcancer.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 02/20/2024]
Abstract
Accurate and complete DNA duplication is critical for maintaining genome integrity. Multiple mechanisms regulate when and where DNA replication takes place, to ensure that the entire genome is duplicated once and only once per cell cycle. Although the bulk of the genome is copied during the S phase of the cell cycle, increasing evidence suggests that parts of the genome are replicated in G2 or mitosis, in a last attempt to secure that daughter cells inherit an accurate copy of parental DNA. Remaining unreplicated gaps may be passed down to progeny and replicated in the next G1 or S phase. These findings challenge the long-established view that genome duplication occurs strictly during the S phase, bridging DNA replication to DNA repair and providing novel therapeutic strategies for cancer treatment.
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Affiliation(s)
- Spyridoula Bournaka
- Department of General Biology, Medical School, University of Patras, Patras 26504, Greece
| | - Nibal Badra-Fajardo
- Department of General Biology, Medical School, University of Patras, Patras 26504, Greece
| | - Marina Arbi
- Department of General Biology, Medical School, University of Patras, Patras 26504, Greece
| | - Stavros Taraviras
- Department of Physiology, Medical School, University of Patras, Patras 26504, Greece
| | - Zoi Lygerou
- Department of General Biology, Medical School, University of Patras, Patras 26504, Greece.
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6
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Karimian K, Groot A, Huso V, Kahidi R, Tan KT, Sholes S, Keener R, McDyer JF, Alder JK, Li H, Rechtsteiner A, Greider CW. Human telomere length is chromosome specific and conserved across individuals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.21.572870. [PMID: 38187739 PMCID: PMC10769321 DOI: 10.1101/2023.12.21.572870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Short telomeres cause age-related disease and long telomeres predispose to cancer; however, the mechanisms regulating telomere length are unclear. To probe these mechanisms, we developed a nanopore sequencing method, Telomere Profiling, that is easy to implement, precise, and cost effective with broad applications in research and the clinic. We sequenced telomeres from individuals with short telomere syndromes and found similar telomere lengths to the clinical FlowFISH assay. We mapped telomere reads to specific chromosome end and identified both chromosome end-specific and haplotype-specific telomere length distributions. In the T2T HG002 genome, where the average telomere length is 5kb, we found a remarkable 6kb difference in lengths between some telomeres. Further, we found that specific chromosome ends were consistently shorter or longer than the average length across 147 individuals. The presence of conserved chromosome end-specific telomere lengths suggests there are new paradigms in telomere biology that are yet to be explored. Understanding the mechanisms regulating length will allow deeper insights into telomere biology that can lead to new approaches to disease.
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Affiliation(s)
- Kayarash Karimian
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Aljona Groot
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz
| | - Vienna Huso
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | | | - Kar-Tong Tan
- Harvard Medical School, Department of Genetics, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute, Cancer Program, Cambridge, MA
| | - Samantha Sholes
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Present address Merck & Co., 770 Sumneytown Pike, West Point, PA 19486
| | - Rebecca Keener
- Department of Biomedical Engineering, Johns Hopkins University
| | - John F. McDyer
- Pulmonary, Allergy, Critical Care, and Sleep Medicine Division, Department of Medicine, University of Pittsburgh
| | - Jonathan K. Alder
- Pulmonary, Allergy, Critical Care, and Sleep Medicine Division, Department of Medicine, University of Pittsburgh
| | - Heng Li
- Dana-Farber Cancer Institute, Department of Data Sciences, Boston, MA
- Harvard Medical School, Department of Biomedical Informatics, Boston, MA
| | - Andreas Rechtsteiner
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz
| | - Carol W. Greider
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz
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7
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Kalmykova A. Telomere Checkpoint in Development and Aging. Int J Mol Sci 2023; 24:15979. [PMID: 37958962 PMCID: PMC10647821 DOI: 10.3390/ijms242115979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/19/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
The maintenance of genome integrity through generations is largely determined by the stability of telomeres. Increasing evidence suggests that telomere dysfunction may trigger changes in cell fate, independently of telomere length. Telomeric multiple tandem repeats are potentially highly recombinogenic. Heterochromatin formation, transcriptional repression, the suppression of homologous recombination and chromosome end protection are all required for telomere stability. Genetic and epigenetic defects affecting telomere homeostasis may cause length-independent internal telomeric DNA damage. Growing evidence, including that based on Drosophila research, points to a telomere checkpoint mechanism that coordinates cell fate with telomere state. According to this scenario, telomeres, irrespective of their length, serve as a primary sensor of genome instability that is capable of triggering cell death or developmental arrest. Telomeric factors released from shortened or dysfunctional telomeres are thought to mediate these processes. Here, we discuss a novel signaling role for telomeric RNAs in cell fate and early development. Telomere checkpoint ensures genome stability in multicellular organisms but aggravates the aging process, promoting the accumulation of damaged and senescent cells.
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Affiliation(s)
- Alla Kalmykova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
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8
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Delourme M, Charlene C, Gerard L, Ganne B, Perrin P, Vovan C, Bertaux K, Nguyen K, Bernard R, Magdinier F. Complex 4q35 and 10q26 Rearrangements: A Challenge for Molecular Diagnosis of Patients With Facioscapulohumeral Dystrophy. Neurol Genet 2023; 9:e200076. [PMID: 37200893 PMCID: PMC10188231 DOI: 10.1212/nxg.0000000000200076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/23/2023] [Indexed: 05/20/2023]
Abstract
Background and Objectives After clinical evaluation, the molecular diagnosis of type 1 facioscapulohumeral dystrophy (FSHD1) relies in most laboratories on the detection of a shortened D4Z4 array at the 4q35 locus by Southern blotting. In many instances, this molecular diagnosis remains inconclusive and requires additional experiments to determine the number of D4Z4 units or identify somatic mosaicism, 4q-10q translocations, and proximal p13E-11 deletions. These limitations highlight the need for alternative methodologies, illustrated by the recent emergence of novel technologies such as molecular combing (MC), single molecule optical mapping (SMOM), or Oxford Nanopore-based long-read sequencing providing a more comprehensive analysis of 4q and 10q loci. Over the last decade, MC revealed a further increasing complexity in the organization of the 4q and 10q distal regions in patients with FSHD with cis-duplication of D4Z4 arrays in approximately 1%-2% of cases. Methods By using MC, we investigated in our center 2,363 cases for molecular diagnosis of FSHD. We also evaluated whether previously reported cis-duplications might be identified by SMOM using the Bionano EnFocus FSHD 1.0 algorithm. Results In our cohort of 2,363 samples, we identified 147 individuals carrying an atypical organization of the 4q35 or 10q26 loci. Mosaicism is the most frequent category followed by cis-duplications of the D4Z4 array. We report here chromosomal abnormalities of the 4q35 or 10q26 loci in 54 patients clinically described as FSHD, which are not present in the healthy population. In one-third of the 54 patients, these rearrangements are the only genetic defect suggesting that they might be causative of the disease. By analyzing DNA samples from 3 patients carrying a complex rearrangement of the 4q35 region, we further showed that the SMOM direct assembly of the 4q and 10q alleles failed to reveal these abnormalities and lead to negative results for FSHD molecular diagnosis. Discussion This work further highlights the complexity of the 4q and 10q subtelomeric regions and the need of in-depth analyses in a significant number of cases. This work also highlights the complexity of the 4q35 region and interpretation issues with consequences on the molecular diagnosis of patients or genetic counseling.
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Affiliation(s)
- Megane Delourme
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Chaix Charlene
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Laurene Gerard
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Benjamin Ganne
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Pierre Perrin
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Catherine Vovan
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Karine Bertaux
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Karine Nguyen
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Rafaëlle Bernard
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
| | - Frederique Magdinier
- From the Aix Marseille University (M.D., B.G., P.P., K.N., R.B., F.M.), INSERM; Département de Génétique Médicale (C.C., L.G., C.V., K.B., K.N., R.B.), and Centre de Ressources Biologiques (K.B.), AP-HM, Hôpital d'enfants de la Timone, Marseille, France
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9
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Pennarun G, Picotto J, Bertrand P. Close Ties between the Nuclear Envelope and Mammalian Telomeres: Give Me Shelter. Genes (Basel) 2023; 14:genes14040775. [PMID: 37107534 PMCID: PMC10137478 DOI: 10.3390/genes14040775] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
The nuclear envelope (NE) in eukaryotic cells is essential to provide a protective compartment for the genome. Beside its role in connecting the nucleus with the cytoplasm, the NE has numerous important functions including chromatin organization, DNA replication and repair. NE alterations have been linked to different human diseases, such as laminopathies, and are a hallmark of cancer cells. Telomeres, the ends of eukaryotic chromosomes, are crucial for preserving genome stability. Their maintenance involves specific telomeric proteins, repair proteins and several additional factors, including NE proteins. Links between telomere maintenance and the NE have been well established in yeast, in which telomere tethering to the NE is critical for their preservation and beyond. For a long time, in mammalian cells, except during meiosis, telomeres were thought to be randomly localized throughout the nucleus, but recent advances have uncovered close ties between mammalian telomeres and the NE that play important roles for maintaining genome integrity. In this review, we will summarize these connections, with a special focus on telomere dynamics and the nuclear lamina, one of the main NE components, and discuss the evolutionary conservation of these mechanisms.
