51
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Behrens YL, Thomay K, Hagedorn M, Ebersold J, Henrich L, Nustede R, Schlegelberger B, Göhring G. Comparison of different methods for telomere length measurement in whole blood and blood cell subsets: Recommendations for telomere length measurement in hematological diseases. Genes Chromosomes Cancer 2017; 56:700-708. [DOI: 10.1002/gcc.22475] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 05/29/2017] [Accepted: 05/30/2017] [Indexed: 12/12/2022] Open
Affiliation(s)
- Yvonne Lisa Behrens
- Department of Human Genetics; Hannover Medical School; Carl-Neuberg-Str.1 Hannover 30625 Germany
| | - Kathrin Thomay
- Department of Human Genetics; Hannover Medical School; Carl-Neuberg-Str.1 Hannover 30625 Germany
| | - Maike Hagedorn
- Department of Human Genetics; Hannover Medical School; Carl-Neuberg-Str.1 Hannover 30625 Germany
| | - Juliane Ebersold
- Department of Human Genetics; Hannover Medical School; Carl-Neuberg-Str.1 Hannover 30625 Germany
| | - Lea Henrich
- Department of Human Genetics; Hannover Medical School; Carl-Neuberg-Str.1 Hannover 30625 Germany
| | - Rainer Nustede
- Pediatric surgery, Hannover Medical School; Carl-Neuberg-Str.1 Hannover 30625 Germany
| | - Brigitte Schlegelberger
- Department of Human Genetics; Hannover Medical School; Carl-Neuberg-Str.1 Hannover 30625 Germany
| | - Gudrun Göhring
- Department of Human Genetics; Hannover Medical School; Carl-Neuberg-Str.1 Hannover 30625 Germany
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Ariffin H, Azanan MS, Abd Ghafar SS, Oh L, Lau KH, Thirunavakarasu T, Sedan A, Ibrahim K, Chan A, Chin TF, Liew FF, Jeyamogan S, Rosli ES, Baharudin R, Yap TY, Skinner R, Lum SH, Hainaut P. Young adult survivors of childhood acute lymphoblastic leukemia show evidence of chronic inflammation and cellular aging. Cancer 2017; 123:4207-4214. [PMID: 28654149 DOI: 10.1002/cncr.30857] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/28/2017] [Accepted: 05/29/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND Large epidemiologic studies have reported the premature onset of age-related conditions, such as ischemic heart disease and diabetes mellitus, in childhood cancer survivors, decades earlier than in their peers. The authors investigated whether young adult survivors of childhood acute lymphoblastic leukemia (ALL) have a biologic phenotype of cellular ageing and chronic inflammation. METHODS Plasma inflammatory cytokines were measured using a cytometric bead array in 87 asymptomatic young adult survivors of childhood ALL (median age, 25 years; age range, 18-35 years) who attended annual follow-up clinic and compared with healthy, age-matched and sex-matched controls. Leukocyte telomere length (LTL) was measured using Southern blot analysis. RESULTS Survivors had significant elevation of plasma interleukin-2 (IL-2), IL-10, IL-17a, and high-sensitivity C-reactive protein levels (all P < .05). A raised high-sensitivity C-reactive protein level (>0.8 mg/dL) was related to increased odds of having metabolic syndrome (odds ratio, 7.256; 95% confidence interval, 1.501-35.074). Survivors also had significantly shorter LTL compared with controls (median, 9866 vs 10,392 base pairs; P = .021). Compared with published data, LTL in survivors was similar to that in healthy individuals aged 20 years older. Survivors who received cranial irradiation had shorter LTL compared with those who had not (P = .013). CONCLUSIONS Asymptomatic young adult survivors of childhood ALL demonstrate a biologic profile of chronic inflammation and telomere attrition, consistent with an early onset of cellular processes that drive accelerated aging. These processes may explain the premature development of age-related chronic conditions in childhood cancer survivors. Understanding their molecular basis may facilitate targeted interventions to disrupt the accelerated aging process and its long-term impact on overall health. Cancer 2017;123:4207-4214. © 2017 American Cancer Society.
