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Ding Y, Hou D, Yin Y, Chen K, He J, Yan S, Li H, Xiong Y, Zhou W, Li M. Genetic dissection of Brassica napus seed vigor after aging. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:141. [PMID: 38789698 DOI: 10.1007/s00122-024-04648-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
KEY MESSAGE Stable and novel QTLs that affect seed vigor under different storage durations were discovered, and BnaOLE4, located in the interval of cqSW-C2-3, increased seed vigor after aging. Seed vigor is an important trait in crop breeding; however, the underlying molecular regulatory mechanisms governing this trait in rapeseed remain largely unknown. In the present study, vigor-related traits were analyzed in seeds from a doubled haploid (DH) rapeseed (Brassica napus) population grown in 2 different environments using seeds stored for 7, 5, and 3 years under natural storage conditions. A total of 229 quantitative trait loci (QTLs) were identified and were found to explain 3.78%-17.22% of the phenotypic variance for seed vigor-related traits after aging. We further demonstrated that seed vigor-related traits were positively correlated with oil content (OC) but negatively correlated with unsaturated fatty acids (FAs). Some pleiotropic QTLs that collectively regulate OC, FAs, and seed vigor, such as uq.A8, uq.A3-2, uq.A9-2, and uq.C3-1, were identified. The transcriptomic results from extreme pools of DH lines with distinct seed vigor phenotypes during accelerated aging revealed that various biological pathways and metabolic processes (such as glutathione metabolism and reactive oxygen species) were involved in seed vigor. Through integration of QTL analysis and RNA-Seq, a regulatory network for the control of seed vigor was constructed. Importantly, a candidate (BnaOLE4) from cqSW-C2-3 was selected for functional analysis, and transgenic lines overexpressing BnaOLE4 showed increased seed vigor after artificial aging. Collectively, these results provide novel information on QTL and potential candidate genes for molecular breeding for improved seed storability.
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Affiliation(s)
- Yiran Ding
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Dalin Hou
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Yongtai Yin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Kang Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Shuxiang Yan
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Yiyi Xiong
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Weixian Zhou
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan, 430074, China.
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Sears RG, Rigoulot SB, Occhialini A, Morgan B, Kakeshpour T, Brabazon H, Barnes CN, Seaberry EM, Jacobs B, Brown C, Yang Y, Schimel TM, Lenaghan SC, Neal Stewart C. Engineered gamma radiation phytosensors for environmental monitoring. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1745-1756. [PMID: 37224108 PMCID: PMC10440981 DOI: 10.1111/pbi.14072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/13/2023] [Accepted: 04/24/2023] [Indexed: 05/26/2023]
Abstract
Nuclear energy, already a practical solution for supplying energy on a scale similar to fossil fuels, will likely increase its footprint over the next several decades to meet current climate goals. Gamma radiation is produced during fission in existing nuclear reactors and thus the need to detect leakage from nuclear plants, and effects of such leakage on ecosystems will likely also increase. At present, gamma radiation is detected using mechanical sensors that have several drawbacks, including: (i) limited availability; (ii) reliance on power supply; and (iii) requirement of human presence in dangerous areas. To overcome these limitations, we have developed a plant biosensor (phytosensor) to detect low-dose ionizing radiation. The system utilizes synthetic biology to engineer a dosimetric switch into potato utilizing the plant's native DNA damage response (DDR) machinery to produce a fluorescent output. In this work, the radiation phytosensor was shown to respond to a wide range of gamma radiation exposure (10-80 Grey) producing a reporter signal that was detectable at >3 m. Further, a pressure test of the top radiation phytosensor in a complex mesocosm demonstrated full function of the system in a 'real world' scenario.
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Affiliation(s)
- Robert G. Sears
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Stephen B. Rigoulot
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Alessandro Occhialini
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
- Department of Food ScienceThe University of TennesseeKnoxvilleTennesseeUSA
| | - Britany Morgan
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Tayebeh Kakeshpour
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Holly Brabazon
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Caitlin N. Barnes
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Erin M. Seaberry
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Brianna Jacobs
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Chandler Brown
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Yongil Yang
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Tayler M. Schimel
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
- Department of Food ScienceThe University of TennesseeKnoxvilleTennesseeUSA
| | - Scott C. Lenaghan
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
- Department of Food ScienceThe University of TennesseeKnoxvilleTennesseeUSA
| | - C. Neal Stewart
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
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3
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Teano G, Concia L, Wolff L, Carron L, Biocanin I, Adamusová K, Fojtová M, Bourge M, Kramdi A, Colot V, Grossniklaus U, Bowler C, Baroux C, Carbone A, Probst AV, Schrumpfová PP, Fajkus J, Amiard S, Grob S, Bourbousse C, Barneche F. Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis. Cell Rep 2023; 42:112894. [PMID: 37515769 DOI: 10.1016/j.celrep.2023.112894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 12/02/2022] [Accepted: 07/13/2023] [Indexed: 07/31/2023] Open
Abstract
While the pivotal role of linker histone H1 in shaping nucleosome organization is well established, its functional interplays with chromatin factors along the epigenome are just starting to emerge. Here we show that, in Arabidopsis, as in mammals, H1 occupies Polycomb Repressive Complex 2 (PRC2) target genes where it favors chromatin condensation and H3K27me3 deposition. We further show that, contrasting with its conserved function in PRC2 activation at genes, H1 selectively prevents H3K27me3 accumulation at telomeres and large pericentromeric interstitial telomeric repeat (ITR) domains by restricting DNA accessibility to Telomere Repeat Binding (TRB) proteins, a group of H1-related Myb factors mediating PRC2 cis recruitment. This study provides a mechanistic framework by which H1 avoids the formation of gigantic H3K27me3-rich domains at telomeric sequences and contributes to safeguard nucleus architecture.
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Affiliation(s)
- Gianluca Teano
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France; Université Paris-Saclay, 91190 Orsay, France
| | - Lorenzo Concia
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Léa Wolff
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Léopold Carron
- Sorbonne Université, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
| | - Ivona Biocanin
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France; Université Paris-Saclay, 91190 Orsay, France
| | - Kateřina Adamusová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michael Bourge
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Amira Kramdi
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Vincent Colot
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Chris Bowler
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Célia Baroux
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Alessandra Carbone
- Sorbonne Université, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
| | - Aline V Probst
- CNRS UMR6293, Université Clermont Auvergne, INSERM U1103, GReD, CRBC, Clermont-Ferrand, France
| | - Petra Procházková Schrumpfová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Simon Amiard
- CNRS UMR6293, Université Clermont Auvergne, INSERM U1103, GReD, CRBC, Clermont-Ferrand, France
| | - Stefan Grob
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Clara Bourbousse
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Fredy Barneche
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France.