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Affiliation(s)
- Gaëlle Pennarun
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
| | - Julien Picotto
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
| | - Pascale Bertrand
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
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10
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Brenner KA, Nandakumar J. Consequences of telomere replication failure: the other end-replication problem. Trends Biochem Sci 2022; 47:506-517. [PMID: 35440402 PMCID: PMC9106919 DOI: 10.1016/j.tibs.2022.03.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/28/2022] [Accepted: 03/17/2022] [Indexed: 01/14/2023]
Abstract
Telomeres are chromosome-capping structures that protect ends of the linear genome from DNA damage sensors. However, these structures present obstacles during DNA replication. Incomplete telomere replication accelerates telomere shortening and limits replicative lifespan. Therefore, continued proliferation under conditions of replication stress requires a means of telomere repair, particularly in the absence of telomerase. It was recently revealed that replication stress triggers break-induced replication (BIR) and mitotic DNA synthesis (MiDAS) at mammalian telomeres; however, these mechanisms are error prone and primarily utilized in tumorigenic contexts. In this review article, we discuss the consequences of replication stress at telomeres and how use of available repair pathways contributes to genomic instability. Current research suggests that fragile telomeres are ultimately tumor-suppressive and thus may be better left unrepaired.
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Affiliation(s)
- Kirsten A Brenner
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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11
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Lu R, Pickett HA. Telomeric replication stress: the beginning and the end for alternative lengthening of telomeres cancers. Open Biol 2022; 12:220011. [PMID: 35259951 PMCID: PMC8905155 DOI: 10.1098/rsob.220011] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Telomeres are nucleoprotein structures that cap the ends of linear chromosomes. Telomeric DNA comprises terminal tracts of G-rich tandem repeats, which are inherently difficult for the replication machinery to navigate. Structural aberrations that promote activation of the alternative lengthening of telomeres (ALT) pathway of telomere maintenance exacerbate replication stress at ALT telomeres, driving fork stalling and fork collapse. This form of telomeric DNA damage perpetuates recombination-mediated repair pathways and break-induced telomere synthesis. The relationship between replication stress and DNA repair is tightly coordinated for the purpose of regulating telomere length in ALT cells, but has been shown to be experimentally manipulatable. This raises the intriguing possibility that induction of replication stress can be used as a means to cause toxic levels of DNA damage at ALT telomeres, thereby selectively disrupting the viability of ALT cancers.
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Affiliation(s)
- Robert Lu
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Hilda A. Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
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12
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Pennarun G, Picotto J, Etourneaud L, Redavid AR, Certain A, Gauthier LR, Fontanilla-Ramirez P, Busso D, Chabance-Okumura C, Thézé B, Boussin FD, Bertrand P. Increase in lamin B1 promotes telomere instability by disrupting the shelterin complex in human cells. Nucleic Acids Res 2021; 49:9886-9905. [PMID: 34469544 PMCID: PMC8464066 DOI: 10.1093/nar/gkab761] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 08/04/2021] [Accepted: 08/31/2021] [Indexed: 12/19/2022] Open
Abstract
Telomere maintenance is essential to preserve genomic stability and involves telomere-specific proteins, DNA replication and repair proteins. Lamins are key components of the nuclear envelope and play numerous roles, including maintenance of the nuclear integrity, regulation of transcription, and DNA replication. Elevated levels of lamin B1, one of the major lamins, have been observed in some human pathologies and several cancers. Yet, the effect of lamin B1 dysregulation on telomere maintenance remains unknown. Here, we unveil that lamin B1 overexpression drives telomere instability through the disruption of the shelterin complex. Indeed, lamin B1 dysregulation leads to an increase in telomere dysfunction-induced foci, telomeric fusions and telomere losses in human cells. Telomere aberrations were preceded by mislocalizations of TRF2 and its binding partner RAP1. Interestingly, we identified new interactions between lamin B1 and these shelterin proteins, which are strongly enhanced at the nuclear periphery upon lamin B1 overexpression. Importantly, chromosomal fusions induced by lamin B1 in excess were rescued by TRF2 overexpression. These data indicated that lamin B1 overexpression triggers telomere instability through a mislocalization of TRF2. Altogether our results point to lamin B1 as a new interacting partner of TRF2, that is involved in telomere stability.
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Affiliation(s)
- Gaëlle Pennarun
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Julien Picotto
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Laure Etourneaud
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Anna-Rita Redavid
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Anaïs Certain
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Laurent R Gauthier
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “Radiopathology” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Paula Fontanilla-Ramirez
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Didier Busso
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- Genetic Engineering and Expression Platform (CIGEX), iRCM, DRF, CEA, Fontenay-aux-Roses, France
| | - Caroline Chabance-Okumura
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Benoît Thézé
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - François D Boussin
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “Radiopathology” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
| | - Pascale Bertrand
- Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, F-92265 Fontenay-aux-Roses, France
- “DNA Repair and Ageing” Team, iRCM/IBFJ, DRF, CEA, Fontenay-aux-Roses, France
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13
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Kychygina A, Dall'Osto M, Allen JAM, Cadoret JC, Piras V, Pickett HA, Crabbe L. Progerin impairs 3D genome organization and induces fragile telomeres by limiting the dNTP pools. Sci Rep 2021; 11:13195. [PMID: 34162976 PMCID: PMC8222272 DOI: 10.1038/s41598-021-92631-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/11/2021] [Indexed: 11/09/2022] Open
Abstract
Chromatin organization within the nuclear volume is essential to regulate many aspects of its function and to safeguard its integrity. A key player in this spatial scattering of chromosomes is the nuclear envelope (NE). The NE tethers large chromatin domains through interaction with the nuclear lamina and other associated proteins. This organization is perturbed in cells from Hutchinson–Gilford progeria syndrome (HGPS), a genetic disorder characterized by premature aging features. Here, we show that HGPS-related lamina defects trigger an altered 3D telomere organization with increased contact sites between telomeres and the nuclear lamina, and an altered telomeric chromatin state. The genome-wide replication timing signature of these cells is perturbed, with a shift to earlier replication for regions that normally replicate late. As a consequence, we detected a higher density of replication forks traveling simultaneously on DNA fibers, which relies on limiting cellular dNTP pools to support processive DNA synthesis. Remarkably, increasing dNTP levels in HGPS cells rescued fragile telomeres, and improved the replicative capacity of the cells. Our work highlights a functional connection between NE dysfunction and telomere homeostasis in the context of premature aging.
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Affiliation(s)
- Anna Kychygina
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France.,INSERM UMR1291, CNRS UMR5051, UT3, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), 31059, Toulouse, France
| | - Marina Dall'Osto
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | | | - Vincent Piras
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Laure Crabbe
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France.
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14
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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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15
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Dumbović G, Braunschweig U, Langner HK, Smallegan M, Biayna J, Hass EP, Jastrzebska K, Blencowe B, Cech TR, Caruthers MH, Rinn JL. Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA is driven by intron retention. Nat Commun 2021; 12:3308. [PMID: 34083519 PMCID: PMC8175569 DOI: 10.1038/s41467-021-23221-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 04/07/2021] [Indexed: 12/27/2022] Open
Abstract
The spatial partitioning of the transcriptome in the cell is an important form of gene-expression regulation. Here, we address how intron retention influences the spatio-temporal dynamics of transcripts from two clinically relevant genes: TERT (Telomerase Reverse Transcriptase) pre-mRNA and TUG1 (Taurine-Upregulated Gene 1) lncRNA. Single molecule RNA FISH reveals that nuclear TERT transcripts uniformly and robustly retain specific introns. Our data suggest that the splicing of TERT retained introns occurs during mitosis. In contrast, TUG1 has a bimodal distribution of fully spliced cytoplasmic and intron-retained nuclear transcripts. We further test the functionality of intron-retention events using RNA-targeting thiomorpholino antisense oligonucleotides to block intron excision. We show that intron retention is the driving force for the nuclear compartmentalization of these RNAs. For both RNAs, altering this splicing-driven subcellular distribution has significant effects on cell viability. Together, these findings show that stable retention of specific introns can orchestrate spatial compartmentalization of these RNAs within the cell. This process reveals that modulating RNA localization via targeted intron retention can be utilized for RNA-based therapies.
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Affiliation(s)
- Gabrijela Dumbović
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| | | | - Heera K Langner
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Michael Smallegan
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Josep Biayna
- Institute for Research in Biomedicine, Parc Científic de Barcelona, Barcelona, Spain
| | - Evan P Hass
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Katarzyna Jastrzebska
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | | | - Thomas R Cech
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Marvin H Caruthers
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA.
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16
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Willaume S, Rass E, Fontanilla-Ramirez P, Moussa A, Wanschoor P, Bertrand P. A Link between Replicative Stress, Lamin Proteins, and Inflammation. Genes (Basel) 2021; 12:genes12040552. [PMID: 33918867 PMCID: PMC8070205 DOI: 10.3390/genes12040552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/23/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022] Open
Abstract
Double-stranded breaks (DSB), the most toxic DNA lesions, are either a consequence of cellular metabolism, programmed as in during V(D)J recombination, or induced by anti-tumoral therapies or accidental genotoxic exposure. One origin of DSB sources is replicative stress, a major source of genome instability, especially when the integrity of the replication forks is not properly guaranteed. To complete stalled replication, restarting the fork requires complex molecular mechanisms, such as protection, remodeling, and processing. Recently, a link has been made between DNA damage accumulation and inflammation. Indeed, defects in DNA repair or in replication can lead to the release of DNA fragments in the cytosol. The recognition of this self-DNA by DNA sensors leads to the production of inflammatory factors. This beneficial response activating an innate immune response and destruction of cells bearing DNA damage may be considered as a novel part of DNA damage response. However, upon accumulation of DNA damage, a chronic inflammatory cellular microenvironment may lead to inflammatory pathologies, aging, and progression of tumor cells. Progress in understanding the molecular mechanisms of DNA damage repair, replication stress, and cytosolic DNA production would allow to propose new therapeutical strategies against cancer or inflammatory diseases associated with aging. In this review, we describe the mechanisms involved in DSB repair, the replicative stress management, and its consequences. We also focus on new emerging links between key components of the nuclear envelope, the lamins, and DNA repair, management of replicative stress, and inflammation.