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Affiliation(s)
- Hany Ariffin
- Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohamad Shafiq Azanan
- Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Lixian Oh
- Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kee Hie Lau
- Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Atiqah Sedan
- Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kamariah Ibrahim
- Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Adelyne Chan
- Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Tong Foh Chin
- Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Fong Fong Liew
- Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Shareni Jeyamogan
- Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Erda Syerena Rosli
- Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Rashidah Baharudin
- Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Tsiao Yi Yap
- Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Roderick Skinner
- Department of Pediatric and Adolescent Hematology/Oncology, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals, University of Newcastle, Newcastle, United Kingdom
| | - Su Han Lum
- Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Pierre Hainaut
- Institute of Advanced Biosciences, University of Grenoble-Alpes, Grenoble, France
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53
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Valuchova S, Fulnecek J, Prokop Z, Stolt-Bergner P, Janouskova E, Hofr C, Riha K. Protection of Arabidopsis Blunt-Ended Telomeres Is Mediated by a Physical Association with the Ku Heterodimer. THE PLANT CELL 2017; 29:1533-1545. [PMID: 28584163 PMCID: PMC5502450 DOI: 10.1105/tpc.17.00064] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 05/01/2017] [Accepted: 06/02/2017] [Indexed: 05/15/2023]
Abstract
Telomeres form specialized chromatin that protects natural chromosome termini from being recognized as DNA double-strand breaks. Plants possess unusual blunt-ended telomeres that are unable to form t-loops or complex with single-strand DNA binding proteins, raising the question of the mechanism behind their protection. We have previously suggested that blunt-ended telomeres in Arabidopsis thaliana are protected by Ku, a DNA repair factor with a high affinity for DNA ends. In nonhomologous end joining, Ku loads onto broken DNA via a channel consisting of positively charged amino acids. Here, we demonstrate that while association of Ku with plant telomeres also depends on this channel, Ku's requirements for DNA binding differ between DNA repair and telomere protection. We show that a Ku complex proficient in DNA loading but impaired in translocation along DNA is able to protect blunt-ended telomeres but is deficient in DNA repair. This suggests that Ku physically sequesters blunt-ended telomeres within its DNA binding channel, shielding them from other DNA repair machineries.
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Affiliation(s)
- Sona Valuchova
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
- Gregor Mendel Institute, Austrian Academy of Sciences (OEAW), Vienna Biocenter, 1030 Vienna, Austria
| | - Jaroslav Fulnecek
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | | | - Eliska Janouskova
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Ctirad Hofr
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Karel Riha
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
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54
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Rice C, Shastrula PK, Kossenkov AV, Hills R, Baird DM, Showe LC, Doukov T, Janicki S, Skordalakes E. Structural and functional analysis of the human POT1-TPP1 telomeric complex. Nat Commun 2017; 8:14928. [PMID: 28393830 PMCID: PMC5394233 DOI: 10.1038/ncomms14928] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 02/14/2017] [Indexed: 12/15/2022] Open
Abstract
POT1 and TPP1 are part of the shelterin complex and are essential for telomere length regulation and maintenance. Naturally occurring mutations of the telomeric POT1-TPP1 complex are implicated in familial glioma, melanoma and chronic lymphocytic leukaemia. Here we report the atomic structure of the interacting portion of the human telomeric POT1-TPP1 complex and suggest how several of these mutations contribute to malignant cancer. The POT1 C-terminus (POT1C) forms a bilobal structure consisting of an OB-fold and a holiday junction resolvase domain. TPP1 consists of several loops and helices involved in extensive interactions with POT1C. Biochemical data shows that several of the cancer-associated mutations, partially disrupt the POT1-TPP1 complex, which affects its ability to bind telomeric DNA efficiently. A defective POT1-TPP1 complex leads to longer and fragile telomeres, which in turn promotes genomic instability and cancer.