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Genetic Variations in Nucleotide Excision Repair Pathway Genes and Risk of Allergic Rhinitis. Mediators Inflamm 2022; 2022:7815283. [PMID: 35693108 PMCID: PMC9187482 DOI: 10.1155/2022/7815283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 05/14/2022] [Accepted: 05/26/2022] [Indexed: 11/24/2022] Open
Abstract
Background Allergic rhinitis (AR) is the most frequent inflammatory disorder in the nasal mucosa that remains unclear etiology. Mounting studies suggested that genetic instability could trigger and worsen the inflammatory response. The nucleotide excision repair (NER) system is an important pathway in maintaining the stability of the genome. Therefore, the genetic variations in NER pathway genes may have potential effects on AR risk. Methods We evaluated the correlation between 19 candidate single nucleotide polymorphisms (SNPs) in NER pathway genes and AR susceptibility by a case-control study in a Chinese population, which contains 508 AR cases and 526 controls. Results Three independent SNPs were identified as significantly associated with AR susceptibility, including ERCC1 rs2298881 C > A (recessive model: adjusted odds ratios (OR) = 0.30, 95%confidence interval (CI) = 0.18–0.50, P < 0.0001), ERCC1 rs11615 G > A (dominant model: adjusted OR = 1.44, 95%CI = 1.04–2.01, P = 0.030), and XPC rs2228001 A > C (dominant model: adjusted OR = 0.68, 95%CI = 0.49–0.95, P = 0.024). Stratified analysis showed that ERCC1 rs2298881 AA genotype was correlated with a lower risk of AR among all the subgroups compared with rs2298881 CC/CA genotype. XPC rs2228001 AC/CC genotype reduced AR risk among the following subgroups: age > 60 months, clinical stage I and III. Conclusion Our finding showed that genetic variations in NER pathway genes: ERCC1 and XPC may affect the risk of AR, which will provide new insights into the genetics of AR from the perspective of DNA damage repair.
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The Power of Stress: The Telo-Hormesis Hypothesis. Cells 2021; 10:cells10051156. [PMID: 34064566 PMCID: PMC8151059 DOI: 10.3390/cells10051156] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
Adaptative response to stress is a strategy conserved across evolution to promote survival. In this context, the groundbreaking findings of Miroslav Radman on the adaptative value of changing mutation rates opened new avenues in our understanding of stress response. Inspired by this work, we explore here the putative beneficial effects of changing the ends of eukaryotic chromosomes, the telomeres, in response to stress. We first summarize basic principles in telomere biology and then describe how various types of stress can alter telomere structure and functions. Finally, we discuss the hypothesis of stress-induced telomere signaling with hormetic effects.
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Kolářová K, Nešpor Dadejová M, Loja T, Lochmanová G, Sýkorová E, Dvořáčková M. Disruption of NAP1 genes in Arabidopsis thaliana suppresses the fas1 mutant phenotype, enhances genome stability and changes chromatin compaction. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:56-73. [PMID: 33368779 DOI: 10.1111/tpj.15145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/21/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Histone chaperones mediate the assembly and disassembly of nucleosomes and participate in essentially all DNA-dependent cellular processes. In Arabidopsis thaliana, loss-of-function of FAS1 or FAS2 subunits of the H3-H4 histone chaperone complex CHROMATIN ASSEMBLY FACTOR 1 (CAF-1) has a dramatic effect on plant morphology, growth and overall fitness. CAF-1 dysfunction can lead to altered chromatin compaction, systematic loss of repetitive elements or increased DNA damage, clearly demonstrating its severity. How chromatin composition is maintained without functional CAF-1 remains elusive. Here we show that disruption of the H2A-H2B histone chaperone NUCLEOSOME ASSEMBLY PROTEIN 1 (NAP1) suppresses the FAS1 loss-of-function phenotype. The quadruple mutant fas1 nap1;1 nap1;2 nap1;3 shows wild-type growth, decreased sensitivity to genotoxic stress and suppression of telomere and 45S rDNA loss. Chromatin of fas1 nap1;1 nap1;2 nap1;3 plants is less accessible to micrococcal nuclease and the nuclear H3.1 and H3.3 histone pools change compared to fas1. Consistently, association between NAP1 and H3 occurs in the cytoplasm and nucleus in vivo in protoplasts. Altogether we show that NAP1 proteins play an essential role in DNA repair in fas1, which is coupled to nucleosome assembly through modulation of H3 levels in the nucleus.
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Affiliation(s)
- Karolína Kolářová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ-61137, Czech Republic
- Molecular Cytology and Cytometry, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, Brno, CZ-61265, Czech Republic
| | - Martina Nešpor Dadejová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology/Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic
| | - Tomáš Loja
- Centre for Molecular Medicine, Central European Institute of Technology/Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic
| | - Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology/Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic
| | - Eva Sýkorová
- Molecular Cytology and Cytometry, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, Brno, CZ-61265, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology/Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic
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Barbero Barcenilla B, Shippen DE. Back to the future: The intimate and evolving connection between telomere-related factors and genotoxic stress. J Biol Chem 2019; 294:14803-14813. [PMID: 31434740 DOI: 10.1074/jbc.aw119.008145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The conversion of circular genomes to linear chromosomes during molecular evolution required the invention of telomeres. This entailed the acquisition of factors necessary to fulfill two new requirements: the need to fully replicate terminal DNA sequences and the ability to distinguish chromosome ends from damaged DNA. Here we consider the multifaceted functions of factors recruited to perpetuate and stabilize telomeres. We discuss recent theories for how telomere factors evolved from existing cellular machineries and examine their engagement in nontelomeric functions such as DNA repair, replication, and transcriptional regulation. We highlight the remarkable versatility of protection of telomeres 1 (POT1) proteins that was fueled by gene duplication and divergence events that occurred independently across several eukaryotic lineages. Finally, we consider the relationship between oxidative stress and telomeres and the enigmatic role of telomere-associated proteins in mitochondria. These findings point to an evolving and intimate connection between telomeres and cellular physiology and the strong drive to maintain chromosome integrity.