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17
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Baxley RM, Leung W, Schmit MM, Matson JP, Yin L, Oram MK, Wang L, Taylor J, Hedberg J, Rogers CB, Harvey AJ, Basu D, Taylor JC, Pagnamenta AT, Dreau H, Craft J, Ormondroyd E, Watkins H, Hendrickson EA, Mace EM, Orange JS, Aihara H, Stewart GS, Blair E, Cook JG, Bielinsky AK. Bi-allelic MCM10 variants associated with immune dysfunction and cardiomyopathy cause telomere shortening. Nat Commun 2021; 12:1626. [PMID: 33712616 PMCID: PMC7955084 DOI: 10.1038/s41467-021-21878-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 02/11/2021] [Indexed: 12/22/2022] Open
Abstract
Minichromosome maintenance protein 10 (MCM10) is essential for eukaryotic DNA replication. Here, we describe compound heterozygous MCM10 variants in patients with distinctive, but overlapping, clinical phenotypes: natural killer (NK) cell deficiency (NKD) and restrictive cardiomyopathy (RCM) with hypoplasia of the spleen and thymus. To understand the mechanism of MCM10-associated disease, we modeled these variants in human cell lines. MCM10 deficiency causes chronic replication stress that reduces cell viability due to increased genomic instability and telomere erosion. Our data suggest that loss of MCM10 function constrains telomerase activity by accumulating abnormal replication fork structures enriched with single-stranded DNA. Terminally-arrested replication forks in MCM10-deficient cells require endonucleolytic processing by MUS81, as MCM10:MUS81 double mutants display decreased viability and accelerated telomere shortening. We propose that these bi-allelic variants in MCM10 predispose specific cardiac and immune cell lineages to prematurely arrest during differentiation, causing the clinical phenotypes observed in both NKD and RCM patients.
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Affiliation(s)
- Ryan M Baxley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Wendy Leung
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Megan M Schmit
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jacob Peter Matson
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Lulu Yin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Marissa K Oram
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Liangjun Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - John Taylor
- Oxford Medical Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jack Hedberg
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Colette B Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Adam J Harvey
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Debashree Basu
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jenny C Taylor
- Wellcome Centre Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford NIHR Biomedical Research Centre, Oxford, OX3 7BN, UK
| | - Alistair T Pagnamenta
- Wellcome Centre Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford NIHR Biomedical Research Centre, Oxford, OX3 7BN, UK
| | - Helene Dreau
- Department of Haematology, University of Oxford, Oxford, OX3 7BN, UK
| | - Jude Craft
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Elizabeth Ormondroyd
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Emily M Mace
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Jordan S Orange
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Edward Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jeanette Gowen Cook
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.
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18
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Yang J, Liu X, Huang Y, He L, Zhang W, Ren J, Wang Y, Wu J, Wu X, Shan L, Yang X, Sun L, Liang J, Zhang Y, Shang Y. TRPS1 drives heterochromatic origin refiring and cancer genome evolution. Cell Rep 2021; 34:108814. [PMID: 33691114 DOI: 10.1016/j.celrep.2021.108814] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 12/18/2020] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
Exploitation of naturally occurring genetic mutations could empower the discovery of novel aspects of established cancer genes. We report here that TRPS1, a gene linked to the tricho-rhino-phalangeal syndrome (TRPS) and recently identified as a potential breast cancer driver, promotes breast carcinogenesis through regulating replication. Epigenomic decomposition of TRPS1 landscape reveals nearly half of H3K9me3-marked heterochromatic origins are occupied by TRPS1, where it encourages the chromatin loading of APC/C, resulting in uncontrolled origin refiring. TRPS1 binds to the genome through its atypical H3K9me3 reading via GATA and IKAROS domains, while TRPS-related mutations affect its chromatin binding, replication boosting, and tumorigenicity. Concordantly, overexpression of wild-type but not TRPS-associated mutants of TRPS1 is sufficient to drive cancer genome amplifications, which experience an extrachromosomal route and dynamically evolve to confer therapeutic resistance. Together, these results uncover a critical function of TRPS1 in driving heterochromatin origin firing and breast cancer genome evolution.
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Affiliation(s)
- Jianguo Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Xiaoping Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yunchao Huang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Lin He
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Wenting Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Jie Ren
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yue Wang
- Department of Biochemistry and Molecular Biology, School of Medicine, Hangzhou Normal University, Hangzhou 311121, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Jiajing Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xiaodi Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Lin Shan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xiaohan Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Jing Liang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yu Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China.
| | - Yongfeng Shang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China; Department of Biochemistry and Molecular Biology, School of Medicine, Hangzhou Normal University, Hangzhou 311121, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China.
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19
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Liddiard K, Grimstead JW, Cleal K, Evans A, Baird DM. Tracking telomere fusions through crisis reveals conflict between DNA transcription and the DNA damage response. NAR Cancer 2021; 3:zcaa044. [PMID: 33447828 PMCID: PMC7787266 DOI: 10.1093/narcan/zcaa044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/02/2020] [Accepted: 12/17/2020] [Indexed: 12/20/2022] Open
Abstract
Identifying attributes that distinguish pre-malignant from senescent cells provides opportunities for targeted disease eradication and revival of anti-tumour immunity. We modelled a telomere-driven crisis in four human fibroblast lines, sampling at multiple time points to delineate genomic rearrangements and transcriptome developments that characterize the transition from dynamic proliferation into replicative crisis. Progression through crisis was associated with abundant intra-chromosomal telomere fusions with increasing asymmetry and reduced microhomology usage, suggesting shifts in DNA repair capacity. Eroded telomeres also fused with genomic loci actively engaged in transcription, with particular enrichment in long genes. Both gross copy number alterations and transcriptional responses to crisis likely underpin the elevated frequencies of telomere fusion with chromosomes 9, 16, 17, 19 and most exceptionally, chromosome 12. Juxtaposition of crisis-regulated genes with loci undergoing de novo recombination exposes the collusive contributions of cellular stress responses to the evolving cancer genome.
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Affiliation(s)
- Kate Liddiard
- Division of Cancer and Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Julia W Grimstead
- Division of Cancer and Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Kez Cleal
- Division of Cancer and Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Anna Evans
- Wales Gene Park, Institute of Medical Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Duncan M Baird
- Division of Cancer and Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
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20
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Rausch C, Weber P, Prorok P, Hörl D, Maiser A, Lehmkuhl A, Chagin VO, Casas-Delucchi CS, Leonhardt H, Cardoso MC. Developmental differences in genome replication program and origin activation. Nucleic Acids Res 2021; 48:12751-12777. [PMID: 33264404 PMCID: PMC7736824 DOI: 10.1093/nar/gkaa1124] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/09/2020] [Accepted: 11/04/2020] [Indexed: 12/17/2022] Open
Abstract
To ensure error-free duplication of all (epi)genetic information once per cell cycle, DNA replication follows a cell type and developmental stage specific spatio-temporal program. Here, we analyze the spatio-temporal DNA replication progression in (un)differentiated mouse embryonic stem (mES) cells. Whereas telomeres replicate throughout S-phase, we observe mid S-phase replication of (peri)centromeric heterochromatin in mES cells, which switches to late S-phase replication upon differentiation. This replication timing reversal correlates with and depends on an increase in condensation and a decrease in acetylation of chromatin. We further find synchronous duplication of the Y chromosome, marking the end of S-phase, irrespectively of the pluripotency state. Using a combination of single-molecule and super-resolution microscopy, we measure molecular properties of the mES cell replicon, the number of replication foci active in parallel and their spatial clustering. We conclude that each replication nanofocus in mES cells corresponds to an individual replicon, with up to one quarter representing unidirectional forks. Furthermore, with molecular combing and genome-wide origin mapping analyses, we find that mES cells activate twice as many origins spaced at half the distance than somatic cells. Altogether, our results highlight fundamental developmental differences on progression of genome replication and origin activation in pluripotent cells.
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Affiliation(s)
- Cathia Rausch
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Patrick Weber
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Paulina Prorok
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - David Hörl
- Department of Biology II, LMU Munich, 81377 Munich, Germany
| | - Andreas Maiser
- Department of Biology II, LMU Munich, 81377 Munich, Germany
| | - Anne Lehmkuhl
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Vadim O Chagin
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany.,Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | | | | | - M Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
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21
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Viceconte N, Loriot A, Lona Abreu P, Scheibe M, Fradera Sola A, Butter F, De Smet C, Azzalin CM, Arnoult N, Decottignies A. PAR-TERRA is the main contributor to telomeric repeat-containing RNA transcripts in normal and cancer mouse cells. RNA (NEW YORK, N.Y.) 2021; 27:106-121. [PMID: 33127860 PMCID: PMC7749631 DOI: 10.1261/rna.076281.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/28/2020] [Indexed: 05/12/2023]
Abstract
Telomeric repeat-containing RNA (TERRA) molecules play important roles at telomeres, from heterochromatin regulation to telomerase activity control. In human cells, TERRA is transcribed from subtelomeric promoters located on most chromosome ends and associates with telomeres. The origin of mouse TERRA molecules is, however, unclear, as transcription from the pseudoautosomal PAR locus was recently suggested to account for the vast majority of TERRA in embryonic stem cells (ESC). Here, we confirm the production of TERRA from both the chromosome 18q telomere and the PAR locus in mouse embryonic fibroblasts, ESC, and various mouse cancer and immortalized cell lines, and we identify two novel sources of TERRA on mouse chromosome 2 and X. Using various approaches, we show that PAR-TERRA molecules account for the majority of TERRA transcripts, displaying an increase of two to four orders of magnitude compared to the telomeric 18q transcript. Finally, we present a SILAC-based pull-down screen revealing a large overlap between TERRA-interacting proteins in human and mouse cells, including PRC2 complex subunits, chromatin remodeling factors, DNA replication proteins, Aurora kinases, shelterin complex subunits, Bloom helicase, Coilin, and paraspeckle proteins. Hence, despite originating from distinct genomic regions, mouse and human TERRA are likely to play similar functions in cells.