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Affiliation(s)
- Cory Rice
- The Wistar Institute, 3601 Spruce St, Philadelphia, Pennsylvania 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | | | | | - Robert Hills
- The Wistar Institute, 3601 Spruce St, Philadelphia, Pennsylvania 19104, USA
| | - Duncan M. Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF10 3AT, UK
| | - Louise C. Showe
- The Wistar Institute, 3601 Spruce St, Philadelphia, Pennsylvania 19104, USA
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA
| | - Susan Janicki
- The Wistar Institute, 3601 Spruce St, Philadelphia, Pennsylvania 19104, USA
| | - Emmanuel Skordalakes
- The Wistar Institute, 3601 Spruce St, Philadelphia, Pennsylvania 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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55
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A balance between elongation and trimming regulates telomere stability in stem cells. Nat Struct Mol Biol 2016; 24:30-39. [PMID: 27918544 PMCID: PMC5215970 DOI: 10.1038/nsmb.3335] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 11/06/2016] [Indexed: 02/07/2023]
Abstract
Telomere length maintenance ensures self-renewal of human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs), however the mechanisms governing telomere length homeostasis in these cell types are unclear. Here, we report that telomere length is determined by the balance between telomere elongation mediated by telomerase and telomere trimming, controlled by the homologous recombination proteins XRCC3 and Nbs1 that generate single-stranded C-rich telomeric DNA and double-stranded telomeric circular DNA (T-circles), respectively. We found that reprogramming of differentiated cells induces T-circle and single stranded C-rich telomeric DNA accumulation, indicating the activation of telomere trimming pathways that compensate telomerase dependent telomere elongation in hiPSCs. Excessive telomere elongation compromises telomere stability and promotes the formation of partially single-stranded telomeric DNA circles (C-circles) in hESCs, suggesting heightened sensitivity of stem cells to replication stress at overly long telomeres. Thus, tight control of telomere length homeostasis is essential to maintain telomere stability in hESCs.
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56
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Dilley RL, Verma P, Cho NW, Winters HD, Wondisford AR, Greenberg RA. Break-induced telomere synthesis underlies alternative telomere maintenance. Nature 2016; 539:54-58. [PMID: 27760120 PMCID: PMC5384111 DOI: 10.1038/nature20099] [Citation(s) in RCA: 299] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 09/16/2016] [Indexed: 12/22/2022]
Abstract
Homology-directed DNA repair is essential for genome maintenance through templated DNA synthesis. Alternative lengthening of telomeres (ALT) necessitates homology-directed DNA repair to maintain telomeres in about 10-15% of human cancers. How DNA damage induces assembly and execution of a DNA replication complex (break-induced replisome) at telomeres or elsewhere in the mammalian genome is poorly understood. Here we define break-induced telomere synthesis and demonstrate that it utilizes a specialized replisome, which underlies ALT telomere maintenance. DNA double-strand breaks enact nascent telomere synthesis by long-tract unidirectional replication. Proliferating cell nuclear antigen (PCNA) loading by replication factor C (RFC) acts as the initial sensor of telomere damage to establish predominance of DNA polymerase δ (Pol δ) through its POLD3 subunit. Break-induced telomere synthesis requires the RFC-PCNA-Pol δ axis, but is independent of other canonical replisome components, ATM and ATR, or the homologous recombination protein Rad51. Thus, the inception of telomere damage recognition by the break-induced replisome orchestrates homology-directed telomere maintenance.
