1
|
Tang S, Roberts RD, Cheng L, Li L. Osteosarcoma Multi-Omics Landscape and Subtypes. Cancers (Basel) 2023; 15:4970. [PMID: 37894336 PMCID: PMC10605601 DOI: 10.3390/cancers15204970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/12/2023] [Accepted: 09/17/2023] [Indexed: 10/29/2023] Open
Abstract
Osteosarcoma (OS) is the most common primary bone malignancy that exhibits remarkable histologic diversity and genetic heterogeneity. The complex nature of osteosarcoma has confounded precise molecular categorization, prognosis, and prediction for this disease. In this study, we performed a comprehensive multiplatform analysis on 86 osteosarcoma tumors, including somatic copy-number alteration, gene expression and methylation, and identified three molecularly distinct and clinically relevant subtypes of osteosarcoma. The subgrouping criteria was validated on another cohort of osteosarcoma tumors. Previously unappreciated osteosarcoma-type-specific changes in specific genes' copy number, expression and methylation were revealed based on the subgrouping. The subgrouping and novel gene signatures provide insights into refining osteosarcoma therapy and relationships to other types of cancer.
Collapse
Affiliation(s)
- Shan Tang
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Ryan D. Roberts
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Lijun Cheng
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Lang Li
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA;
| |
Collapse
|
2
|
Shakirov EV, Chen JJL, Shippen DE. Plant telomere biology: The green solution to the end-replication problem. THE PLANT CELL 2022; 34:2492-2504. [PMID: 35511166 PMCID: PMC9252485 DOI: 10.1093/plcell/koac122] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/14/2022] [Indexed: 05/04/2023]
Abstract
Telomere maintenance is a fundamental cellular process conserved across all eukaryotic lineages. Although plants and animals diverged over 1.5 billion years ago, lessons learned from plants continue to push the boundaries of science, revealing detailed molecular mechanisms in telomere biology with broad implications for human health, aging biology, and stress responses. Recent studies of plant telomeres have unveiled unexpected divergence in telomere sequence and architecture, and the proteins that engage telomeric DNA and telomerase. The discovery of telomerase RNA components in the plant kingdom and some algae groups revealed new insight into the divergent evolution and the universal core of telomerase across major eukaryotic kingdoms. In addition, resources cataloging the abundant natural variation in Arabidopsis thaliana, maize (Zea mays), and other plants are providing unparalleled opportunities to understand the genetic networks that govern telomere length polymorphism and, as a result, are uncovering unanticipated crosstalk between telomeres, environmental factors, organismal fitness, and plant physiology. Here we recap current advances in plant telomere biology and put this field in perspective relative to telomere and telomerase research in other eukaryotic lineages.
Collapse
Affiliation(s)
- Eugene V Shakirov
- Department of Biological Sciences, College of Science, Marshall University, Huntington, West Virginia 25701, USA
| | - Julian J -L Chen
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | | |
Collapse
|
3
|
Telomeres and Cancer. Life (Basel) 2021; 11:life11121405. [PMID: 34947936 PMCID: PMC8704776 DOI: 10.3390/life11121405] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 12/18/2022] Open
Abstract
Telomeres cap the ends of eukaryotic chromosomes and are indispensable chromatin structures for genome protection and replication. Telomere length maintenance has been attributed to several functional modulators, including telomerase, the shelterin complex, and the CST complex, synergizing with DNA replication, repair, and the RNA metabolism pathway components. As dysfunctional telomere maintenance and telomerase activation are associated with several human diseases, including cancer, the molecular mechanisms behind telomere length regulation and protection need particular emphasis. Cancer cells exhibit telomerase activation, enabling replicative immortality. Telomerase reverse transcriptase (TERT) activation is involved in cancer development through diverse activities other than mediating telomere elongation. This review describes the telomere functions, the role of functional modulators, the implications in cancer development, and the future therapeutic opportunities.