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Affiliation(s)
- Borja Barbero Barcenilla
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
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8
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Panier S, Maric M, Hewitt G, Mason-Osann E, Gali H, Dai A, Labadorf A, Guervilly JH, Ruis P, Segura-Bayona S, Belan O, Marzec P, Gaillard PHL, Flynn RL, Boulton SJ. SLX4IP Antagonizes Promiscuous BLM Activity during ALT Maintenance. Mol Cell 2019; 76:27-43.e11. [PMID: 31447390 PMCID: PMC6863466 DOI: 10.1016/j.molcel.2019.07.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 06/03/2019] [Accepted: 07/08/2019] [Indexed: 12/18/2022]
Abstract
Cancer cells acquire unlimited proliferative capacity by either re-expressing telomerase or inducing alternative lengthening of telomeres (ALT), which relies on telomere recombination. Here, we show that ALT recombination requires coordinate regulation of the SMX and BTR complexes to ensure the appropriate balance of resolution and dissolution activities at recombining telomeres. Critical to this control is SLX4IP, which accumulates at ALT telomeres and interacts with SLX4, XPF, and BLM. Loss of SLX4IP increases ALT-related phenotypes, which is incompatible with cell growth following concomitant loss of SLX4. Inactivation of BLM is sufficient to rescue telomere aggregation and the synthetic growth defect in this context, suggesting that SLX4IP favors SMX-dependent resolution by antagonizing promiscuous BLM activity during ALT recombination. Finally, we show that SLX4IP is inactivated in a subset of ALT-positive osteosarcomas. Collectively, our findings uncover an SLX4IP-dependent regulatory mechanism critical for telomere maintenance in ALT cancer cells.
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Affiliation(s)
| | - Marija Maric
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Graeme Hewitt
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Emily Mason-Osann
- Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Himabindu Gali
- Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Anqi Dai
- Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Adam Labadorf
- Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Jean-Hugues Guervilly
- Centre de Recherche en Cancérologie de Marseille, CRCM, CNRS, Aix Marseille Université, INSERM, Institut Paoli-Calmettes, 27 Boulevard Leï Roure, 13009 Marseille, France
| | - Philip Ruis
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Ondrej Belan
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Paulina Marzec
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Pierre-Henri L Gaillard
- Centre de Recherche en Cancérologie de Marseille, CRCM, CNRS, Aix Marseille Université, INSERM, Institut Paoli-Calmettes, 27 Boulevard Leï Roure, 13009 Marseille, France
| | - Rachel L Flynn
- Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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Olivier M, Charbonnel C, Amiard S, White CI, Gallego ME. RAD51 and RTEL1 compensate telomere loss in the absence of telomerase. Nucleic Acids Res 2019; 46:2432-2445. [PMID: 29346668 PMCID: PMC5861403 DOI: 10.1093/nar/gkx1322] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/09/2018] [Indexed: 11/23/2022] Open
Abstract
Replicative erosion of telomeres is naturally compensated by telomerase and studies in yeast and vertebrates show that homologous recombination can compensate for the absence of telomerase. We show that RAD51 protein, which catalyzes the key strand-invasion step of homologous recombination, is localized at Arabidopsis telomeres in absence of telomerase. Blocking the strand-transfer activity of the RAD51 in telomerase mutant plants results in a strikingly earlier onset of developmental defects, accompanied by increased numbers of end-to-end chromosome fusions. Imposing replication stress through knockout of RNaseH2 increases numbers of chromosome fusions and reduces the survival of these plants deficient for telomerase and homologous recombination. This finding suggests that RAD51-dependent homologous recombination acts as an essential backup to the telomerase for compensation of replicative telomere loss to ensure genome stability. Furthermore, we show that this positive role of RAD51 in telomere stability is dependent on the RTEL1 helicase. We propose that a RAD51 dependent break-induced replication process is activated in cells lacking telomerase activity, with RTEL1 responsible for D-loop dissolution after telomere replication.
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Affiliation(s)
- Margaux Olivier
- Génétique, Reproduction et Développement, UMR CNRS 6293 - INSERM U1103 - Université Clermont Auvergne, Faculté de Médecine. 28, place Henri Dunant - BP38 63001 Clermont-Ferrand Cedex 1, France
| | - Cyril Charbonnel
- Génétique, Reproduction et Développement, UMR CNRS 6293 - INSERM U1103 - Université Clermont Auvergne, Faculté de Médecine. 28, place Henri Dunant - BP38 63001 Clermont-Ferrand Cedex 1, France
| | - Simon Amiard
- Génétique, Reproduction et Développement, UMR CNRS 6293 - INSERM U1103 - Université Clermont Auvergne, Faculté de Médecine. 28, place Henri Dunant - BP38 63001 Clermont-Ferrand Cedex 1, France
| | - Charles I White
- Génétique, Reproduction et Développement, UMR CNRS 6293 - INSERM U1103 - Université Clermont Auvergne, Faculté de Médecine. 28, place Henri Dunant - BP38 63001 Clermont-Ferrand Cedex 1, France
| | - Maria E Gallego
- Génétique, Reproduction et Développement, UMR CNRS 6293 - INSERM U1103 - Université Clermont Auvergne, Faculté de Médecine. 28, place Henri Dunant - BP38 63001 Clermont-Ferrand Cedex 1, France
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Smith ED, Garza-Gongora AG, MacQuarrie KL, Kosak ST. Interstitial telomeric loops and implications of the interaction between TRF2 and lamin A/C. Differentiation 2018; 102:19-26. [PMID: 29979997 DOI: 10.1016/j.diff.2018.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/11/2018] [Accepted: 06/12/2018] [Indexed: 11/19/2022]
Abstract
The protein-DNA complexes that compose the end of mammalian chromosomes-telomeres-serve to stabilize linear genomic DNA and are involved in cellular and organismal aging. One mechanism that protects telomeres from premature degradation is the formation of structures called t-loops, in which the single-stranded 3' overhang present at the terminal end of telomeres loops back and invades medial double-stranded telomeric DNA. We identified looped structures formed between terminal chromosome ends and interstitial telomeric sequences (ITSs), which are found throughout the human genome, that we have termed interstitial telomeric loops (ITLs). While they form in a TRF2-dependent manner similar to t-loops, ITLs further require the physical interaction of TRF2 with the nuclear intermediate filament protein lamin A/C. Our findings suggest that interactions between telomeres and the nucleoskeleton broadly impact genomic integrity, including telomere stability, chromosome structure, and chromosome fragility. Here, we review the roles of TRF2 and lamin A/C in telomere biology and consider how their interaction may relate telomere homeostasis to cellular and organismal aging.
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Affiliation(s)
- Erica D Smith
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Arturo G Garza-Gongora
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Kyle L MacQuarrie
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Division of Hematology, Oncology and Stem Cell Transplantation, Ann & Robert H. Lurie Children's Hospital of Chicago, USA
| | - Steven T Kosak
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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11
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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.