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Affiliation(s)
- Robert L Dilley
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Priyanka Verma
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Nam Woo Cho
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Harrison D Winters
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Anne R Wondisford
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Roger A Greenberg
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA
- Department of Pathology, Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA
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57
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Zhou W, Gao J, Ma J, Cao L, Zhang C, Zhu Y, Dong A, Shen WH. Distinct roles of the histone chaperones NAP1 and NRP and the chromatin-remodeling factor INO80 in somatic homologous recombination in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:397-410. [PMID: 27352805 DOI: 10.1111/tpj.13256] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/24/2016] [Indexed: 05/10/2023]
Abstract
Homologous recombination (HR) of nuclear DNA occurs within the context of a highly complex chromatin structure. Despite extensive studies of HR in diverse organisms, mechanisms regulating HR within the chromatin context remain poorly elucidated. Here we investigate the role and interplay of the histone chaperones NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) and NAP1-RELATED PROTEIN (NRP) and the ATP-dependent chromatin-remodeling factor INOSITOL AUXOTROPHY80 (INO80) in regulating somatic HR in Arabidopsis thaliana. We show that simultaneous knockout of the four AtNAP1 genes and the two NRP genes in the sextuple mutant m123456-1 barely affects normal plant growth and development. Interestingly, compared with the respective AtNAP1 (m123-1 and m1234-1) or NRP (m56-1) loss-of-function mutants, the sextuple mutant m123456-1 displays an enhanced plant hypersensitivity to UV or bleomycin treatments. Using HR reporter constructs, we show that AtNAP1 and NRP act in parallel to synergistically promote somatic HR. Distinctively, the AtINO80 loss-of-function mutation (atino80-5) is epistatic to m56-1 in plant phenotype and telomere length but hypostatic to m56-1 in HR determinacy. Further analyses show that expression of HR machinery genes and phosphorylation of H2A.X (γ-H2A.X) are not impaired in the mutants. Collectively, our study indicates that NRP and AtNAP1 synergistically promote HR upstream of AtINO80-mediated chromatin remodeling after the formation of γ-H2A.X foci during DNA damage repair.
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Affiliation(s)
- Wangbin Zhou
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, 20043, China
| | - Juan Gao
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, 20043, China
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg Cédex, 67084, France
- School of Life Sciences, Shanghai Key Laboratory of Bio-Energy Crops, Shanghai University, Shanghai, 200444, China
| | - Jing Ma
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, 20043, China
| | - Lin Cao
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, 20043, China
| | - Chi Zhang
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, 20043, China
| | - Yan Zhu
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, 20043, China
| | - Aiwu Dong
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, 20043, China
| | - Wen-Hui Shen
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, 20043, China
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 CNRS, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg Cédex, 67084, France
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58
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Nigmatullina LR, Sharipova MR, Shakirov EV. Non-radioactive TRF assay modifications to improve telomeric DNA detection efficiency in plants. BIONANOSCIENCE 2016; 6:325-328. [PMID: 28133587 DOI: 10.1007/s12668-016-0223-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The length of telomeric DNA is often considered a cellular biomarker of aging and general health status. Several telomere length measuring assays have been developed, of which the most common is the Telomere Restriction Fragment (TRF) analysis, which typically involves the use of radioactively labeled oligonucleotide probes. While highly effective, this method potentially poses substantial health concerns and generates radioactive waste. Digoxigenin (DIG) alternatives to radioactive probes have been developed and used successfully in a number of assays. Here we optimize the DIG protocol to measure telomere length in the model plant Arabidopsis thaliana and present evidence that this approach can be used successfully to efficiently and accurately measure telomere length in plants. Specifically, hybridization temperature of 42 °C instead of the typical 55 °C appears to generate stronger signals. In addition, DIG incorporation at 5'-end instead of 3'-end of the labeled oligonucleotide greatly enhances signal. We conclude that non-radioactive TRF assays can be as efficient as radioactive methods in detecting and measuring telomere length in plants, making this assay suitable for medical and research laboratories unable to utilize radioactivity due to hazardous waste disposal and safety concerns.
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Affiliation(s)
- Liliia R Nigmatullina
- Laboratory of Microbial Biotechnology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 9 Parizhskaya Communa str., Kazan, 420021, Russia
| | - Margarita R Sharipova
- Laboratory of Microbial Biotechnology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 9 Parizhskaya Communa str., Kazan, 420021, Russia
| | - Eugene V Shakirov
- Laboratory of Microbial Biotechnology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 9 Parizhskaya Communa str., Kazan, 420021, Russia; Department of Integrative Biology, University of Texas at Austin, Austin, 78712, TX, USA
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59
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Nersisyan L. Integration of Telomere Length Dynamics into Systems Biology Framework: A Review. GENE REGULATION AND SYSTEMS BIOLOGY 2016; 10:35-42. [PMID: 27346946 PMCID: PMC4912229 DOI: 10.4137/grsb.s39836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/11/2016] [Accepted: 05/21/2016] [Indexed: 01/02/2023]
Abstract
Telomere length dynamics plays a crucial role in regulation of cellular processes and cell fate. In contrast to epidemiological studies revealing the association of telomere length with age, age-related diseases, and cancers, the role of telomeres in regulation of transcriptome and epigenome and the role of genomic variations in telomere lengthening are not extensively analyzed. This is explained by the fact that experimental assays for telomere length measurement are resource consuming, and there are very few studies where high-throughput genomics, transcriptomics, and/or epigenomics experiments have been coupled with telomere length measurements. Recent development of computational approaches for assessment of telomere length from whole genome sequencing data pave a new perspective on integration of telomeres into high-throughput systems biology analysis framework. Herein, we review existing methodologies for telomere length measurement and compare them to computational approaches, as well as discuss their applications in large-scale studies on telomere length dynamics.