Collapse
|
4
|
Eekhout T, Dvorackova M, Pedroza Garcia JA, Nespor Dadejova M, Kalhorzadeh P, Van den Daele H, Vercauteren I, Fajkus J, De Veylder L. G2/M-checkpoint activation in fasciata1 rescues an aberrant S-phase checkpoint but causes genome instability. PLANT PHYSIOLOGY 2021; 186:1893-1907. [PMID: 34618100 PMCID: PMC8331141 DOI: 10.1093/plphys/kiab201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/05/2021] [Indexed: 05/13/2023]
Abstract
The WEE1 and ATM AND RAD3-RELATED (ATR) kinases are important regulators of the plant intra-S-phase checkpoint; consequently, WEE1KO and ATRKO roots are hypersensitive to replication-inhibitory drugs. Here, we report on a loss-of-function mutant allele of the FASCIATA1 (FAS1) subunit of the chromatin assembly factor 1 (CAF-1) complex that suppresses the phenotype of WEE1- or ATR-deficient Arabidopsis (Arabidopsis thaliana) plants. We demonstrate that lack of FAS1 activity results in the activation of an ATAXIA TELANGIECTASIA MUTATED (ATM)- and SUPPRESSOR OF GAMMA-RESPONSE 1 (SOG1)-mediated G2/M-arrest that renders the ATR and WEE1 checkpoint regulators redundant. This ATM activation accounts for the telomere erosion and loss of ribosomal DNA that are described for fas1 plants. Knocking out SOG1 in the fas1 wee1 background restores replication stress sensitivity, demonstrating that SOG1 is an important secondary checkpoint regulator in plants that fail to activate the intra-S-phase checkpoint.
Collapse
Affiliation(s)
- Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Martina Dvorackova
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
| | - José Antonio Pedroza Garcia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Martina Nespor Dadejova
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Pooneh Kalhorzadeh
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Hilde Van den Daele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Jiri Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| |
Collapse
|
5
|
Bose S, Suescún AV, Song J, Castillo-González C, Aklilu BB, Branham E, Lynch R, Shippen DE. tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana. PLANT CELL REPORTS 2020; 39:1669-1685. [PMID: 32959123 PMCID: PMC7655638 DOI: 10.1007/s00299-020-02594-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/04/2020] [Indexed: 05/05/2023]
Abstract
KEY MESSAGE: tRNA Adenosine Deaminase 3 helps to sustain telomere tracts in a telomerase-independent fashion, likely through regulating cellular metabolism. Telomere length maintenance is influenced by a complex web of chromatin and metabolism-related factors. We previously reported that a lncRNA termed AtTER2 regulates telomerase activity in Arabidopsis thaliana in response to DNA damage. AtTER2 was initially shown to partially overlap with the 5' UTR of the tRNA ADENOSINE DEAMINASE 3 (TAD3) gene. However, updated genome annotation showed that AtTER2 was completely embedded in TAD3, raising the possibility that phenotypes ascribed to AtTER2 could be derived from TAD3. Here we show through strand-specific RNA-Seq, strand-specific qRT-PCR and bioinformatic analyses that AtTER2 does not encode a stable lncRNA. Further examination of the original tad3 (ter2-1/tad3-1) mutant revealed expression of an antisense transcript driven by a cryptic promoter in the T-DNA. Hence, a new hypomorphic allele of TAD3 (tad3-2) was examined. tad3-2 mutants showed hypersensitivity to DNA damage, but no deregulation of telomerase, suggesting that the telomerase phenotype of tad3-1 mutants reflects an off-target effect. Unexpectedly, however, tad3-2 plants displayed progressive loss of telomeric DNA over successive generations that was not accompanied by alteration of terminal architecture or end protection. The phenotype was exacerbated in plants lacking the telomerase processivity factor POT1a, indicating that TAD3 promotes telomere maintenance through a non-canonical, telomerase-independent pathway. The transcriptome of tad3-2 mutants revealed significant dysregulation of genes involved in auxin signaling and glucosinolate biosynthesis, pathways that intersect the stress response, cell cycle regulation and DNA metabolism. These findings indicate that the TAD3 locus indirectly contributes to telomere length homeostasis by altering the metabolic profile in Arabidopsis.