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Affiliation(s)
- Nikenza Viceconte
- Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Université catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Axelle Loriot
- Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Université catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Patrícia Lona Abreu
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Marion Scheibe
- Quantitative Proteomics, Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Albert Fradera Sola
- Quantitative Proteomics, Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Falk Butter
- Quantitative Proteomics, Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Charles De Smet
- Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Université catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Claus M Azzalin
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Nausica Arnoult
- MCBD-University of Colorado Boulder, Boulder, Colorado 80309-0347, USA
| | - Anabelle Decottignies
- Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Université catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
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22
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Chromatin and Nuclear Architecture: Shaping DNA Replication in 3D. Trends Genet 2020; 36:967-980. [PMID: 32713597 DOI: 10.1016/j.tig.2020.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 12/13/2022]
Abstract
In eukaryotes, DNA replication progresses through a finely orchestrated temporal and spatial program. The 3D genome structure and nuclear architecture have recently emerged as fundamental determinants of the replication program. Factors with established roles in replication have been recognized as genome organization regulators. Exploiting paradigms from yeasts and mammals, we discuss how DNA replication is regulated in time and space through DNA-associated trans-acting factors, diffusible limiting replication initiation factors, higher-order chromatin folding, dynamic origin localization, and specific nuclear microenvironments. We present an integrated model for the regulation of DNA replication in 3D and highlight the importance of accurate spatio-temporal regulation of DNA replication in physiology and disease.
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23
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Towards delineating the chain of events that cause premature senescence in the accelerated aging syndrome Hutchinson-Gilford progeria (HGPS). Biochem Soc Trans 2020; 48:981-991. [PMID: 32539085 PMCID: PMC7329345 DOI: 10.1042/bst20190882] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 11/17/2022]
Abstract
The metazoan nucleus is equipped with a meshwork of intermediate filament proteins called the A- and B-type lamins. Lamins lie beneath the inner nuclear membrane and serve as a nexus to maintain the architectural integrity of the nucleus, chromatin organization, DNA repair and replication and to regulate nucleocytoplasmic transport. Perturbations or mutations in various components of the nuclear lamina result in a large spectrum of human diseases collectively called laminopathies. One of the most well-characterized laminopathies is Hutchinson-Gilford progeria (HGPS), a rare segmental premature aging syndrome that resembles many features of normal human aging. HGPS patients exhibit alopecia, skin abnormalities, osteoporosis and succumb to cardiovascular complications in their teens. HGPS is caused by a mutation in LMNA, resulting in a mutated form of lamin A, termed progerin. Progerin expression results in a myriad of cellular phenotypes including abnormal nuclear morphology, loss of peripheral heterochromatin, transcriptional changes, DNA replication defects, DNA damage and premature cellular senescence. A key challenge is to elucidate how these different phenotypes are causally and mechanistically linked. In this mini-review, we highlight some key findings and present a model on how progerin-induced phenotypes may be temporally and mechanistically linked.
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24
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DNA methylation in satellite repeats disorders. Essays Biochem 2020; 63:757-771. [PMID: 31387943 DOI: 10.1042/ebc20190028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023]
Abstract
Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.
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25
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Martins F, Sousa J, Pereira CD, Cruz e Silva OAB, Rebelo S. Nuclear envelope dysfunction and its contribution to the aging process. Aging Cell 2020; 19:e13143. [PMID: 32291910 PMCID: PMC7253059 DOI: 10.1111/acel.13143] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/28/2020] [Accepted: 03/09/2020] [Indexed: 12/25/2022] Open
Abstract
The nuclear envelope (NE) is the central organizing unit of the eukaryotic cell serving as a genome protective barrier and mechanotransduction interface between the cytoplasm and the nucleus. The NE is mainly composed of a nuclear lamina and a double membrane connected at specific points where the nuclear pore complexes (NPCs) form. Physiological aging might be generically defined as a functional decline across lifespan observed from the cellular to organismal level. Therefore, during aging and premature aging, several cellular alterations occur, including nuclear‐specific changes, particularly, altered nuclear transport, increased genomic instability induced by DNA damage, and telomere attrition. Here, we highlight and discuss proteins associated with nuclear transport dysfunction induced by aging, particularly nucleoporins, nuclear transport factors, and lamins. Moreover, changes in the structure of chromatin and consequent heterochromatin rearrangement upon aging are discussed. These alterations correlate with NE dysfunction, particularly lamins’ alterations. Finally, telomere attrition is addressed and correlated with altered levels of nuclear lamins and nuclear lamina‐associated proteins. Overall, the identification of molecular mechanisms underlying NE dysfunction, including upstream and downstream events, which have yet to be unraveled, will be determinant not only to our understanding of several pathologies, but as here discussed, in the aging process.
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Affiliation(s)
- Filipa Martins
- Neuroscience and Signaling Laboratory Institute of Biomedicine (iBiMED) Department of Medical Sciences University of Aveiro Aveiro Portugal
| | - Jéssica Sousa
- Neuroscience and Signaling Laboratory Institute of Biomedicine (iBiMED) Department of Medical Sciences University of Aveiro Aveiro Portugal
| | - Cátia D. Pereira
- Neuroscience and Signaling Laboratory Institute of Biomedicine (iBiMED) Department of Medical Sciences University of Aveiro Aveiro Portugal
| | - Odete A. B. Cruz e Silva
- Neuroscience and Signaling Laboratory Institute of Biomedicine (iBiMED) Department of Medical Sciences University of Aveiro Aveiro Portugal
- The Discoveries CTR Aveiro Portugal
| | - Sandra Rebelo
- Neuroscience and Signaling Laboratory Institute of Biomedicine (iBiMED) Department of Medical Sciences University of Aveiro Aveiro Portugal
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26
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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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27
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Chojnowski A, Ong PF, Foo MXR, Liebl D, Hor L, Stewart CL, Dreesen O. Heterochromatin loss as a determinant of progerin-induced DNA damage in Hutchinson-Gilford Progeria. Aging Cell 2020; 19:e13108. [PMID: 32087607 PMCID: PMC7059134 DOI: 10.1111/acel.13108] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 12/15/2019] [Accepted: 01/02/2020] [Indexed: 12/13/2022] Open
Abstract
Hutchinson-Gilford progeria is a premature aging syndrome caused by a truncated form of lamin A called progerin. Progerin expression results in a variety of cellular defects including heterochromatin loss, DNA damage, impaired proliferation and premature senescence. It remains unclear how these different progerin-induced phenotypes are temporally and mechanistically linked. To address these questions, we use a doxycycline-inducible system to restrict progerin expression to different stages of the cell cycle. We find that progerin expression leads to rapid and widespread loss of heterochromatin in G1-arrested cells, without causing DNA damage. In contrast, progerin triggers DNA damage exclusively during late stages of DNA replication, when heterochromatin is normally replicated, and preferentially in cells that have lost heterochromatin. Importantly, removal of progerin from G1-arrested cells restores heterochromatin levels and results in no permanent proliferative impediment. Taken together, these results delineate the chain of events that starts with progerin expression and ultimately results in premature senescence. Moreover, they provide a proof of principle that removal of progerin from quiescent cells restores heterochromatin levels and their proliferative capacity to normal levels.
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Affiliation(s)
- Alexandre Chojnowski
- Developmental and Regenerative BiologyInstitute of Medical BiologySingaporeSingapore
| | - Peh Fern Ong
- Cell Ageing, Skin Research Institute SingaporeSingaporeSingapore
| | | | - David Liebl
- A*STAR Microscopy PlatformSingaporeSingapore
| | - Louis‐Peter Hor
- Cell Ageing, Skin Research Institute SingaporeSingaporeSingapore
| | - Colin L. Stewart
- Developmental and Regenerative BiologyInstitute of Medical BiologySingaporeSingapore
| | - Oliver Dreesen
- Cell Ageing, Skin Research Institute SingaporeSingaporeSingapore
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28
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Sobecki M, Souaid C, Boulay J, Guerineau V, Noordermeer D, Crabbe L. MadID, a Versatile Approach to Map Protein-DNA Interactions, Highlights Telomere-Nuclear Envelope Contact Sites in Human Cells. Cell Rep 2019; 25:2891-2903.e5. [PMID: 30517874 PMCID: PMC6293860 DOI: 10.1016/j.celrep.2018.11.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/26/2018] [Accepted: 11/04/2018] [Indexed: 11/19/2022] Open
Abstract
Mapping the binding sites of DNA- or chromatin-interacting proteins is essential to understanding biological processes. DNA adenine methyltransferase identification (DamID) has emerged as a comprehensive method to map genome-wide occupancy of proteins of interest. A caveat of DamID is the specificity of Dam methyltransferase for GATC motifs that are not homogenously distributed in the genome. Here, we developed an optimized method named MadID, using proximity labeling of DNA by the methyltransferase M.EcoGII. M.EcoGII mediates N6-adenosine methylation in any DNA sequence context, resulting in deeper and unbiased coverage of the genome. We demonstrate, using m6A-specific immunoprecipitation and deep sequencing, that MadID is a robust method to identify protein-DNA interactions at the whole-genome level. Using MadID, we revealed contact sites between human telomeres, repetitive sequences devoid of GATC sites, and the nuclear envelope. Overall, MadID opens the way to identification of binding sites in genomic regions that were largely inaccessible. MadID: mapping of protein-DNA interactions in vivo using proximity labeling Deeper and unbiased genome-wide coverage using M.EcoGII, a methyltransferase Identification of binding sites in previously inaccessible regions of the genome Identification of telomere-nuclear envelope contact sites
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Affiliation(s)
- Michal Sobecki
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Charbel Souaid
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Jocelyne Boulay
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Vincent Guerineau
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Daan Noordermeer
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Laure Crabbe
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France; LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS/UPS, 31062 Toulouse Cedex, France.