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Affiliation(s)
- Lilit Nersisyan
- Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, Republic of Armenia
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60
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Lacroix T, Thérond S, Rugeri M, Nicolas P, Gendrault A, Loux V, Gibrat JF. Synchronized navigation and comparative analyses across Ensembl complete bacterial genomes with INSYGHT. Bioinformatics 2016; 32:1083-4. [PMID: 26607491 PMCID: PMC4896367 DOI: 10.1093/bioinformatics/btv689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/16/2015] [Indexed: 11/24/2022] Open
Abstract
Motivation: High-throughput sequencing technologies provide access to an increasing number of bacterial genomes. Today, many analyses involve the comparison of biological properties among many strains of a given species, or among species of a particular genus. Tools that can help the microbiologist with these tasks become increasingly important. Results: Insyght is a comparative visualization tool whose core features combine a synchronized navigation across genomic data of multiple organisms with a versatile interoperability between complementary views. In this work, we have greatly increased the scope of the Insyght public dataset by including 2688 complete bacterial genomes available in Ensembl thus vastly improving its phylogenetic coverage. We also report the development of a virtual machine that allows users to easily set up and customize their own local Insyght server. Availability and implementation:http://genome.jouy.inra.fr/Insyght Contact:Thomas.Lacroix@jouy.inra.fr
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Affiliation(s)
- Thomas Lacroix
- INRA, UR1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, 78350 Jouy-en-Josas, France and
| | | | | | - Pierre Nicolas
- INRA, UR1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, 78350 Jouy-en-Josas, France and
| | - Annie Gendrault
- INRA, UR1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, 78350 Jouy-en-Josas, France and
| | - Valentin Loux
- INRA, UR1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, 78350 Jouy-en-Josas, France and
| | - Jean-François Gibrat
- INRA, UR1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, 78350 Jouy-en-Josas, France and
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61
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Fulcher N, Riha K. Using Centromere Mediated Genome Elimination to Elucidate the Functional Redundancy of Candidate Telomere Binding Proteins in Arabidopsis thaliana. Front Genet 2016; 6:349. [PMID: 26779251 PMCID: PMC4700174 DOI: 10.3389/fgene.2015.00349] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 11/29/2015] [Indexed: 12/23/2022] Open
Abstract
Proteins that bind to telomeric DNA form the key structural and functional constituents of telomeres. While telomere binding proteins have been described in the majority of organisms, their identity in plants remains unknown. Several protein families containing a telomere binding motif known as the telobox have been previously described in Arabidopsis thaliana. Nonetheless, functional evidence for their involvement at telomeres has not been obtained, likely due to functional redundancy. Here we performed genetic analysis on the TRF-like family consisting of six proteins (TRB1, TRP1, TRFL1, TRFL2, TRFL4, and TRF9) which have previously shown to bind telomeric DNA in vitro. We used haploid genetics to create multiple knock-out plants deficient for all six proteins of this gene family. These plants did not exhibit changes in telomere length, or phenotypes associated with telomere dysfunction. This data demonstrates that this telobox protein family is not involved in telomere maintenance in Arabidopsis. Phylogenetic analysis in major plant lineages revealed early diversification of telobox proteins families indicating that telomere function may be associated with other telobox proteins.