Collapse
Affiliation(s)
- Sreyashree Bose
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Ana Victoria Suescún
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Facultad de Ciencias, Instituto de Ciencias Ambientales Y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Jiarui Song
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | | | - Behailu Birhanu Aklilu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- KWS Gateway Research Center, LLC, 1005 N Warson Rd, BRDG Park, St. Louis, MO, 63132, USA
| | - Erica Branham
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Ryan Lynch
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
- Department of Biochemistry and Biophysics, 300 Olsen Blvd, Room 413, College Station, TX, 77843-2128, USA.
| |
Collapse
|
6
|
Li G, Zou W, Jian L, Qian J, Zhao J. AtNSE1 and AtNSE3 are required for embryo pattern formation and maintenance of cell viability during Arabidopsis embryogenesis. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6229-6244. [PMID: 31408172 PMCID: PMC6859727 DOI: 10.1093/jxb/erz373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 08/06/2019] [Indexed: 05/30/2023]
Abstract
Embryogenesis is an essential process during seed development in higher plants. It has previously been shown that mutation of the Arabidopsis non-SMC element genes AtNSE1 or AtNSE3 leads to early embryo abortion, and their proteins can interact with each other directly. However, the crucial regions of these proteins in this interaction and how the proteins are cytologically involved in Arabidopsis embryo development are unknown. In this study, we found that the C-terminal including the Ring-like motif of AtNSE1 can interact with the N-terminal of AtNSE3, and only the Ring-like motif is essential for binding with three α motifs of AtNSE2 (homologous to AtMMS21). Using genetic assays and by analysing molecular markers of cell fate decisions (STM, WOX5, and WOX8) in mutant nse1 and nse3 embryos, we found that AtNSE1 and AtNSE3 work non-redundantly in early embryo development, and that differentiation of the apical meristem and the hypophysis fails in the mutants, which have disrupted auxin transportation and responses. However, the upper cells of the suspensor in the mutants seem to have proper embryo cell identity. Cytological examination showed that cell death occurred from the early embryo stage, and that vacuolar programmed cell death and necrosis in the nse1 and nse3 mutant embryos led to ovule abortion. Thus, AtNSE1 and AtNSE3 are essential for maintaining cell viability and growth during early embryogenesis. Our results improve our understanding of the functions of SMC5/6 complex in early embryogenesis in Arabidopsis.
Collapse
Affiliation(s)
- Gang Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wenxuan Zou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Liufang Jian
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jie Qian
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| |
Collapse
|
7
|
Charbonnel C, Rymarenko O, Da Ines O, Benyahya F, White CI, Butter F, Amiard S. The Linker Histone GH1-HMGA1 Is Involved in Telomere Stability and DNA Damage Repair. PLANT PHYSIOLOGY 2018; 177:311-327. [PMID: 29622687 PMCID: PMC5933147 DOI: 10.1104/pp.17.01789] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/28/2018] [Indexed: 05/19/2023]
Abstract
Despite intensive searches, few proteins involved in telomere homeostasis have been identified in plants. Here, we used pull-down assays to identify potential telomeric interactors in the model plant species Arabidopsis (Arabidopsis thaliana). We identified the candidate protein GH1-HMGA1 (also known as HON4), an uncharacterized linker histone protein of the High Mobility Group Protein A (HMGA) family in plants. HMGAs are architectural transcription factors and have been suggested to function in DNA damage repair, but their precise biological roles remain unclear. Here, we show that GH1-HMGA1 is required for efficient DNA damage repair and telomere integrity in Arabidopsis. GH1-HMGA1 mutants exhibit developmental and growth defects, accompanied by ploidy defects, increased telomere dysfunction-induced foci, mitotic anaphase bridges, and degraded telomeres. Furthermore, mutants have a higher sensitivity to genotoxic agents such as mitomycin C and γ-irradiation. Our work also suggests that GH1-HMGA1 is involved directly in the repair process by allowing the completion of homologous recombination.