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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
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12
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Nataliia L, Volodymyr L. Cold Resistance of Plant Species of the Genus Vitex l. Introduced in M.M. GRYSHKO National Botanic Garden of NAS of Ukraine. INTERNATIONAL JOURNAL OF SECONDARY METABOLITE 2018. [DOI: 10.21448/ijsm.416258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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13
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Litvinov S, Rashydov N. Transgenerational Transmission of Radiation-Induced Expression Patterns of Arabidopsis Thaliana (L.) Heynh. Rad51 and Rad1 Genes. INTERNATIONAL JOURNAL OF SECONDARY METABOLITE 2018. [DOI: 10.21448/ijsm.415191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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14
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Dehé PM, Gaillard PHL. Control of structure-specific endonucleases to maintain genome stability. Nat Rev Mol Cell Biol 2017; 18:315-330. [PMID: 28327556 DOI: 10.1038/nrm.2016.177] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Structure-specific endonucleases (SSEs) have key roles in DNA replication, recombination and repair, and emerging roles in transcription. These enzymes have specificity for DNA secondary structure rather than for sequence, and therefore their activity must be precisely controlled to ensure genome stability. In this Review, we discuss how SSEs are controlled as part of genome maintenance pathways in eukaryotes, with an emphasis on the elaborate mechanisms that regulate the members of the major SSE families - including the xeroderma pigmentosum group F-complementing protein (XPF) and MMS and UV-sensitive protein 81 (MUS81)-dependent nucleases, and the flap endonuclease 1 (FEN1), XPG and XPG-like endonuclease 1 (GEN1) enzymes - during processes such as DNA adduct repair, Holliday junction processing and replication stress. We also discuss newly characterized connections between SSEs and other classes of DNA-remodelling enzymes and cell cycle control machineries, which reveal the importance of SSE scaffolds such as the synthetic lethal of unknown function 4 (SLX4) tumour suppressor for the maintenance of genome stability.
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Affiliation(s)
- Pierre-Marie Dehé
- Centre de Recherche en Cancérologie de Marseille, CRCM, CNRS, Aix Marseille Université, INSERM, Institut Paoli-Calmettes, 27 Boulevard Leï Roure, 13009 Marseille, France
| | - Pierre-Henri L Gaillard
- Centre de Recherche en Cancérologie de Marseille, CRCM, CNRS, Aix Marseille Université, INSERM, Institut Paoli-Calmettes, 27 Boulevard Leï Roure, 13009 Marseille, France
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15
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Fouquerel E, Opresko P. Convergence of The Nobel Fields of Telomere Biology and DNA Repair. Photochem Photobiol 2017; 93:229-237. [PMID: 27861975 PMCID: PMC5315637 DOI: 10.1111/php.12672] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/26/2016] [Indexed: 02/02/2023]
Abstract
The fields of telomere biology and DNA repair have enjoyed a great deal of cross-fertilization and convergence in recent years. Telomeres function at chromosome ends to prevent them from being falsely recognized as chromosome breaks by the DNA damage response and repair machineries. Conversely, both canonical and nonconical functions of numerous DNA repair proteins have been found to be critical for preserving telomere structure and function. In 2009, Elizabeth Blackburn, Carol Greider and Jack Szostak were awarded the Nobel prize in Physiology or Medicine for the discovery of telomeres and telomerase. Four years later, pioneers in the field of DNA repair, Aziz Sancar, Tomas Lindahl and Paul Modrich were recognized for their seminal contributions by being awarded the Nobel Prize in Chemistry. This review is part of a special issue meant to celebrate this amazing achievement, and will focus in particular on the convergence of nucleotide excision repair and telomere biology, and will discuss the profound implications for human health.
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Affiliation(s)
- Elise Fouquerel
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh Cancer Institute Research Pavilion, 5117 Centre Avenue, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Patricia Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh Cancer Institute Research Pavilion, 5117 Centre Avenue, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
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16
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Fujimoto S, Sugano SS, Kuwata K, Osakabe K, Matsunaga S. Visualization of specific repetitive genomic sequences with fluorescent TALEs in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6101-6110. [PMID: 27811079 PMCID: PMC5100022 DOI: 10.1093/jxb/erw371] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Live imaging of the dynamics of nuclear organization provides the opportunity to uncover the mechanisms responsible for four-dimensional genome architecture. Here, we describe the use of fluorescent protein (FP) fusions of transcription activator-like effectors (TALEs) to visualize endogenous genomic sequences in Arabidopsis thaliana. The ability to engineer sequence-specific TALEs permits the investigation of precise genomic sequences. We could detect TALE-FP signals associated with centromeric, telomeric, and rDNA repeats and the signal distribution was consistent with that observed by fluorescent in situ hybridization. TALE-FPs are advantageous because they permit the observation of intact tissues. We used our TALE-FP method to investigate the nuclei of several multicellular plant tissues including roots, hypocotyls, leaves, and flowers. Because TALE-FPs permit live-cell imaging, we successfully observed the temporal dynamics of centromeres and telomeres in plant organs. Fusing TALEs to multimeric FPs enhanced the signal intensity when observing telomeres. We found that the mobility of telomeres was different in sub-nuclear regions. Transgenic plants stably expressing TALE-FPs will provide new insights into chromatin organization and dynamics in multicellular organisms.
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Affiliation(s)
- Satoru Fujimoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Shigeo S Sugano
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
- PRESTO, JST, Saitama 332-0012, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Keishi Osakabe
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima 770-8513, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
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17
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Gu Y, Xing S, He C. Genome-Wide Analysis Indicates Lineage-Specific Gene Loss during Papilionoideae Evolution. Genome Biol Evol 2016; 8:635-48. [PMID: 26868598 PMCID: PMC4824202 DOI: 10.1093/gbe/evw021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2016] [Indexed: 02/07/2023] Open
Abstract
Gene loss is the driving force for changes in genome and morphology; however, this particular evolutionary event has been poorly investigated in leguminous plants. Legumes (Fabaceae) have some lineage-specific and diagnostic characteristics that are distinct from other angiosperms. To understand the potential role of gene loss in the evolution of legumes, we compared six genome-sequenced legume species of Papilionoideae, the largest representative clade of Fabaceae, such as Glycine max, with 34 nonlegume plant species, such as Arabidopsis thaliana. The results showed that the putative orthologs of the 34 Arabidopsis genes belonging to 29 gene families were absent in these legume species but these were conserved in the sequenced nonlegume angiosperm lineages. Further evolutionary analyses indicated that the orthologs of these genes were almost completely lost in the Papillionoideae ancestors, thus designated as the legume lost genes (LLGs), and these underwent purifying selection in nonlegume plants. Most LLGs were functionally unknown. In Arabidopsis, two LLGs were well-known genes that played a role in plant immunity such as HARMLESS TO OZONE LAYER 1 and HOPZ-ACTIVATED RESISTANCE 1, and 16 additional LLGs were predicted to participate in plant-pathogen interactions in in silico expression and protein-protein interaction network analyses. Most of these LLGs' orthologs in various plants were also found to be associated with biotic stress response, indicating the conserved role of these genes in plant defense. The evolutionary implication of LLGs during the development of the ability of symbiotic nitrogen fixation involving plant and bacterial interactions, which is a well-known characteristic of most legumes, is also discussed. Our work sheds light on the evolutionary implication of gene loss events in Papilionoideae evolution, as well as provides new insights into crop design to improve nitrogen fixation capacity.