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29
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Gaillard MC, Broucqsault N, Morere J, Laberthonnière C, Dion C, Badja C, Roche S, Nguyen K, Magdinier F, Robin JD. Analysis of the 4q35 chromatin organization reveals distinct long-range interactions in patients affected with Facio-Scapulo-Humeral Dystrophy. Sci Rep 2019; 9:10327. [PMID: 31316120 PMCID: PMC6637155 DOI: 10.1038/s41598-019-46861-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/25/2019] [Indexed: 12/15/2022] Open
Abstract
Facio-Scapulo Humeral dystrophy (FSHD) is the third most common myopathy, affecting 1 amongst 10,000 individuals (FSHD1, OMIM #158900). This autosomal dominant pathology is associated in 95% of cases with genetic and epigenetic alterations in the subtelomeric region at the extremity of the long arm of chromosome 4 (q arm). A large proportion of the remaining 5% of cases carry a mutation in the SMCHD1 gene (FSHD2, OMIM #158901). Here, we explored the 3D organization of the 4q35 locus by three-dimensions DNA in situ fluorescent hybridization (3D-FISH) in primary fibroblasts isolated from patients and healthy donors. We found that D4Z4 contractions and/or SMCHD1 mutations impact the spatial organization of the 4q35 region and trigger changes in the expression of different genes. Changes in gene expression were corroborated in muscle biopsies suggesting that the modified chromatin landscape impelled a modulation in the level of expression of a number of genes across the 4q35 locus in FSHD. Using induced pluripotent stem cells (hIPSC), we further examined whether chromatin organization is inherited after reprogramming or acquired during differentiation and showed that folding of the 4q35 region is modified upon differentiation. These results together with previous findings highlight the role of the D4Z4 macrosatellite repeat in the topological organization of chromatin and further indicate that the D4Z4-dependent 3D structure induces transcriptional changes of 4q35 genes expression.
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Affiliation(s)
| | | | - Julia Morere
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France
| | | | - Camille Dion
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France
| | - Cherif Badja
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France
| | - Stéphane Roche
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France
| | - Karine Nguyen
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France.,APHM, Laboratoire de Génétique Médicale, Hôpital de la Timone, Marseille, France
| | | | - Jérôme D Robin
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France.
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30
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Nguyen K, Broucqsault N, Chaix C, Roche S, Robin JD, Vovan C, Gerard L, Mégarbané A, Urtizberea JA, Bellance R, Barnérias C, David A, Eymard B, Fradin M, Manel V, Sacconi S, Tiffreau V, Zagnoli F, Cuisset JM, Salort-Campana E, Attarian S, Bernard R, Lévy N, Magdinier F. Deciphering the complexity of the 4q and 10q subtelomeres by molecular combing in healthy individuals and patients with facioscapulohumeral dystrophy. J Med Genet 2019; 56:590-601. [PMID: 31010831 DOI: 10.1136/jmedgenet-2018-105949] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/28/2019] [Accepted: 03/24/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Subtelomeres are variable regions between telomeres and chromosomal-specific regions. One of the most studied pathologies linked to subtelomeric imbalance is facioscapulohumeral dystrophy (FSHD). In most cases, this disease involves shortening of an array of D4Z4 macrosatellite elements at the 4q35 locus. The disease also segregates with a specific A-type haplotype containing a degenerated polyadenylation signal distal to the last repeat followed by a repetitive array of β-satellite elements. This classification applies to most patients with FSHD. A subset of patients called FSHD2 escapes this definition and carries a mutation in the SMCHD1 gene. We also recently described patients carrying a complex rearrangement consisting of a cis-duplication of the distal 4q35 locus identified by molecular combing. METHODS Using this high-resolution technology, we further investigated the organisation of the 4q35 region linked to the disease and the 10q26 locus presenting with 98% of homology in controls and patients. RESULTS Our analyses reveal a broad variability in size of the different elements composing these loci highlighting the complexity of these subtelomeres and the difficulty for genomic assembly. Out of the 1029 DNA samples analysed in our centre in the last 7 years, we also identified 54 cases clinically diagnosed with FSHD carrying complex genotypes. This includes mosaic patients, patients with deletions of the proximal 4q region and 23 cases with an atypical chromosome 10 pattern, infrequently found in the control population and never reported before. CONCLUSION Overall, this work underlines the complexity of these loci challenging the diagnosis and genetic counselling for this disease.
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Affiliation(s)
- Karine Nguyen
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Natacha Broucqsault
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Charlene Chaix
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France
| | - Stephane Roche
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Jérôme D Robin
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Catherine Vovan
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France
| | - Laurene Gerard
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France
| | | | - Jon Andoni Urtizberea
- Pôle Soins de suite et réadaptation handicaps lourds et maladies rares neurologiques, Hôpital Marin, Assistance publique des hopitaux de Paris, Hendaye, France
| | - Remi Bellance
- Hopital Pierre Zobda-Quitman, Fort-de-France, France
| | - Christine Barnérias
- Service de Neurologie infantile, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France.,Centre de Référence de Maladies Neuromusculaires Garches-Necker-Mondor-Hendaye (GNMH), Réseau National Français de la Filière Neuromusculaire (FILNEMUS), Paris, France
| | | | - Bruno Eymard
- Assistance Publique - Hopitaux de Paris, Paris, Île-de-France, France
| | - Melanie Fradin
- Service de Génétique Médicale, Centre De Référence Anomalies du Développement, CHU de Rennes, Rennes, France
| | - Véronique Manel
- Centre référent maladies neuromusculaires rares, Hospices Civils de Lyon, Hôpital Femme Mère Enfant, Bron, France
| | - Sabrina Sacconi
- Peripheral Nervous System, Muscle and ALS Department, Université Côte d'Azur, Nice, France.,Institute for Research on Cancer and Aging of Nice, Université Côte d'Azur, Faculty of Medicine, Nice, France
| | - Vincent Tiffreau
- Centre de Référence des Maladies Neuromusculaires, service de Médecine Physique et de Réadaptation, Centre hospitalier régionale de Lille, Lille, France
| | - Fabien Zagnoli
- Centre de Référence des Maladies Neuromusculaires, CHU Morvan, Brest, France
| | | | - Emmanuelle Salort-Campana
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France.,Centre de reference des maladies neuromusculaires, Assistance Publique Hopitaux de Marseille, Marseille, France
| | - Shahram Attarian
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France.,Centre de reference des maladies neuromusculaires, Assistance Publique Hopitaux de Marseille, Marseille, France
| | - Rafaëlle Bernard
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Nicolas Lévy
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Frederique Magdinier
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
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31
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The Emerging Roles of TERRA in Telomere Maintenance and Genome Stability. Cells 2019; 8:cells8030246. [PMID: 30875900 PMCID: PMC6468625 DOI: 10.3390/cells8030246] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 12/20/2022] Open
Abstract
The finding that transcription occurs at chromosome ends has opened new fields of study on the roles of telomeric transcripts in chromosome end maintenance and genome stability. Indeed, the ends of chromosomes are required to be protected from activation of DNA damage response and DNA repair pathways. Chromosome end protection is achieved by the activity of specific proteins that associate with chromosome ends, forming telomeres. Telomeres need to be constantly maintained as they are in a heterochromatic state and fold into specific structures (T-loops), which may hamper DNA replication. In addition, in the absence of maintenance mechanisms, chromosome ends shorten at every cell division due to limitations in the DNA replication machinery, which is unable to fully replicate the extremities of chromosomes. Altered telomere structure or critically short chromosome ends generate dysfunctional telomeres, ultimately leading to replicative senescence or chromosome instability. Telomere biology is thus implicated in multiple human diseases, including cancer. Emerging evidence indicates that a class of long noncoding RNAs transcribed at telomeres, known as TERRA for “TElomeric Repeat-containing RNA,” actively participates in the mechanisms regulating telomere maintenance and chromosome end protection. However, the molecular details of TERRA activities remain to be elucidated. In this review, we discuss recent findings on the emerging roles of TERRA in telomere maintenance and genome stability and their implications in human diseases.
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Aksenova AY, Mirkin SM. At the Beginning of the End and in the Middle of the Beginning: Structure and Maintenance of Telomeric DNA Repeats and Interstitial Telomeric Sequences. Genes (Basel) 2019; 10:genes10020118. [PMID: 30764567 PMCID: PMC6410037 DOI: 10.3390/genes10020118] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 02/07/2023] Open
Abstract
Tandem DNA repeats derived from the ancestral (TTAGGG)n run were first detected at chromosome ends of the majority of living organisms, hence the name telomeric DNA repeats. Subsequently, it has become clear that telomeric motifs are also present within chromosomes, and they were suitably called interstitial telomeric sequences (ITSs). It is well known that telomeric DNA repeats play a key role in chromosome stability, preventing end-to-end fusions and precluding the recurrent DNA loss during replication. Recent data suggest that ITSs are also important genomic elements as they confer its karyotype plasticity. In fact, ITSs appeared to be among the most unstable microsatellite sequences as they are highly length polymorphic and can trigger chromosomal fragility and gross chromosomal rearrangements. Importantly, mechanisms responsible for their instability appear to be similar to the mechanisms that maintain the length of genuine telomeres. This review compares the mechanisms of maintenance and dynamic properties of telomeric repeats and ITSs and discusses the implications of these dynamics on genome stability.
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Affiliation(s)
- Anna Y Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02421, USA.