Collapse
Affiliation(s)
- Cyril Charbonnel
- Génétique, Reproduction, et Dévélopement, Université Clermont Auvergne-Centre National de la Recherche Scientifique Unité Mixte de Recherche 6293-INSERM U1103, F-63000 Clermont-Ferrand, France
| | | | - Olivier Da Ines
- Génétique, Reproduction, et Dévélopement, Université Clermont Auvergne-Centre National de la Recherche Scientifique Unité Mixte de Recherche 6293-INSERM U1103, F-63000 Clermont-Ferrand, France
| | - Fatiha Benyahya
- Génétique, Reproduction, et Dévélopement, Université Clermont Auvergne-Centre National de la Recherche Scientifique Unité Mixte de Recherche 6293-INSERM U1103, F-63000 Clermont-Ferrand, France
| | - Charles I White
- Génétique, Reproduction, et Dévélopement, Université Clermont Auvergne-Centre National de la Recherche Scientifique Unité Mixte de Recherche 6293-INSERM U1103, F-63000 Clermont-Ferrand, France
| | - Falk Butter
- Institute of Molecular Biology, 455128 Mainz, Germany
| | - Simon Amiard
- Génétique, Reproduction, et Dévélopement, Université Clermont Auvergne-Centre National de la Recherche Scientifique Unité Mixte de Recherche 6293-INSERM U1103, F-63000 Clermont-Ferrand, France
| |
Collapse
|
8
|
Stewart JA, Wang Y, Ackerson SM, Schuck PL. Emerging roles of CST in maintaining genome stability and human disease. Front Biosci (Landmark Ed) 2018; 23:1564-1586. [PMID: 29293451 DOI: 10.2741/4661] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The human CTC1-STN1-TEN1 (CST) complex is a single-stranded DNA binding protein that shares homology with RPA and interacts with DNA polymerase alpha/primase. CST complexes are conserved from yeasts to humans and function in telomere maintenance. A common role of CST across species is in the regulation of telomere extension by telomerase and C-strand fill-in synthesis. However, recent studies also indicate that CST promotes telomere duplex replication as well the rescue of stalled DNA replication at non-telomeric sites. Furthermore, CST dysfunction and mutation is associated with several genetic diseases and cancers. In this review, we will summarize what is known about CST with a particular focus on the emerging roles of CST in DNA replication and human disease.
Collapse
Affiliation(s)
- Jason A Stewart
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA,
| | - Yilin Wang
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Stephanie M Ackerson
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Percy Logan Schuck
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| |
Collapse
|
9
|
Xie X, Shippen DE. DDM1 guards against telomere truncation in Arabidopsis. PLANT CELL REPORTS 2018; 37:501-513. [PMID: 29392401 PMCID: PMC5880217 DOI: 10.1007/s00299-017-2245-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/26/2017] [Indexed: 05/20/2023]
Abstract
Prolonged hypomethylation of DNA leads to telomere truncation correlated with increased telomere recombination, transposon mobilization and stem cell death. Epigenetic pathways, including DNA methylation, are crucial for telomere maintenance. Deficient in DNA Methylation 1 (DDM1) encodes a nucleosome remodeling protein, required to maintain DNA methylation in Arabidopsis thaliana. Plants lacking DDM1 can be self-propagated, but in the sixth generation (G6) hypomethylation leads to rampant transposon activation and infertility. Here we examine the role of DDM1 in telomere length homeostasis through a longitudinal study of successive generations of ddm1-2 mutants. We report that bulk telomere length remains within the wild-type range for the first five generations (G1-G5), and then precipitously drops in G6. While telomerase activity becomes more variable in later generation ddm1-2 mutants, there is no correlation between enzyme activity and telomere length. Plants lacking DDM1 also exhibit no dysregulation of several known telomere-associated transcripts, including TERRA. Instead, telomere shortening coincides with increased G-overhangs and extra-chromosomal circles, consistent with deletional recombination. Telomere shortening also correlates with transcriptional activation of retrotransposons, and a hypersensitive DNA damage response in root apical meristems. Since abiotic stresses, including DNA damage, stimulate homologous recombination, we hypothesize that telomere deletion in G6 ddm1-2 mutants is a by-product of elevated genome-wide recombination in response to transposon mobilization. Further, we speculate that telomere truncation may be beneficial in adverse environmental conditions by accelerating the elimination of stem cells with aberrant genomes.
Collapse
Affiliation(s)
- Xiaoyuan Xie
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843-2128, USA
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843-2128, USA.
| |
Collapse
|
10
|
Abstract
Because the genome stores all genetic information required for growth and development, it is of pivotal importance to maintain DNA integrity, especially during cell division, when the genome is prone to replication errors and damage. Although over the last two decades it has become evident that the basic cell cycle toolbox of plants shares several similarities with those of fungi and mammals, plants appear to have evolved a set of distinct checkpoint regulators in response to different types of DNA stress. This might be a consequence of plants' sessile lifestyle, which exposes them to a set of unique DNA damage-inducing conditions. In this review, we highlight the types of DNA stress that plants typically experience and describe the plant-specific molecular mechanisms that control cell division in response to these stresses.