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Affiliation(s)
- Yongzhe Gu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing 100093, China Graduate University, Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
| | - Shilai Xing
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing 100093, China Graduate University, Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing 100093, China
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18
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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.
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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
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19
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Olivier M, Da Ines O, Amiard S, Serra H, Goubely C, White CI, Gallego ME. The Structure-Specific Endonucleases MUS81 and SEND1 Are Essential for Telomere Stability in Arabidopsis. THE PLANT CELL 2016; 28:74-86. [PMID: 26704385 PMCID: PMC4746687 DOI: 10.1105/tpc.15.00898] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 12/23/2015] [Indexed: 05/02/2023]
Abstract
Structure-specific endonucleases act to repair potentially toxic structures produced by recombination and DNA replication, ensuring proper segregation of the genetic material to daughter cells during mitosis and meiosis. Arabidopsis thaliana has two putative homologs of the resolvase (structure-specific endonuclease): GEN1/Yen1. Knockout of resolvase genes GEN1 and SEND1, individually or together, has no detectable effect on growth, fertility, or sensitivity to DNA damage. However, combined absence of the endonucleases MUS81 and SEND1 results in severe developmental defects, spontaneous cell death, and genome instability. A similar effect is not seen in mus81 gen1 plants, which develop normally and are fertile. Absence of RAD51 does not rescue mus81 send1, pointing to roles of these proteins in DNA replication rather than DNA break repair. The enrichment of S-phase histone γ-H2AX foci and a striking loss of telomeric DNA in mus81 send1 further support this interpretation. SEND1 has at most a minor role in resolution of the Holliday junction but acts as an essential backup to MUS81 for resolution of toxic replication structures to ensure genome stability and to maintain telomere integrity.
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Affiliation(s)
- Margaux Olivier
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Olivier Da Ines
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Simon Amiard
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Heïdi Serra
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Chantal Goubely
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Charles I White
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Maria E Gallego
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
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20
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Gao J, Roy S, Tong L, Argos M, Jasmine F, Rahaman R, Rakibuz-Zaman M, Parvez F, Ahmed A, Hore SK, Sarwar G, Slavkovich V, Yunus M, Rahman M, Baron JA, Graziano JH, Ahsan H, Pierce BL. Arsenic exposure, telomere length, and expression of telomere-related genes among Bangladeshi individuals. ENVIRONMENTAL RESEARCH 2015; 136:462-9. [PMID: 25460668 PMCID: PMC4264833 DOI: 10.1016/j.envres.2014.09.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 08/11/2014] [Accepted: 09/22/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND Inorganic arsenic is a carcinogen whose mode of action may involve telomere dysfunction. Recent epidemiological studies suggest that chronic arsenic exposure is associated with longer telomeres and altered expression of telomere-related genes in peripheral blood. In this study, we evaluated the association of urinary arsenic concentration with expression of telomere-related genes and telomere length in Bangladeshi individuals with a wide range of arsenic exposure through naturally contaminated drinking water. METHODS We used linear regression models to estimate associations between urinary arsenic and array-based expression measures for 69 telomere related genes using mononuclear cell RNA samples from 1799 individuals. Association between arsenic exposure and a qPCR-based telomere length measure was assessed among 167 individuals. RESULTS Urinary arsenic was positively associated with expression of WRN, and negatively associated with TERF2, DKC1, TERF2IP and OBFC1 (all P<0.00035, Bonferroni-corrected threshold). We detected interaction between urinary arsenic and arsenic metabolism efficiency in relation to expression of WRN (P for interaction =0.00008). In addition, we observed that very high arsenic exposure was associated with longer telomeres compared to very low exposure (P=0.02). DISCUSSION Our findings suggest that arsenic's carcinogenic mode of action may involve alteration of telomere maintenance and/or telomere damage. This study extends our knowledge regarding the effect of arsenic on telomere length and expression of telomere-related genes.
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Affiliation(s)
- Jianjun Gao
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Shantanu Roy
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Lin Tong
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Maria Argos
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Farzana Jasmine
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Ronald Rahaman
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | | | - Faruque Parvez
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | | | - Samar K Hore
- International Center for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - Vesna Slavkovich
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Mohammad Yunus
- International Center for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - John A Baron
- University of North Carolina, Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27514, USA
| | - Joseph H Graziano
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Habibul Ahsan
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA; Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA; Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Brandon L Pierce
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA; Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA.
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21
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Muchová V, Amiard S, Mozgová I, Dvořáčková M, Gallego ME, White C, Fajkus J. Homology-dependent repair is involved in 45S rDNA loss in plant CAF-1 mutants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:198-209. [PMID: 25359579 PMCID: PMC4309414 DOI: 10.1111/tpj.12718] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 10/23/2014] [Accepted: 10/24/2014] [Indexed: 05/19/2023]
Abstract
Arabidopsis thaliana mutants in FAS1 and FAS2 subunits of chromatin assembly factor 1 (CAF1) show progressive loss of 45S rDNA copies and telomeres. We hypothesized that homology-dependent DNA damage repair (HDR) may contribute to the loss of these repeats in fas mutants. To test this, we generated double mutants by crossing fas mutants with knock-out mutants in RAD51B, one of the Rad51 paralogs of A. thaliana. Our results show that the absence of RAD51B decreases the rate of rDNA loss, confirming the implication of RAD51B-dependent recombination in rDNA loss in the CAF1 mutants. Interestingly, this effect is not observed for telomeric repeat loss, which thus differs from that acting in rDNA loss. Involvement of DNA damage repair in rDNA dynamics in fas mutants is further supported by accumulation of double-stranded breaks (measured as γ-H2AX foci) in 45S rDNA. Occurrence of the foci is not specific for S-phase, and is ATM-independent. While the foci in fas mutants occur both in the transcribed (intranucleolar) and non-transcribed (nucleoplasmic) fraction of rDNA, double fas rad51b mutants show a specific increase in the number of the intranucleolar foci. These results suggest that the repair of double-stranded breaks present in the transcribed rDNA region is RAD51B dependent and that this contributes to rDNA repeat loss in fas mutants, presumably via the single-stranded annealing recombination pathway. Our results also highlight the importance of proper chromatin assembly in the maintenance of genome stability.
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Affiliation(s)
- Veronika Muchová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
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22
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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.
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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
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Abstract
Telomeres protect chromosome ends from degradation and inappropriate DNA damage response activation through their association with specific factors. Interestingly, these telomeric factors are able to localize outside telomeric regions, where they can regulate the transcription of genes involved in metabolism, immunity and differentiation. These findings delineate a signalling pathway by which telomeric changes control the ability of their associated factors to regulate transcription. This mechanism is expected to enable a greater diversity of cellular responses that are adapted to specific cell types and telomeric changes, and may therefore represent a pivotal aspect of development, ageing and telomere-mediated diseases.