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Laberthonnière C, Magdinier F, Robin JD. Bring It to an End: Does Telomeres Size Matter? Cells 2019; 8:E30. [PMID: 30626097 PMCID: PMC6356554 DOI: 10.3390/cells8010030] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/01/2019] [Accepted: 01/04/2019] [Indexed: 12/22/2022] Open
Abstract
Telomeres are unique nucleoprotein structures. Found at the edge of each chromosome, their main purpose is to mask DNA ends from the DNA-repair machinery by formation of protective loops. Through life and cell divisions, telomeres shorten and bring cells closer to either cell proliferation crisis or senescence. Beyond this mitotic clock role attributed to the need for telomere to be maintained over a critical length, the very tip of our DNA has been shown to impact transcription by position effect. TPE and a long-reach counterpart, TPE-OLD, are mechanisms recently described in human biology. Still in infancy, the mechanism of action of these processes and their respective genome wide impact remain to be resolved. In this review, we will discuss recent findings on telomere dynamics, TPE, TPE-OLD, and lessons learnt from model organisms.
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Affiliation(s)
| | - Frédérique Magdinier
- Aix Marseille Univ, MMG, Marseille Medical Genetics U1251, 13385 Marseille, France.
| | - Jérôme D Robin
- Aix Marseille Univ, MMG, Marseille Medical Genetics U1251, 13385 Marseille, France.
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34
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Coluzzi E, Leone S, Sgura A. Oxidative Stress Induces Telomere Dysfunction and Senescence by Replication Fork Arrest. Cells 2019; 8:cells8010019. [PMID: 30609792 PMCID: PMC6356380 DOI: 10.3390/cells8010019] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 12/29/2018] [Indexed: 12/12/2022] Open
Abstract
Oxidative DNA damage, particularly 8-oxoguanine, represents the most frequent DNA damage in human cells, especially at the telomeric level. The presence of oxidative lesions in the DNA can hinder the replication fork and is able to activate the DNA damage response. In this study, we wanted to understand the mechanisms by which oxidative damage causes telomere dysfunction and senescence in human primary fibroblasts. After acute oxidative stress at telomeres, our data demonstrated a reduction in TRF1 and TRF2, which are involved in proper telomere replication and T-loop formation, respectively. Furthermore, we observed a higher level of γH2AX with respect to 53BP1 at telomeres, suggesting a telomeric replication fork stall rather than double-strand breaks. To confirm this finding, we studied the replication of telomeres by Chromosome Orientation-FISH (CO-FISH). The data obtained show an increase in unreplicated telomeres after hydrogen peroxide treatment, corroborating the idea that the presence of 8-oxoG can induce replication fork arrest at telomeres. Lastly, we analyzed the H3K9me3 histone mark after oxidative stress at telomeres, and our results showed an increase of this marker, most likely inducing the heterochromatinization of telomeres. These results suggest that 8-oxoG is fundamental in oxidative stress-induced telomeric damage, principally causing replication fork arrest.
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Affiliation(s)
- Elisa Coluzzi
- Department of Science, University of Rome "Roma TRE", Viale Guglielmo Marconi, 446, 00146 Rome, Italy.
| | - Stefano Leone
- Department of Science, University of Rome "Roma TRE", Viale Guglielmo Marconi, 446, 00146 Rome, Italy.
| | - Antonella Sgura
- Department of Science, University of Rome "Roma TRE", Viale Guglielmo Marconi, 446, 00146 Rome, Italy.
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35
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Gali H, Mason-Osann E, Flynn RL. Direct Visualization of DNA Replication at Telomeres Using DNA Fiber Combing Combined with Telomere FISH. Methods Mol Biol 2019; 1999:319-325. [PMID: 31127588 DOI: 10.1007/978-1-4939-9500-4_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The ability to analyze individual DNA fibers undergoing active DNA synthesis has emerged as a powerful technique in the field of DNA replication. Much of the initial analysis has focused on replication throughout the genome. However, more recent advancements in this technique have allowed for the visualization of replication patterns at distinct loci or regions within the genome. This type of locus-specific resolution will greatly enhance our understanding of the dynamics of DNA replication in regions that provide a challenge to the replication machinery. Here, we describe a protocol that will allow for the visualization of DNA replication through one of the most structurally complex regions in the human genome, the telomeric DNA.
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Affiliation(s)
- Himabindu Gali
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA
| | - Emily Mason-Osann
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA
| | - Rachel Litman Flynn
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA.
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA.
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36
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Minina JM, Karamysheva TV, Rubtsov NB, Zhdanova NS. Replication timing of large Sorex granarius (Soricidae, Eulipotyphla) telomeres. PROTOPLASMA 2018; 255:1477-1486. [PMID: 29627866 DOI: 10.1007/s00709-018-1244-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
Previously, we described the unique feature of telomeric regions in Iberian shrew Sorex granarius: its telomeres have two ranges of size, very small (3.8 kb of telomeric repeats on average) and very large discontinuous telomeres (213 kb) interrupted with 18S rDNA. In this study, we have demonstrated extraordinary replication pattern of S. granarius large telomeres that have not been shown before in other studied mammal. Using the ReD-FISH procedure, we observed prolonged, through S period, large telomere replication. Furthermore, revealed ReD-FISH asymmetric signals were probably caused by partial replication of telomeres within an hour of 5-bromodeoxyuridine treatment due to the large size and special organization. We also found that in contrast to the telomeric halo from primary fibroblasts of bovine, mink, and common shrew, telomere halo of S. granarius consists of multiple loops bundled together, some of which contain rDNA. Here, we suggested several replicons firing possibly stochastic in each large telomere. Finally, we performed the TIF assay to reveal DNA damage responses at the telomeres, and along with TIF in nuclei, we found large bodies of telomeric DNA and ɤ-H2AX in the cytoplasm and on the surface of fibroblasts. We discuss the possibility of additional origin activation together with recombination-dependent replication pathways, mainly homologous recombination including BIR for replication fork stagnation overcoming and further S. granarius large telomere replication.
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Affiliation(s)
- Julia M Minina
- The Federal Research Center Institute of Cytology and Genetics of SB RAS, Lavrentjeva av. 10, 630090, Novosibirsk, Russia.
| | - Tatjana V Karamysheva
- The Federal Research Center Institute of Cytology and Genetics of SB RAS, Lavrentjeva av. 10, 630090, Novosibirsk, Russia
| | - Nicolaj B Rubtsov
- The Federal Research Center Institute of Cytology and Genetics of SB RAS, Lavrentjeva av. 10, 630090, Novosibirsk, Russia
| | - Natalia S Zhdanova
- The Federal Research Center Institute of Cytology and Genetics of SB RAS, Lavrentjeva av. 10, 630090, Novosibirsk, Russia
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37
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Concia L, Brooks AM, Wheeler E, Zynda GJ, Wear EE, LeBlanc C, Song J, Lee TJ, Pascuzzi PE, Martienssen RA, Vaughn MW, Thompson WF, Hanley-Bowdoin L. Genome-Wide Analysis of the Arabidopsis Replication Timing Program. PLANT PHYSIOLOGY 2018; 176:2166-2185. [PMID: 29301956 PMCID: PMC5841712 DOI: 10.1104/pp.17.01537] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/03/2018] [Indexed: 05/21/2023]
Abstract
Eukaryotes use a temporally regulated process, known as the replication timing program, to ensure that their genomes are fully and accurately duplicated during S phase. Replication timing programs are predictive of genomic features and activity and are considered to be functional readouts of chromatin organization. Although replication timing programs have been described for yeast and animal systems, much less is known about the temporal regulation of plant DNA replication or its relationship to genome sequence and chromatin structure. We used the thymidine analog, 5-ethynyl-2'-deoxyuridine, in combination with flow sorting and Repli-Seq to describe, at high-resolution, the genome-wide replication timing program for Arabidopsis (Arabidopsis thaliana) Col-0 suspension cells. We identified genomic regions that replicate predominantly during early, mid, and late S phase, and correlated these regions with genomic features and with data for chromatin state, accessibility, and long-distance interaction. Arabidopsis chromosome arms tend to replicate early while pericentromeric regions replicate late. Early and mid-replicating regions are gene-rich and predominantly euchromatic, while late regions are rich in transposable elements and primarily heterochromatic. However, the distribution of chromatin states across the different times is complex, with each replication time corresponding to a mixture of states. Early and mid-replicating sequences interact with each other and not with late sequences, but early regions are more accessible than mid regions. The replication timing program in Arabidopsis reflects a bipartite genomic organization with early/mid-replicating regions and late regions forming separate, noninteracting compartments. The temporal order of DNA replication within the early/mid compartment may be modulated largely by chromatin accessibility.
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Affiliation(s)
- Lorenzo Concia
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Ashley M Brooks
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Emily Wheeler
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Gregory J Zynda
- Texas Advanced Computing Center, University of Texas at Austin, Austin, Texas 78758
| | - Emily E Wear
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Chantal LeBlanc
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Jawon Song
- Texas Advanced Computing Center, University of Texas at Austin, Austin, Texas 78758
| | - Tae-Jin Lee
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Pete E Pascuzzi
- Purdue University Libraries, Purdue University, West Lafayette, Indiana 47907
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Matthew W Vaughn
- Texas Advanced Computing Center, University of Texas at Austin, Austin, Texas 78758
| | - William F Thompson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695
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38
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Gunes C, Avila AI, Rudolph KL. Telomeres in cancer. Differentiation 2017; 99:41-50. [PMID: 29291448 DOI: 10.1016/j.diff.2017.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 02/07/2023]
Abstract
Telomere shortening as a consequence of cell divisions during aging and chronic diseases associates with an increased cancer risk. Experimental data revealed that telomere shortening results in telomere dysfunction, which in turn affects tumorigenesis in two ways. First, telomere dysfunction suppresses tumor progression by the activation of DNA damage checkpoints, which induce cell cycle arrest (senescence) or apoptosis, as well as by inducing metabolic compromise and activation of immune responses directed against senescent cells. Second, telomere dysfunction promotes tumorigenesis by inducing chromosomal instability in tumor initiating cells, by inhibiting proliferative competition of non-transformed cells, and possibly, also by influencing tumor cell plasticity. The tumor promoting effects of telomere dysfunction are context dependent and require the loss of p53-dependent DNA damage checkpoints or other genetic modifiers that attenuate DNA damage responses possibly involving complex interactions of different genes. The activation of telomere stabilizing mechanisms appears as a subsequent step, which is required to enable immortal grotwh of emerging cancer cells. Here, we conceptually discuss our current knowledge and new, unpublished experimental data on telomere dependent influences on tumor initiation and progression.