Collapse
Affiliation(s)
- Zhubing Hu
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
| | - Toon Cools
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
| | | |
Collapse
|
11
|
Procházková Schrumpfová P, Schořová Š, Fajkus J. Telomere- and Telomerase-Associated Proteins and Their Functions in the Plant Cell. FRONTIERS IN PLANT SCIENCE 2016; 7:851. [PMID: 27446102 PMCID: PMC4924339 DOI: 10.3389/fpls.2016.00851] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 05/31/2016] [Indexed: 05/20/2023]
Abstract
Telomeres, as physical ends of linear chromosomes, are targets of a number of specific proteins, including primarily telomerase reverse transcriptase. Access of proteins to the telomere may be affected by a number of diverse factors, e.g., protein interaction partners, local DNA or chromatin structures, subcellular localization/trafficking, or simply protein modification. Knowledge of composition of the functional nucleoprotein complex of plant telomeres is only fragmentary. Moreover, the plant telomeric repeat binding proteins that were characterized recently appear to also be involved in non-telomeric processes, e.g., ribosome biogenesis. This interesting finding was not totally unexpected since non-telomeric functions of yeast or animal telomeric proteins, as well as of telomerase subunits, have been reported for almost a decade. Here we summarize known facts about the architecture of plant telomeres and compare them with the well-described composition of telomeres in other organisms.
Collapse
Affiliation(s)
- Petra Procházková Schrumpfová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityBrno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrno, Czech Republic
- *Correspondence: Petra Procházková Schrumpfová,
| | - Šárka Schořová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityBrno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i.Brno, Czech Republic
| |
Collapse
|
12
|
González-García MP, Pavelescu I, Canela A, Sevillano X, Leehy KA, Nelson ADL, Ibañes M, Shippen DE, Blasco MA, Caño-Delgado AI. Single-cell telomere-length quantification couples telomere length to meristem activity and stem cell development in Arabidopsis. Cell Rep 2015; 11:977-989. [PMID: 25937286 PMCID: PMC4827700 DOI: 10.1016/j.celrep.2015.04.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 02/19/2015] [Accepted: 04/05/2015] [Indexed: 01/14/2023] Open
Abstract
Telomeres are specialized nucleoprotein caps that protect chromosome ends assuring cell division. Single-cell telomere quantification in animals established a critical role for telomerase in stem cells, yet, in plants, telomere-length quantification has been reported only at the organ level. Here, a quantitative analysis of telomere length of single cells in Arabidopsis root apex uncovered a heterogeneous telomere-length distribution of different cell lineages showing the longest telomeres at the stem cells. The defects in meristem and stem cell renewal observed in tert mutants demonstrate that telomere lengthening by TERT sets a replicative limit in the root meristem. Conversely, the long telomeres of the columella cells and the premature stem cell differentiation plt1,2 mutants suggest that differentiation can prevent telomere erosion. Overall, our results indicate that telomere dynamics are coupled to meristem activity and continuous growth, disclosing a critical association between telomere length, stem cell function, and the extended lifespan of plants.
Collapse
Affiliation(s)
- Mary-Paz González-García
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona 08193, Spain; Centro Nacional de Biotecnología (CSIC), Cantoblanco, 28049 Madrid, Spain
| | - Irina Pavelescu
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona 08193, Spain; Department of Structure and Constituents of Matter, Faculty of Physics, University of Barcelona, Barcelona 08024, Spain
| | - Andrés Canela
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid 28029, Spain
| | - Xavier Sevillano
- Grup de Recerca en Tecnologies Mèdia, La Salle - Universitat Ramon Llull, Barcelona 08022, Spain
| | - Katherine A Leehy
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Andrew D L Nelson
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Marta Ibañes
- Department of Structure and Constituents of Matter, Faculty of Physics, University of Barcelona, Barcelona 08024, Spain
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Maria A Blasco
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid 28029, Spain
| | - Ana I Caño-Delgado
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona 08193, Spain.