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Affiliation(s)
- Nick Fulcher
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Austria
| | - Karel Riha
- Central European Institute of Technology, Masaryk University, Brno Czech Republic
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62
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Nguyen D, Grenier St-Sauveur V, Bergeron D, Dupuis-Sandoval F, Scott MS, Bachand F. A Polyadenylation-Dependent 3' End Maturation Pathway Is Required for the Synthesis of the Human Telomerase RNA. Cell Rep 2015; 13:2244-57. [PMID: 26628368 DOI: 10.1016/j.celrep.2015.11.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/02/2015] [Accepted: 10/29/2015] [Indexed: 12/19/2022] Open
Abstract
Telomere maintenance by the telomerase reverse transcriptase requires a noncoding RNA subunit that acts as a template for the synthesis of telomeric repeats. In humans, the telomerase RNA (hTR) is a non-polyadenylated transcript produced from an independent transcriptional unit. As yet, the mechanism and factors responsible for hTR 3' end processing have remained largely unknown. Here, we show that hTR is matured via a polyadenylation-dependent pathway that relies on the nuclear poly(A)-binding protein PABPN1 and the poly(A)-specific RNase PARN. Depletion of PABPN1 and PARN results in telomerase RNA deficiency and the accumulation of polyadenylated precursors. Accordingly, a deficiency in PABPN1 leads to impaired telomerase activity and telomere shortening. In contrast, we find that hTRAMP-dependent polyadenylation and exosome-mediated degradation function antagonistically to hTR maturation, thereby limiting telomerase RNA accumulation. Our findings unveil a critical requirement for RNA polyadenylation in telomerase RNA biogenesis, providing alternative approaches for telomerase inhibition in cancer.
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Affiliation(s)
- Duy Nguyen
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | | | - Danny Bergeron
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Fabien Dupuis-Sandoval
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Michelle S Scott
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - François Bachand
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
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63
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Dokládal L, Honys D, Rana R, Lee LY, Gelvin SB, Sýkorová E. cDNA Library Screening Identifies Protein Interactors Potentially Involved in Non-Telomeric Roles of Arabidopsis Telomerase. FRONTIERS IN PLANT SCIENCE 2015; 6:985. [PMID: 26617625 PMCID: PMC4641898 DOI: 10.3389/fpls.2015.00985] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/27/2015] [Indexed: 05/27/2023]
Abstract
Telomerase-reverse transcriptase (TERT) plays an essential catalytic role in maintaining telomeres. However, in animal systems telomerase plays additional non-telomeric functional roles. We previously screened an Arabidopsis cDNA library for proteins that interact with the C-terminal extension (CTE) TERT domain and identified a nuclear-localized protein that contains an RNA recognition motif (RRM). This RRM-protein forms homodimers in both plants and yeast. Mutation of the gene encoding the RRM-protein had no detectable effect on plant growth and development, nor did it affect telomerase activity or telomere length in vivo, suggesting a non-telomeric role for TERT/RRM-protein complexes. The gene encoding the RRM-protein is highly expressed in leaf and reproductive tissues. We further screened an Arabidopsis cDNA library for proteins that interact with the RRM-protein and identified five interactors. These proteins are involved in numerous non-telomere-associated cellular activities. In plants, the RRM-protein, both alone and in a complex with its interactors, localizes to nuclear speckles. Transcriptional analyses in wild-type and rrm mutant plants, as well as transcriptional co-analyses, suggest that TERT, the RRM-protein, and the RRM-protein interactors may play important roles in non-telomeric cellular functions.