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Affiliation(s)
| | - Alush Irene Avila
- Research Group on Stem Cell Aging, Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745 Jena, Germany
| | - K Lenhard Rudolph
- Research Group on Stem Cell Aging, Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745 Jena, Germany.
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39
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CTCF driven TERRA transcription facilitates completion of telomere DNA replication. Nat Commun 2017; 8:2114. [PMID: 29235471 PMCID: PMC5727389 DOI: 10.1038/s41467-017-02212-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 11/14/2017] [Indexed: 12/20/2022] Open
Abstract
Telomere repeat DNA forms a nucleo-protein structure that can obstruct chromosomal DNA replication, especially under conditions of replication stress. Transcription of telomere repeats can initiate at subtelomeric CTCF-binding sites to generate telomere repeat-encoding RNA (TERRA), but the role of transcription, CTCF, and TERRA in telomere replication is not known. Here, we have used CRISPR/Cas9 gene editing to mutate CTCF-binding sites at the putative start site of TERRA transcripts for a class of subtelomeres. Under replication stress, telomeres lacking CTCF-driven TERRA exhibit sister-telomere loss and upon entry into mitosis, exhibit the formation of ultra-fine anaphase bridges and micronuclei. Importantly, these phenotypes could be rescued by the forced transcription of TERRA independent of CTCF binding. Our findings indicate that subtelomeric CTCF facilitates telomeric DNA replication by promoting TERRA transcription. Our findings also demonstrate that CTCF-driven TERRA transcription acts in cis to facilitate telomere repeat replication and chromosome stability. TERRA RNA is involved in maintaining stability during telomere repeat replication. Here the authors, by using CRISPR/Cas9, mutate CTCF-binding sites at start site of TERRA transcripts and find that subtelomeric CTCF facilitates telomeric DNA replication by promoting TERRA transcription.
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40
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Sagie S, Edni O, Weinberg J, Toubiana S, Kozlovski T, Frostig T, Katzin N, Bar-Am I, Selig S. Non-random length distribution of individual telomeres in immunodeficiency, centromeric instability and facial anomalies syndrome, type I. Hum Mol Genet 2017; 26:4244-4256. [PMID: 28973513 DOI: 10.1093/hmg/ddx313] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/03/2017] [Indexed: 12/30/2022] Open
Abstract
Mutations in the de novo DNA methyltransferase DNMT3B lead to Immunodeficiency, Centromeric Instability and Facial anomalies (ICF) syndrome, type I. This syndrome is characterized, among other hypomethylated genomic loci, by severe subtelomeric hypomethylation that is associated with abnormally short telomere length. While it was demonstrated that the mean telomere length is significantly shorter in ICF type I cells, it is unknown whether all telomeres are equally vulnerable to shortening. To study this question we determined by combined telomere-FISH and spectral karyotyping the relative length of each individual telomere in lymphoblastoid cell lines (LCLs) generated from multiple ICF syndrome patients and control individuals. Here we confirm the short telomere lengths, and demonstrate that telomere length variance in the ICF patient group is much larger than in the control group, suggesting that not all telomeres shorten in a uniform manner. We identified a subgroup of telomeres whose relatively short lengths can distinguish with a high degree of certainty between a control and an ICF metaphase, proposing that in ICF syndrome cells, certain individual telomeres are consistently at greater risk to shorten than others. The majority of these telomeres display high sequence identity at the distal 2 kb of their subtelomeres, suggesting that the attenuation in DNMT3B methylation capacity affects individual telomeres to different degrees based, at least in part, on the adjacent subtelomeric sequence composition.
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Affiliation(s)
- Shira Sagie
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Omer Edni
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Joseph Weinberg
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Shir Toubiana
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Tal Kozlovski
- Department of Statistics and Operations Research, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 39040, Israel
| | - Tzviel Frostig
- Department of Statistics and Operations Research, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 39040, Israel
| | - Nirit Katzin
- Applied Spectral Imaging Ltd., Yokneam 2069200, Israel
| | - Irit Bar-Am
- Applied Spectral Imaging Ltd., Yokneam 2069200, Israel
| | - Sara Selig
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
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41
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Serebryannyy L, Misteli T. Protein sequestration at the nuclear periphery as a potential regulatory mechanism in premature aging. J Cell Biol 2017; 217:21-37. [PMID: 29051264 PMCID: PMC5748986 DOI: 10.1083/jcb.201706061] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/10/2017] [Accepted: 08/17/2017] [Indexed: 12/19/2022] Open
Abstract
Serebryannyy and Misteli provide a perspective on how protein sequestration at the inner nuclear membrane and nuclear lamina might influence aging. Despite the extensive description of numerous molecular changes associated with aging, insights into the driver mechanisms of this fundamental biological process are limited. Based on observations in the premature aging syndrome Hutchinson–Gilford progeria, we explore the possibility that protein regulation at the inner nuclear membrane and the nuclear lamina contributes to the aging process. In support, sequestration of nucleoplasmic proteins to the periphery impacts cell stemness, the response to cytotoxicity, proliferation, changes in chromatin state, and telomere stability. These observations point to the nuclear periphery as a central regulator of the aging phenotype.
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Affiliation(s)
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD
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Nguyen K, Puppo F, Roche S, Gaillard MC, Chaix C, Lagarde A, Pierret M, Vovan C, Olschwang S, Salort-Campana E, Attarian S, Bartoli M, Bernard R, Magdinier F, Levy N. Molecular combing reveals complex 4q35 rearrangements in Facioscapulohumeral dystrophy. Hum Mutat 2017; 38:1432-1441. [DOI: 10.1002/humu.23304] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 07/19/2017] [Accepted: 07/22/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Karine Nguyen
- Aix Marseille Université; INSERM GMGF UMR S_910; Marseille 13385 France
- APHM; Département de Génétique Médicale; Hôpital d'enfants de la Timone; Marseille 13385 France
| | - Francesca Puppo
- Aix Marseille Université; INSERM GMGF UMR S_910; Marseille 13385 France
| | - Stéphane Roche
- Aix Marseille Université; INSERM GMGF UMR S_910; Marseille 13385 France
| | | | - Charlène Chaix
- APHM; Département de Génétique Médicale; Hôpital d'enfants de la Timone; Marseille 13385 France
| | - Arnaud Lagarde
- Aix Marseille Université; INSERM GMGF UMR S_910; Marseille 13385 France
| | | | - Catherine Vovan
- APHM; Département de Génétique Médicale; Hôpital d'enfants de la Timone; Marseille 13385 France
| | - Sylviane Olschwang
- Aix Marseille Université; INSERM GMGF UMR S_910; Marseille 13385 France
- APHM; Département de Génétique Médicale; Hôpital d'enfants de la Timone; Marseille 13385 France
- Groupe Ramsay Générale de Santé; Hôpital Clairval; Marseille France
| | - Emmanuelle Salort-Campana
- Aix Marseille Université; INSERM GMGF UMR S_910; Marseille 13385 France
- APHM; Centre de Référence des Maladies Neuromusculaires et de la SLA; Hôpital de la Timone; Marseille 13385 France
| | - Shahram Attarian
- Aix Marseille Université; INSERM GMGF UMR S_910; Marseille 13385 France
- APHM; Centre de Référence des Maladies Neuromusculaires et de la SLA; Hôpital de la Timone; Marseille 13385 France
| | - Marc Bartoli
- Aix Marseille Université; INSERM GMGF UMR S_910; Marseille 13385 France
| | - Rafaëlle Bernard
- Aix Marseille Université; INSERM GMGF UMR S_910; Marseille 13385 France
- APHM; Département de Génétique Médicale; Hôpital d'enfants de la Timone; Marseille 13385 France
| | | | - Nicolas Levy
- Aix Marseille Université; INSERM GMGF UMR S_910; Marseille 13385 France
- APHM; Département de Génétique Médicale; Hôpital d'enfants de la Timone; Marseille 13385 France
- APHM; Centre de Ressources Biologiques; Hôpital de la Timone; Marseille 13385 France
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DNA Replication Origins and Fork Progression at Mammalian Telomeres. Genes (Basel) 2017; 8:genes8040112. [PMID: 28350373 PMCID: PMC5406859 DOI: 10.3390/genes8040112] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/23/2017] [Accepted: 03/24/2017] [Indexed: 12/20/2022] Open
Abstract
Telomeres are essential chromosomal regions that prevent critical shortening of linear chromosomes and genomic instability in eukaryotic cells. The bulk of telomeric DNA is replicated by semi-conservative DNA replication in the same way as the rest of the genome. However, recent findings revealed that replication of telomeric repeats is a potential cause of chromosomal instability, because DNA replication through telomeres is challenged by the repetitive telomeric sequences and specific structures that hamper the replication fork. In this review, we summarize current understanding of the mechanisms by which telomeres are faithfully and safely replicated in mammalian cells. Various telomere-associated proteins ensure efficient telomere replication at different steps, such as licensing of replication origins, passage of replication forks, proper fork restart after replication stress, and dissolution of post-replicative structures. In particular, shelterin proteins have central roles in the control of telomere replication. Through physical interactions, accessory proteins are recruited to maintain telomere integrity during DNA replication. Dormant replication origins and/or homology-directed repair may rescue inappropriate fork stalling or collapse that can cause defects in telomere structure and functions.