| |
Collapse
|
13
|
Hu Z, Cools T, Kalhorzadeh P, Heyman J, De Veylder L. Deficiency of the Arabidopsis helicase RTEL1 triggers a SOG1-dependent replication checkpoint in response to DNA cross-links. THE PLANT CELL 2015; 27:149-61. [PMID: 25595823 PMCID: PMC4330584 DOI: 10.1105/tpc.114.134312] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
To maintain genome integrity, DNA replication is executed and regulated by a complex molecular network of numerous proteins, including helicases and cell cycle checkpoint regulators. Through a systematic screening for putative replication mutants, we identified an Arabidopsis thaliana homolog of human Regulator of Telomere Length 1 (RTEL1), which functions in DNA replication, DNA repair, and recombination. RTEL1 deficiency retards plant growth, a phenotype including a prolonged S-phase duration and decreased cell proliferation. Genetic analysis revealed that rtel1 mutant plants show activated cell cycle checkpoints, specific sensitivity to DNA cross-linking agents, and increased homologous recombination, but a lack of progressive shortening of telomeres, indicating that RTEL1 functions have only been partially conserved between mammals and plants. Surprisingly, RTEL1 deficiency induces tolerance to the deoxynucleotide-depleting drug hydroxyurea, which could be mimicked by DNA cross-linking agents. This resistance does not rely on the essential replication checkpoint regulator WEE1 but could be blocked by a mutation in the SOG1 transcription factor. Taken together, our data indicate that RTEL1 is required for DNA replication and that its deficiency activates a SOG1-dependent replication checkpoint.
Collapse
Affiliation(s)
- Zhubing Hu
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Toon Cools
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Pooneh Kalhorzadeh
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Jefri Heyman
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Lieven De Veylder
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| |
Collapse
|
14
|
Amiard S, Olivier M, Allain E, Choi K, Smith-Unna R, Henderson IR, White CI, Gallego ME. Telomere stability and development of ctc1 mutants are rescued by inhibition of EJ recombination pathways in a telomerase-dependent manner. Nucleic Acids Res 2014; 42:11979-91. [PMID: 25274733 PMCID: PMC4231758 DOI: 10.1093/nar/gku897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 12/11/2022] Open
Abstract
The telomeres of linear eukaryotic chromosomes are protected by caps consisting of evolutionarily conserved nucleoprotein complexes. Telomere dysfunction leads to recombination of chromosome ends and this can result in fusions which initiate chromosomal breakage-fusion-bridge cycles, causing genomic instability and potentially cell death or cancer. We hypothesize that in the absence of the recombination pathways implicated in these fusions, deprotected chromosome ends will instead be eroded by nucleases, also leading to the loss of genes and cell death. In this work, we set out to specifically test this hypothesis in the plant, Arabidopsis. Telomere protection in Arabidopsis implicates KU and CST and their absence leads to chromosome fusions, severe genomic instability and dramatic developmental defects. We have analysed the involvement of end-joining recombination pathways in telomere fusions and the consequences of this on genomic instability and growth. Strikingly, the absence of the multiple end-joining pathways eliminates chromosome fusion and restores normal growth and development to cst ku80 mutant plants. It is thus the chromosomal fusions, per se, which are the underlying cause of the severe developmental defects. This rescue is mediated by telomerase-dependent telomere extension, revealing a competition between telomerase and end-joining recombination proteins for access to deprotected telomeres.
Collapse
Affiliation(s)
- Simon Amiard
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, Aubière, France
| | - Margaux Olivier
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, Aubière, France
| | - Elisabeth Allain
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, Aubière, France Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | | | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Charles I White
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, Aubière, France
| | - Maria Eugenia Gallego
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, Aubière, France
| |
Collapse
|
15
|
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.