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Affiliation(s)
- Ladislav Dokládal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology and Faculty of Science, Masaryk UniversityBrno, Czech Republic
- Institute of Biophysics – Academy of Sciences of the Czech Republic v.v.i.Brno, Czech Republic
| | - David Honys
- Institute of Experimental Botany – Academy of Sciences of the Czech Republic v.v.i.Prague, Czech Republic
| | - Rajiv Rana
- Institute of Experimental Botany – Academy of Sciences of the Czech Republic v.v.i.Prague, Czech Republic
| | - Lan-Ying Lee
- Department of Biological Sciences, Purdue University, West LafayetteIN, USA
| | - Stanton B. Gelvin
- Department of Biological Sciences, Purdue University, West LafayetteIN, USA
| | - Eva Sýkorová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology and Faculty of Science, Masaryk UniversityBrno, Czech Republic
- Institute of Biophysics – Academy of Sciences of the Czech Republic v.v.i.Brno, Czech Republic
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64
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Korandová M, Frydrychová RČ. Activity of telomerase and telomeric length in Apis mellifera. Chromosoma 2015; 125:405-11. [DOI: 10.1007/s00412-015-0547-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/23/2015] [Accepted: 10/05/2015] [Indexed: 01/15/2023]
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65
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Bryan C, Rice C, Hoffman H, Harkisheimer M, Sweeney M, Skordalakes E. Structural Basis of Telomerase Inhibition by the Highly Specific BIBR1532. Structure 2015; 23:1934-1942. [PMID: 26365799 DOI: 10.1016/j.str.2015.08.006] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 08/12/2015] [Accepted: 08/13/2015] [Indexed: 01/03/2023]
Abstract
BIBR1532 is a highly specific telomerase inhibitor, although the molecular basis for inhibition is unknown. Here we present the crystal structure of BIBR1532 bound to Tribolium castaneum catalytic subunit of telomerase (tcTERT). BIBR1532 binds to a conserved hydrophobic pocket (FVYL motif) on the outer surface of the thumb domain. The FVYL motif is near TRBD residues that bind the activation domain (CR4/5) of hTER. RNA binding assays show that the human TERT (hTERT) thumb domain binds the P6.1 stem loop of CR4/5 in vitro. hTERT mutations of the FVYL pocket alter wild-type CR4/5 binding and cause telomere attrition in cells. Furthermore, the hTERT FVYL mutations V1025F, N1028H, and V1090M are implicated in dyskeratosis congenita and aplastic anemia, further supporting the biological and clinical relevance of this novel motif. We propose that CR4/5 contacts with the telomerase thumb domain contribute to telomerase ribonucleoprotein assembly and promote enzymatic activity.
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Affiliation(s)
- Christopher Bryan
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA; Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Cory Rice
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA; Department of Biochemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hunter Hoffman
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | | | - Melanie Sweeney
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA; Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Emmanuel Skordalakes
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA; Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA; Department of Biochemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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66
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Fulcher N, Teubenbacher A, Kerdaffrec E, Farlow A, Nordborg M, Riha K. Genetic architecture of natural variation of telomere length in Arabidopsis thaliana. Genetics 2015; 199:625-35. [PMID: 25488978 PMCID: PMC4317667 DOI: 10.1534/genetics.114.172163] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/25/2014] [Indexed: 11/18/2022] Open
Abstract
Telomeres represent the repetitive sequences that cap chromosome ends and are essential for their protection. Telomere length is known to be highly heritable and is derived from a homeostatic balance between telomeric lengthening and shortening activities. Specific loci that form the genetic framework underlying telomere length homeostasis, however, are not well understood. To investigate the extent of natural variation of telomere length in Arabidopsis thaliana, we examined 229 worldwide accessions by terminal restriction fragment analysis. The results showed a wide range of telomere lengths that are specific to individual accessions. To identify loci that are responsible for this variation, we adopted a quantitative trait loci (QTL) mapping approach with multiple recombinant inbred line (RIL) populations. A doubled haploid RIL population was first produced using centromere-mediated genome elimination between accessions with long (Pro-0) and intermediate (Col-0) telomere lengths. Composite interval mapping analysis of this population along with two established RIL populations (Ler-2/Cvi-0 and Est-1/Col-0) revealed a number of shared and unique QTL. QTL detected in the Ler-2/Cvi-0 population were examined using near isogenic lines that confirmed causative regions on chromosomes 1 and 2. In conclusion, this work describes the extent of natural variation of telomere length in A. thaliana, identifies a network of QTL that influence telomere length homeostasis, examines telomere length dynamics in plants with hybrid backgrounds, and shows the effects of two identified regions on telomere length regulation.