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Bilichak A, Yao Y, Titov V, Golubov A, Kovalchuk I. Genome stability in the uvh6 mutant of Arabidopsis thaliana. PLANT CELL REPORTS 2014; 33:979-991. [PMID: 24553752 DOI: 10.1007/s00299-014-1580-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/21/2014] [Accepted: 01/30/2014] [Indexed: 06/03/2023]
Abstract
Plant XPD homolog UVH6 is the protein involved in the repair of strand breaks, and the excision repair and uvh6 mutant is not impaired in transgenerational increase in HRF. While analyzing the transgenerational response to stress in plants, we found that the promoter and gene body of Arabidopsis thaliana (Arabidopsis) XPD homolog UVH6 underwent hypomethylation and showed an increase in the level of transcript. Here, we analyzed the mutant of this gene, uvh6-1, by crossing it to two different reporter lines: one which allows for analysis of homologous recombination frequency (HRF) and another which makes it possible to analyze the frequency of point mutations. We observed that uvh6-1 plants exhibited lower rate of spontaneous homologous recombination but higher frequencies of spontaneous point mutations. The analysis of strand breaks using ROPS and Comet assays showed that the mutant had a much higher level of strand breaks at non-induced conditions. Exposure to stresses such as UVC, heat, cold, flood and drought showed that the mutant was not impaired in an increase in somatic HRF. The analysis of spontaneous HRF in the progeny of control plants compared to that of the progeny of stressed plants demonstrated that uvh6-1 was mildly affected in response to temperature, UV and drought. Our data suggest that UVH6 may be involved in the repair of strand breaks and excision repair, but it is unlikely that UVH6 is required for transgenerational increase in HRF.
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Affiliation(s)
- Andriy Bilichak
- Department of Biological Sciences, University of Lethbridge, University Drive 4401, Lethbridge, AB, T1K 3M4, Canada,
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25
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Machado CR, Vieira-da-Rocha JP, Mendes IC, Rajão MA, Marcello L, Bitar M, Drummond MG, Grynberg P, Oliveira DAA, Marques C, Van Houten B, McCulloch R. Nucleotide excision repair in Trypanosoma brucei: specialization of transcription-coupled repair due to multigenic transcription. Mol Microbiol 2014; 92:756-76. [PMID: 24661334 PMCID: PMC4138998 DOI: 10.1111/mmi.12589] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2014] [Indexed: 02/02/2023]
Abstract
Nucleotide excision repair (NER) is a highly conserved genome repair pathway acting on helix distorting DNA lesions. NER is divided into two subpathways: global genome NER (GG-NER), which is responsible for repair throughout genomes, and transcription-coupled NER (TC-NER), which acts on lesions that impede transcription. The extent of the Trypanosoma brucei genome that is transcribed is highly unusual, since most genes are organized in multigene transcription units, each transcribed from a single promoter. Given this transcription organization, we have addressed the importance of NER to T. brucei genome maintenance by performing RNAi against all predicted contributing factors. Our results indicate that TC-NER is the main pathway of NER repair, but only CSB, XPBz and XPG contribute. Moreover, we show that UV lesions are inefficiently repaired in T. brucei, perhaps due to preferential use of RNA polymerase translesion synthesis. RNAi of XPC and DDB was found to be lethal, and we show that these factors act in inter-strand cross-link repair. XPD and XPB appear only to act in transcription, not repair. This work indicates that the predominance of multigenic transcription in T. brucei has resulted in pronounced adaptation of NER relative to the host and may be an attractive drug target.
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Affiliation(s)
- Carlos R Machado
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Caixa Postal 486, Belo Horizonte, 30161-970, MG, Brazil
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26
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Vaquero-Sedas MI, Vega-Palas MA. Differential association of Arabidopsis telomeres and centromeres with histone H3 variants. Sci Rep 2013; 3:1202. [PMID: 23383372 PMCID: PMC3563029 DOI: 10.1038/srep01202] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 01/11/2013] [Indexed: 01/25/2023] Open
Abstract
Two different groups, using ChIP-seq data, have recently published the genome-wide distribution of histones H3.1 and H3.3 in Arabidopsis thaliana. In one report, Stroud and colleagues determined that, whereas H3.1 was enriched in repetitive pericentromeric and silent chromatin, H3.3 was enriched in transcriptionally active regions. This work was performed using seedlings, which contained dividing and non-dividing cells. In a second report, Wollmann and colleagues found similar results analyzing dividing or non-dividing tissue. None of these reports addressed the analysis of telomeres or centromeres. Our group has recently described an experimental approach that allows the study of the epigenetic status of some Arabidopsis repetitive sequences by analyzing ChIP-seq data. By using this approach and the data generated by Stroud, Wollmann and colleagues, we found that telomeres are enriched in H3.3 with regard to the centromeric 178 bp repeats, whereas the centromeric repeats are enriched in H3.1 with regard to telomeres.
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Affiliation(s)
- María I Vaquero-Sedas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-US), c/Américo Vespucio n° 49, 41092 Seville, Spain
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27
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Vaquero-Sedas MI, Luo C, Vega-Palas MA. Analysis of the epigenetic status of telomeres by using ChIP-seq data. Nucleic Acids Res 2012; 40:e163. [PMID: 22855559 PMCID: PMC3505975 DOI: 10.1093/nar/gks730] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/06/2012] [Indexed: 01/17/2023] Open
Abstract
The chromatin structure of eukaryotic telomeres plays an essential role in telomere functions. However, their study might be impaired by the presence of interstitial telomeric sequences (ITSs), which have a widespread distribution in different model systems. We have developed a simple approach to study the chromatin structure of Arabidopsis telomeres independently of ITSs by analyzing ChIP-seq data. This approach could be used to study the chromatin structure of telomeres in some other eukaryotes. The analysis of ChIP-seq experiments revealed that Arabidopsis telomeres have higher density of histone H3 than centromeres, which might reflects their short nucleosomal organization. These experiments also revealed that Arabidopsis telomeres have lower levels of heterochromatic marks than centromeres (H3K9(Me2) and H3K27(Me)), higher levels of some euchromatic marks (H3K4(Me2) and H3K9Ac) and similar or lower levels of other euchromatic marks (H3K4(Me3), H3K36(Me2), H3K36(Me3) and H3K18Ac). Interestingly, the ChIP-seq experiments also revealed that Arabidopsis telomeres exhibit high levels of H3K27(Me3), a repressive mark that associates with many euchromatic genes. The epigenetic profile of Arabidopsis telomeres is closely related to the previously defined chromatin state 2. This chromatin state is found in 23% of Arabidopsis genes, many of which are repressed or lowly expressed. At least, in part, this scenario is similar in rice.