Collapse
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:
| |
Collapse
|
16
|
Boltz KA, Jasti M, Townley JM, Shippen DE. Analysis of poly(ADP-Ribose) polymerases in Arabidopsis telomere biology. PLoS One 2014; 9:e88872. [PMID: 24551184 PMCID: PMC3923816 DOI: 10.1371/journal.pone.0088872] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 01/17/2014] [Indexed: 11/22/2022] Open
Abstract
Maintaining the length of the telomere tract at chromosome ends is a complex process vital to normal cell division. Telomere length is controlled through the action of telomerase as well as a cadre of telomere-associated proteins that facilitate replication of the chromosome end and protect it from eliciting a DNA damage response. In vertebrates, multiple poly(ADP-ribose) polymerases (PARPs) have been implicated in the regulation of telomere length, telomerase activity and chromosome end protection. Here we investigate the role of PARPs in plant telomere biology. We analyzed Arabidopsis thaliana mutants null for PARP1 and PARP2 as well as plants treated with the PARP competitive inhibitor 3-AB. Plants deficient in PARP were hypersensitive to genotoxic stress, and expression of PARP1 and PARP2 mRNA was elevated in response to MMS or zeocin treatment or by the loss of telomerase. Additionally, PARP1 mRNA was induced in parp2 mutants, and conversely, PARP2 mRNA was induced in parp1 mutants. PARP3 mRNA, by contrast, was elevated in both parp1 and parp2 mutants, but not in seedlings treated with 3-AB or zeocin. PARP mutants and 3-AB treated plants displayed robust telomerase activity, no significant changes in telomere length, and no end-to-end chromosome fusions. Although there remains a possibility that PARPs play a role in Arabidopsis telomere biology, these findings argue that the contribution is a minor one.
Collapse
Affiliation(s)
- Kara A. Boltz
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Madhu Jasti
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Jennifer M. Townley
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Dorothy E. Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
| |
Collapse
|
17
|
Amiard S, Da Ines O, Gallego ME, White CI. Responses to telomere erosion in plants. PLoS One 2014; 9:e86220. [PMID: 24465970 PMCID: PMC3897657 DOI: 10.1371/journal.pone.0086220] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/06/2013] [Indexed: 01/01/2023] Open
Abstract
In striking contrast to animals, plants are able to develop and reproduce in the presence of significant levels of genome damage. This is seen clearly in both the viability of plants carrying knockouts for key recombination and DNA repair genes, which are lethal in vertebrates, and in the impact of telomere dysfunction. Telomerase knockout mice show accelerated ageing and severe developmental phenotypes, with effects on both highly proliferative and on more quiescent tissues, while cell death in Arabidopsis tert mutants is mostly restricted to actively dividing meristematic cells. Through phenotypic and whole-transcriptome RNAseq studies, we present here an analysis of the response of Arabidopsis plants to the continued presence of telomere damage. Comparison of second-generation and seventh-generation tert mutant plants has permitted separation of the effects of the absence of the telomerase enzyme and the ensuing chromosome damage. In addition to identifying a large number of genes affected by telomere damage, many of which are of unknown function, the striking conclusion of this study is the clear difference observed at both cellular and transcriptome levels between the ways in which mammals and plants respond to chronic telomeric damage.
Collapse
Affiliation(s)
- Simon Amiard
- Génétique, Reproduction et Développement, Unité Mixte de Recherche 6293, Centre National de la Recherche Scientifique - Clermont Université - Unité 1103, Institut National de la Santé et de la Recherche Médicale, Aubière, France
| | - Olivier Da Ines
- Génétique, Reproduction et Développement, Unité Mixte de Recherche 6293, Centre National de la Recherche Scientifique - Clermont Université - Unité 1103, Institut National de la Santé et de la Recherche Médicale, Aubière, France
| | - Maria Eugenia Gallego
- Génétique, Reproduction et Développement, Unité Mixte de Recherche 6293, Centre National de la Recherche Scientifique - Clermont Université - Unité 1103, Institut National de la Santé et de la Recherche Médicale, Aubière, France
| | - Charles I White
- Génétique, Reproduction et Développement, Unité Mixte de Recherche 6293, Centre National de la Recherche Scientifique - Clermont Université - Unité 1103, Institut National de la Santé et de la Recherche Médicale, Aubière, France
| |
Collapse
|
18
|
Nelson ADL, Shippen DE. Surprises from the chromosome front: lessons from Arabidopsis on telomeres and telomerase. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2013; 77:7-15. [PMID: 23460576 DOI: 10.1101/sqb.2013.77.017053] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Telomeres serve two vital functions: They act as a buffer against the end-replication problem, and they prevent chromosome ends from being recognized as double-strand DNA (dsDNA) breaks. These functions are orchestrated by the telomerase reverse transcriptase and a variety of telomere protein complexes. Here, we discuss our recent studies with Arabidopsis thaliana that uncovered a new and highly conserved telomere complex called CST (Cdc13/CTC1, STN1, TEN1). Formerly believed to be yeast specific, CST has now been identified as a key component of both plant and vertebrate telomeres, which is essential for genome integrity and stem cell viability. We also describe the unexpected discovery of alternative telomerase ribonucleoprotein complexes in Arabidopsis. Fueled by duplication and diversification of the telomerase RNA subunit and telomerase accessory proteins, these telomerase complexes act in concert to maintain genome stability. In addition to the canonical telomerase enzyme, one of two alternative telomerase ribonucleoprotein (RNP) complexes functions as a novel negative regulator of enzyme activity in response to genotoxic stress. These contributions highlight the immense potential of Arabidopsis in probing the depths of the chromosome end.