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Affiliation(s)
- Nick Fulcher
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria
| | - Astrid Teubenbacher
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria
| | - Envel Kerdaffrec
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria
| | - Ashley Farlow
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria
| | - Karel Riha
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, Czech Republic
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67
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Analysis of the age of Panax ginseng based on telomere length and telomerase activity. Sci Rep 2015; 5:7985. [PMID: 25614145 PMCID: PMC5379010 DOI: 10.1038/srep07985] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 12/24/2014] [Indexed: 11/17/2022] Open
Abstract
Ginseng, which is the root of Panax ginseng (Araliaceae), has been used in Oriental medicine as a stimulant and dietary supplement for more than 7,000 years. Older ginseng plants are substantially more medically potent, but ginseng age can be simulated using unscrupulous cultivation practices. Telomeres progressively shorten with each cell division until they reach a critical length, at which point cells enter replicative senescence. However, in some cells, telomerase maintains telomere length. In this study, to determine whether telomere length reflects ginseng age and which tissue is best for such an analysis, we examined telomerase activity in the main roots, leaves, stems, secondary roots and seeds of ginseng plants of known age. Telomere length in the main root (approximately 1 cm below the rhizome) was found to be the best indicator of age. Telomeric terminal restriction fragment (TRF) lengths, which are indicators of telomere length, were determined for the main roots of plants of different ages through Southern hybridization analysis. Telomere length was shown to be positively correlated with plant age, and a simple mathematical model was formulated to describe the relationship between telomere length and age for P. ginseng.
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68
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Derboven E, Ekker H, Kusenda B, Bulankova P, Riha K. Role of STN1 and DNA polymerase α in telomere stability and genome-wide replication in Arabidopsis. PLoS Genet 2014; 10:e1004682. [PMID: 25299252 PMCID: PMC4191939 DOI: 10.1371/journal.pgen.1004682] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 08/19/2014] [Indexed: 11/18/2022] Open
Abstract
The CST (Cdc13/CTC1-STN1-TEN1) complex was proposed to have evolved kingdom specific roles in telomere capping and replication. To shed light on its evolutionary conserved function, we examined the effect of STN1 dysfunction on telomere structure in plants. STN1 inactivation in Arabidopsis leads to a progressive loss of telomeric DNA and the onset of telomeric defects depends on the initial telomere size. While EXO1 aggravates defects associated with STN1 dysfunction, it does not contribute to the formation of long G-overhangs. Instead, these G-overhangs arise, at least partially, from telomerase-mediated telomere extension indicating a deficiency in C-strand fill-in synthesis. Analysis of hypomorphic DNA polymerase α mutants revealed that the impaired function of a general replication factor mimics the telomeric defects associated with CST dysfunction. Furthermore, we show that STN1-deficiency hinders re-replication of heterochromatic regions to a similar extent as polymerase α mutations. This comparative analysis of stn1 and pol α mutants suggests that STN1 plays a genome-wide role in DNA replication and that chromosome-end deprotection in stn1 mutants may represent a manifestation of aberrant replication through telomeres. Telomeres form an elaborate nucleoprotein structure that may represent an obstacle for replication machinery and renders this region prone to fork stalling. CST is an evolutionary conserved complex that was originally discovered to specifically act at telomeres. Interestingly, the function of CST seems to have diverged in the course of evolution; in yeast it is required for telomere protection, while in mammals it was proposed to facilitate replication through telomeres. In plants, inactivation of CST leads to telomere deprotection and genome instability. Here we show that the telomere deprotection in Arabidopsis deficient in STN1, one of the CST components, is consistent with defects in telomere replication and that STN1 phenotypes can be partially phenocopied by an impairment of a general replication factor, DNA polymerase α. In addition, we provide evidence that STN1 facilitates re-replication at non-telomeric loci. This suggests a more general role of CST in genome maintenance and further infers that its seemingly specific function(s) in telomere protection may rather represent unique requirements for efficient replication of telomeric DNA.
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Affiliation(s)
- Elisa Derboven
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Heinz Ekker
- Campus Science Support Facilities, Next Generation Sequencing Facility, Vienna, Austria
| | - Branislav Kusenda
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Petra Bulankova
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Karel Riha
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- * E-mail:
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