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Maestroni L, Matmati S, Coulon S. Solving the Telomere Replication Problem. Genes (Basel) 2017; 8:genes8020055. [PMID: 28146113 PMCID: PMC5333044 DOI: 10.3390/genes8020055] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/23/2017] [Indexed: 12/12/2022] Open
Abstract
Telomeres are complex nucleoprotein structures that protect the extremities of linear chromosomes. Telomere replication is a major challenge because many obstacles to the progression of the replication fork are concentrated at the ends of the chromosomes. This is known as the telomere replication problem. In this article, different and new aspects of telomere replication, that can threaten the integrity of telomeres, will be reviewed. In particular, we will focus on the functions of shelterin and the replisome for the preservation of telomere integrity.
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Affiliation(s)
- Laetitia Maestroni
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labélisée Ligue Contre le Cancer, 13273 Marseille, France.
| | - Samah Matmati
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labélisée Ligue Contre le Cancer, 13273 Marseille, France.
| | - Stéphane Coulon
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labélisée Ligue Contre le Cancer, 13273 Marseille, France.
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45
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Vasianovich Y, Wellinger RJ. Life and Death of Yeast Telomerase RNA. J Mol Biol 2017; 429:3242-3254. [PMID: 28115201 DOI: 10.1016/j.jmb.2017.01.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/10/2017] [Accepted: 01/14/2017] [Indexed: 12/20/2022]
Abstract
Telomerase reverse transcriptase elongates telomeres to overcome their natural attrition and allow unlimited cellular proliferation, a characteristic shared by stem cells and the majority of malignant cancerous cells. The telomerase holoenzyme comprises a core RNA molecule, a catalytic protein subunit, and other accessory proteins. Malfunction of certain telomerase components can cause serious genetic disorders including dyskeratosis congenita and aplastic anaemia. A hierarchy of tightly regulated steps constitutes the process of telomerase biogenesis, which, if interrupted or misregulated, can impede the production of a functional enzyme and severely affect telomere maintenance. Here, we take a closer look at the budding yeast telomerase RNA component, TLC1, in its long lifetime journey around the cell. We review the extensive knowledge on TLC1 transcription and processing. We focus on exciting recent studies on telomerase assembly, trafficking, and nuclear dynamics, which for the first time unveil striking similarities between the yeast and human telomerase ribonucleoproteins. Finally, we identify questions yet to be answered and new directions to be followed, which, in the future, might improve our knowledge of telomerase biology and trigger the development of new therapies against cancer and other telomerase-related diseases.
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Affiliation(s)
- Yulia Vasianovich
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Applied Cancer Research Pavillion, 3201 rue Jean-Mignault, Sherbrooke, Quebec, J1E 4K8, Canada.
| | - Raymund J Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Applied Cancer Research Pavillion, 3201 rue Jean-Mignault, Sherbrooke, Quebec, J1E 4K8, Canada.
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46
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Rif1-Dependent Regulation of Genome Replication in Mammals. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:259-272. [DOI: 10.1007/978-981-10-6955-0_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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47
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Cortizas EM, Zahn A, Safavi S, Reed JA, Vega F, Di Noia JM, Verdun RE. UNG protects B cells from AID-induced telomere loss. J Exp Med 2016; 213:2459-2472. [PMID: 27697833 PMCID: PMC5068241 DOI: 10.1084/jem.20160635] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/16/2016] [Indexed: 02/05/2023] Open
Abstract
Verdun and colleagues find that the uracil-DNA glycosylase UNG, which promotes DNA breaks in the immunoglobulin genes during class switch recombination and is required for AID-induced chromosomal translocations, protects telomeres from AID-induced DNA damage and subsequent dysfunction. Activation-induced deaminase (AID) initiates antibody gene diversification by creating G:U mismatches in the immunoglobulin loci. However, AID also deaminates nonimmunoglobulin genes, and failure to faithfully repair these off-target lesions can cause B cell lymphoma. In this study, we identify a mechanism by which processing of G:U produced by AID at the telomeres can eliminate B cells at risk of genomic instability. We show that telomeres are off-target substrates of AID and that B cell proliferation depends on protective repair by uracil-DNA glycosylase (UNG). In contrast, in the absence of UNG activity, deleterious processing by mismatch repair leads to telomere loss and defective cell proliferation. Indeed, we show that UNG deficiency reduces B cell clonal expansion in the germinal center in mice and blocks the proliferation of tumor B cells expressing AID. We propose that AID-induced damage at telomeres acts as a fail-safe mechanism to limit the tumor promoting activity of AID when it overwhelms uracil excision repair.
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Affiliation(s)
- Elena M Cortizas
- Department of Medicine, Division of Hematology-Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136
| | - Astrid Zahn
- Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
| | - Shiva Safavi
- Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada.,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 0G4, Canada
| | - Joseph A Reed
- Department of Medicine, Division of Hematology-Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136
| | - Francisco Vega
- Department of Pathology and Laboratory Medicine, Division of Hematopathology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada .,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 0G4, Canada.,Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Ramiro E Verdun
- Department of Medicine, Division of Hematology-Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136 .,Geriatric Research, Education, and Clinical Center, Miami VA Healthcare System, FL 33125
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48
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Piqueret-Stephan L, Ricoul M, Hempel WM, Sabatier L. Replication Timing of Human Telomeres is Conserved during Immortalization and Influenced by Respective Subtelomeres. Sci Rep 2016; 6:32510. [PMID: 27587191 PMCID: PMC5009427 DOI: 10.1038/srep32510] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 08/05/2016] [Indexed: 12/16/2022] Open
Abstract
Telomeres are specific structures that protect chromosome ends and act as a biological clock, preventing normal cells from replicating indefinitely. Mammalian telomeres are replicated throughout S-phase in a predetermined order. However, the mechanism of this regulation is still unknown. We wished to investigate this phenomenon under physiological conditions in a changing environment, such as the immortalization process to better understand the mechanism for its control. We thus examined the timing of human telomere replication in normal and SV40 immortalized cells, which are cytogenetically very similar to cancer cells. We found that the timing of telomere replication was globally conserved under different conditions during the immortalization process. The timing of telomere replication was conserved despite changes in telomere length due to endogenous telomerase reactivation, in duplicated homologous chromosomes, and in rearranged chromosomes. Importantly, translocated telomeres, possessing their initial subtelomere, retained the replication timing of their homolog, independently of the proportion of the translocated arm, even when the remaining flanking DNA is restricted to its subtelomere, the closest chromosome-specific sequences (inferior to 500 kb). Our observations support the notion that subtelomere regions strongly influence the replication timing of the associated telomere.
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Affiliation(s)
- Laure Piqueret-Stephan
- PROCyTOX Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Fontenay-aux-Roses and Université Paris-Saclay, France
| | - Michelle Ricoul
- PROCyTOX Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Fontenay-aux-Roses and Université Paris-Saclay, France
| | - William M Hempel
- PROCyTOX Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Fontenay-aux-Roses and Université Paris-Saclay, France
| | - Laure Sabatier
- PROCyTOX Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Fontenay-aux-Roses and Université Paris-Saclay, France
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Schmidt JC, Zaug AJ, Cech TR. Live Cell Imaging Reveals the Dynamics of Telomerase Recruitment to Telomeres. Cell 2016; 166:1188-1197.e9. [PMID: 27523609 PMCID: PMC5743434 DOI: 10.1016/j.cell.2016.07.033] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 06/14/2016] [Accepted: 07/21/2016] [Indexed: 01/22/2023]
Abstract
Telomerase maintains genome integrity by adding repetitive DNA sequences to the chromosome ends in actively dividing cells, including 90% of all cancer cells. Recruitment of human telomerase to telomeres occurs during S-phase of the cell cycle, but the molecular mechanism of the process is only partially understood. Here, we use CRISPR genome editing and single-molecule imaging to track telomerase trafficking in nuclei of living human cells. We demonstrate that telomerase uses three-dimensional diffusion to search for telomeres, probing each telomere thousands of times each S-phase but only rarely forming a stable association. Both the transient and stable association events depend on the direct interaction of the telomerase protein TERT with the telomeric protein TPP1. Our results reveal that telomerase recruitment to telomeres is driven by dynamic interactions between the rapidly diffusing telomerase and the chromosome end.
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Affiliation(s)
- Jens C Schmidt
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Arthur J Zaug
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Thomas R Cech
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80309, USA.
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50
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Robin JD, Magdinier F. Physiological and Pathological Aging Affects Chromatin Dynamics, Structure and Function at the Nuclear Edge. Front Genet 2016; 7:153. [PMID: 27602048 PMCID: PMC4993774 DOI: 10.3389/fgene.2016.00153] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 08/08/2016] [Indexed: 01/29/2023] Open
Abstract
Lamins are intermediate filaments that form a complex meshwork at the inner nuclear membrane. Mammalian cells express two types of Lamins, Lamins A/C and Lamins B, encoded by three different genes, LMNA, LMNB1, and LMNB2. Mutations in the LMNA gene are associated with a group of phenotypically diverse diseases referred to as laminopathies. Lamins interact with a large number of binding partners including proteins of the nuclear envelope but also chromatin-associated factors. Lamins not only constitute a scaffold for nuclear shape, rigidity and resistance to stress but also contribute to the organization of chromatin and chromosomal domains. We will discuss here the impact of A-type Lamins loss on alterations of chromatin organization and formation of chromatin domains and how disorganization of the lamina contributes to the patho-physiology of premature aging syndromes.
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Affiliation(s)
- Jérôme D Robin
- IRCAN, CNRS UMR 7284/INSERM U1081, Faculté de Médecine Nice, France
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