Collapse
Affiliation(s)
- A D L Nelson
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
| | | |
Collapse
|
19
|
Chueh FS, Chen YL, Hsu SC, Yang JS, Hsueh SC, Ji BC, Lu HF, Chung JG. Triptolide induced DNA damage in A375.S2 human malignant melanoma cells is mediated via reduction of DNA repair genes. Oncol Rep 2012; 29:613-8. [PMID: 23233170 DOI: 10.3892/or.2012.2170] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 11/14/2012] [Indexed: 11/05/2022] Open
Abstract
Numerous studies have demonstrated that triptolide induces cell cycle arrest and apoptosis in human cancer cell lines. However, triptolide-induced DNA damage and inhibition of DNA repair gene expression in human skin cancer cells has not previously been reported. We sought the effects of triptolide on DNA damage and associated gene expression in A375.S2 human malignant melanoma cells in vitro. Comet assay, DAPI staining and DNA gel electrophoresis were used for examining DNA damage and results indicated that triptolide induced a longer DNA migration smear based on single cell electrophoresis and DNA condensation and damage occurred based on the examination of DAPI straining and DNA gel electrophoresis. The real-time PCR technique was used to examine DNA damage and repair gene expression (mRNA) and results indicated that triptolide led to a decrease in the ataxia telangiectasia mutated (ATM), ataxia-telangiectasia and Rad3-related (ATR), breast cancer 1, early onset (BRCA-1), p53, DNA-dependent serine/threonine protein kinase (DNA-PK) and O6-methylguanine-DNA methyltransferase (MGMT) mRNA expression. Thus, these observations indicated that triptolide induced DNA damage and inhibited DNA damage and repair-associated gene expression (mRNA) that may be factors for triptolide-mediated inhibition of cell growth in vitro in A375.S2 cells.
Collapse
Affiliation(s)
- Fu-Shin Chueh
- Departments of Health and Nutrition Biotechnology, Asia University, Taichung 413, Taiwan, ROC
| | | | | | | | | | | | | | | |
Collapse
|
20
|
An alternative telomerase RNA in Arabidopsis modulates enzyme activity in response to DNA damage. Genes Dev 2012; 26:2512-23. [PMID: 23109676 DOI: 10.1101/gad.202960.112] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Telomerase replenishes telomere tracts by reiteratively copying its RNA template, TER. Unlike other model organisms, Arabidopsis thaliana harbors two divergent TER genes. However, only TER1 is required for telomere maintenance. Here we examine the function of TER2. We show that TER2 is spliced and its 3' end is truncated in vivo to generate a third TER isoform, TER2(S). TERT preferentially associates with TER2 > TER1 > TER2(S). Moreover, TER2 and TER2(S) assemble with Ku and POT1b (protection of telomeres), forming RNP (ribonucleoprotein) complexes distinct from TER1 RNP. Plants null for TER2 display increased telomerase enzyme activity, while TER2 overexpression inhibits telomere synthesis from TER1 and leads to telomere shortening. These findings argue that TER2 negatively regulates telomerase by sequestering TERT in a nonproductive RNP complex. Introduction of DNA double-strand breaks by zeocin leads to an immediate and specific spike in TER2 and a concomitant decrease in telomerase enzyme activity. This response is not triggered by replication stress or telomere dysfunction and is abrogated in ter2 mutants. We conclude that Arabidopsis telomerase is modulated by TER2, a novel DNA damage-induced noncoding RNA that works in concert with the canonical TER to promote genome integrity.
Collapse
|