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Affiliation(s)
- María I. Vaquero-Sedas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-USE), c/ Américo Vespucio n° 49, 41092 Seville, Spain and Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Chongyuan Luo
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-USE), c/ Américo Vespucio n° 49, 41092 Seville, Spain and Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Miguel A. Vega-Palas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-USE), c/ Américo Vespucio n° 49, 41092 Seville, Spain and Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, USA
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28
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Taleei R, Weinfeld M, Nikjoo H. Single strand annealing mathematical model for double strand break repair. ACTA ACUST UNITED AC 2012. [DOI: 10.7243/2050-1412-1-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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29
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Amiard S, Depeiges A, Allain E, White CI, Gallego ME. Arabidopsis ATM and ATR kinases prevent propagation of genome damage caused by telomere dysfunction. THE PLANT CELL 2011; 23:4254-65. [PMID: 22158468 PMCID: PMC3269864 DOI: 10.1105/tpc.111.092387] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 11/22/2011] [Accepted: 11/30/2011] [Indexed: 05/18/2023]
Abstract
The ends of linear eukaryotic chromosomes are hidden in nucleoprotein structures called telomeres, and loss of the telomere structure causes inappropriate repair, leading to severe karyotypic and genomic instability. Although it has been shown that DNA damaging agents activate a DNA damage response (DDR), little is known about the signaling of dysfunctional plant telomeres. We show that absence of telomerase in Arabidopsis thaliana elicits an ATAXIA-TELANGIECTASIA MUTATED (ATM) and ATM AND RAD3-RELATED (ATR)-dependent DDR at telomeres, principally through ATM. By contrast, telomere dysfunction induces an ATR-dependent response in telomeric Conserved telomere maintenance component1 (Ctc1)-Suppressor of cdc thirteen (Stn1)-Telomeric pathways in association with Stn1 (CST)-complex mutants. These results uncover a new role for the CST complex in repressing the ATR-dependent DDR pathway in plant cells and show that plant cells use two different DNA damage surveillance pathways to signal telomere dysfunction. The absence of either ATM or ATR in ctc1 and stn1 mutants significantly enhances developmental and genome instability while reducing stem cell death. These data thus give a clear illustration of the action of ATM/ATR-dependent programmed cell death in maintaining genomic integrity through elimination of genetically unstable cells.
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30
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Vaquero-Sedas MI, Vega-Palas MA. On the chromatin structure of eukaryotic telomeres. Epigenetics 2011; 6:1055-8. [PMID: 21822057 PMCID: PMC3225743 DOI: 10.4161/epi.6.9.16845] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 07/05/2011] [Indexed: 01/12/2023] Open
Abstract
Telomeres prevent chromosome fusions and degradation by exonucleases and are implicated in DNA repair, homologous recombination, chromosome pairing and segregation. All these functions of telomeres require the integrity of their chromatin structure, which has been traditionally considered as heterochromatic. In agreement with this idea, different studies have reported that telomeres associate with heterochromatic marks. However, these studies addressed simultaneously the chromatin structures of telomeres and subtelomeric regions or the chromatin structure of telomeres and Interstitial Telomeric Sequences (ITSs). The independent analysis of Arabidopsis telomeres, subtelomeric regions and ITSs has allowed the discovery of euchromatic telomeres. In Arabidopsis, whereas subtelomeric regions and ITSs associate with heterochromatic marks, telomeres exhibit euchromatic features. We think that this scenario could be found in other model systems if the chromatin organizations of telomeres, subtelomeric regions and ITSs are independently analyzed.
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Affiliation(s)
- María I Vaquero-Sedas
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Seville, Spain
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31
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Vaquero-Sedas MI, Gámez-Arjona FM, Vega-Palas MA. Arabidopsis thaliana telomeres exhibit euchromatic features. Nucleic Acids Res 2011; 39:2007-17. [PMID: 21071395 PMCID: PMC3064777 DOI: 10.1093/nar/gkq1119] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 10/19/2010] [Accepted: 10/19/2010] [Indexed: 12/03/2022] Open
Abstract
Telomere function is influenced by chromatin structure and organization, which usually involves epigenetic modifications. We describe here the chromatin structure of Arabidopsis thaliana telomeres. Based on the study of six different epigenetic marks we show that Arabidopsis telomeres exhibit euchromatic features. In contrast, subtelomeric regions and telomeric sequences present at interstitial chromosomal loci are heterochromatic. Histone methyltransferases and the chromatin remodeling protein DDM1 control subtelomeric heterochromatin formation. Whereas histone methyltransferases are required for histone H3K9(2Me) and non-CpG DNA methylation, DDM1 directs CpG methylation but not H3K9(2Me) or non-CpG methylation. These results argue that both kinds of proteins participate in different pathways to reinforce subtelomeric heterochromatin formation.
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Affiliation(s)
| | | | - Miguel A. Vega-Palas
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla – CSIC, c/ Américo Vespucio n° 49, 41092 Seville, Spain
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32
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Abstract
Telomeres are essential structures at the ends of eukaryotic chromosomes. Work on their structure and function began almost 70 years ago in plants and flies, continued through the Nobel Prize winning work on yeast and ciliates, and goes on today in many model and non-model organisms. The basic molecular mechanisms of telomeres are highly conserved throughout evolution, and our current understanding of how telomeres function is a conglomeration of insights gained from many different species. This review will compare the current knowledge of telomeres in plants with other organisms, with special focus on the functional length of telomeric DNA, the search for TRF homologs, the family of POT1 proteins, and the recent discovery of members of the CST complex.
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Affiliation(s)
- J Matthew Watson
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
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33
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Amiard S, Charbonnel C, Allain E, Depeiges A, White CI, Gallego ME. Distinct roles of the ATR kinase and the Mre11-Rad50-Nbs1 complex in the maintenance of chromosomal stability in Arabidopsis. THE PLANT CELL 2010; 22:3020-33. [PMID: 20876831 PMCID: PMC2965537 DOI: 10.1105/tpc.110.078527] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 09/04/2010] [Accepted: 09/13/2010] [Indexed: 05/17/2023]
Abstract
Signaling of chromosomal DNA breaks is of primary importance for initiation of repair and, thus, for global genomic stability. Although the Mre11-Rad50-Nbs1 (MRN) complex is the first sensor of double-strand breaks, its role in double-strand break (DSB) signaling is not fully understood. We report the absence of γ-ray-induced, ATM/ATR-dependent histone H2AX phosphorylation in Arabidopsis thaliana rad50 and mre11 mutants, confirming that the MRN complex is required for H2AX phosphorylation by the ATM and ATR kinases in response to irradiation-induced DSB in Arabidopsis. rad50 and mre11 mutants spontaneously activate a DNA damage response, as shown by the presence of γ-H2AX foci and activation of cell cycle arrest in nonirradiated plants. This response is ATR dependent as shown both by the absence of these spontaneous foci and by the wild-type mitotic indices of double rad50 atr and mre11 atr plants. EdU S-phase labeling and fluorescence in situ hybridization analysis using specific subtelomeric probes point to a replicative S-phase origin of this chromosome damage in the double mutants and not to telomere destabilization. Thus, the data presented here show the exclusive involvement of ATR in DNA damage signaling in MRN mutants and provide evidence for a role for ATR in the avoidance of S-phase DNA damage.
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34
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Ye J, Lenain C, Bauwens S, Rizzo A, Saint-Léger A, Poulet A, Benarroch D, Magdinier F, Morere J, Amiard S, Verhoeyen E, Britton S, Calsou P, Salles B, Bizard A, Nadal M, Salvati E, Sabatier L, Wu Y, Biroccio A, Londoño-Vallejo A, Giraud-Panis MJ, Gilson E. TRF2 and apollo cooperate with topoisomerase 2alpha to protect human telomeres from replicative damage. Cell 2010; 142:230-42. [PMID: 20655466 DOI: 10.1016/j.cell.2010.05.032] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 12/21/2009] [Accepted: 05/17/2010] [Indexed: 10/19/2022]
Abstract
Human telomeres are protected from DNA damage by a nucleoprotein complex that includes the repeat-binding factor TRF2. Here, we report that TRF2 regulates the 5' exonuclease activity of its binding partner, Apollo, a member of the metallo-beta-lactamase family that is required for telomere integrity during S phase. TRF2 and Apollo also suppress damage to engineered interstitial telomere repeat tracts that were inserted far away from chromosome ends. Genetic data indicate that DNA topoisomerase 2alpha acts in the same pathway of telomere protection as TRF2 and Apollo. Moreover, TRF2, which binds preferentially to positively supercoiled DNA substrates, together with Apollo, negatively regulates the amount of TOP1, TOP2alpha, and TOP2beta at telomeres. Our data are consistent with a model in which TRF2 and Apollo relieve topological stress during telomere replication. Our work also suggests that cellular senescence may be caused by topological problems that occur during the replication of the inner portion of telomeres.
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Affiliation(s)
- Jing Ye
- Shanghai Ruijin Hospital, School of Medicine of Shanghai Jiaotong University, 200025 Shanghai, China
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35
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Rahn JJ, Adair GM, Nairn RS. Multiple roles of ERCC1-XPF in mammalian interstrand crosslink repair. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2010; 51:567-581. [PMID: 20658648 DOI: 10.1002/em.20583] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
DNA interstrand crosslinks (ICLs) are among the most deleterious cytotoxic lesions encountered by cells, mainly due to the covalent linkage these lesions create between the two strands of DNA which effectively blocks replication and transcription. Although ICL repair in mammalian cells is not fully understood, processing of these lesions is thought to begin by "unhooking" at the site of the damaged base accompanied by the generation of a double strand break and ultimately repair through translesion synthesis and homologous recombination. A key player in this repair process is the heterodimeric protein complex ERCC1-XPF. Although some models of ICL repair restrict ERCC1-XPF activity to the unhooking step, recent data suggest that this protein complex acts in additional downstream steps. Here, we review the evidence implicating ERCC1-XPF in multiple steps of ICL repair.
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Affiliation(s)
- Jennifer J Rahn
- Department of Carcinogenesis, Science Park-Research Division, University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA.
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36
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Watson JM, Riha K. Comparative biology of telomeres: where plants stand. FEBS Lett 2010; 584:3752-9. [PMID: 20580356 PMCID: PMC3767043 DOI: 10.1016/j.febslet.2010.06.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 06/11/2010] [Accepted: 06/14/2010] [Indexed: 01/02/2023]
Abstract
Telomeres are essential structures at the ends of eukaryotic chromosomes. Work on their structure and function began almost 70 years ago in plants and flies, continued through the Nobel Prize winning work on yeast and ciliates, and goes on today in many model and non-model organisms. The basic molecular mechanisms of telomeres are highly conserved throughout evolution, and our current understanding of how telomeres function is a conglomeration of insights gained from many different species. This review will compare the current knowledge of telomeres in plants with other organisms, with special focus on the functional length of telomeric DNA, the search for TRF homologs, the family of POT1 proteins, and the recent discovery of members of the CST complex.
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Affiliation(s)
- J Matthew Watson
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
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37
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Lou J, Chu G, Zhou G, Jiang J, Huang F, Xu J, Zheng S, Jiang W, Lu Y, Li X, Chen Z, He J. Comparison between two kinds of cigarette smoke condensates (CSCs) of the cytogenotoxicity and protein expression in a human B-cell lymphoblastoid cell line using CCK-8 assay, comet assay and protein microarray. Mutat Res 2010; 697:55-9. [PMID: 20139030 DOI: 10.1016/j.mrgentox.2010.01.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 12/02/2009] [Accepted: 01/31/2010] [Indexed: 12/21/2022]
Abstract
The differences of the cytogenotoxicity and proteins expression of human B-cell lymphoblastoid cells exposed to cigarette smoke condensates (CSCs) from two kinds of cigarettes were detected with CCK-8 assay, comet assay, protein microarray and western blot assay in vitro. Human B-cell lymphoblastoid cell line was exposed to CSCs from two cigarettes (which delivers approximately 3mg tar, 0.3mg nicotine, 3mg CO per cigarette for cigarette 1 and 15mg tar, 1.3mg nicotine, 15mg CO per cigarette for cigarette 2), and the exposure doses were 2.5, 5.0, 7.5, 10.0 and 12.5x10(-3)cigarettes/ml of CSCs for 24h in CCK-8 assay, 6.0, 8.0, 10.0, 12.0 and 14.0x10(-3)cigarettes/ml of CSCs for 4h in comet assay, and 10.0x10(-3)cigarettes/ml of CSCs for 4h in protein levels analysis. The results of CCK-8 assay and comet assay in the present study suggested that the cytogenotoxicity in cigarette 2 group was significantly higher than that in cigarette 1 group. The results of protein microarray and western blot assay showed that there were the differences of the expression levels of four proteins (i.e., RAR-beta, 14-3-3 sigma, XPF, and p57(Kip2) Ab-7) between cigarette 1 group and cigarette 2 group. Hence, it is possible that the RAR-beta, 14-3-3 sigma, XPF, and p57(Kip2) Ab-7 proteins serve as the molecular biomarkers in studying the cytogenotoxicity induced by CSCs.
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Affiliation(s)
- Jianlin Lou
- Technology Center, China Tobacco Zhejiang Industrial Co. Ltd, Hangzhou 310008, Zhejiang, PR China
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