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Bozděchová L, Rudolfová A, Hanáková K, Fojtová M, Fajkus J. Optimizing ChIRP-MS for Comprehensive Profiling of RNA-Protein Interactions in Arabidopsis thaliana: A Telomerase RNA Case Study. Plants (Basel) 2024; 13:850. [PMID: 38592918 PMCID: PMC10975786 DOI: 10.3390/plants13060850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/05/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024]
Abstract
The current repertoire of methods available for studying RNA-protein interactions in plants is somewhat limited. Employing an RNA-centric approach, particularly with less abundant RNAs, presents various challenges. Many of the existing methods were initially designed for different model systems, with their application in plants receiving limited attention thus far. The Comprehensive Identification of RNA-Binding Proteins by Mass Spectrometry (ChIRP-MS) technique, initially developed for mammalian cells, has been adapted in this study for application in Arabidopsis thaliana. The procedures have been meticulously modified and optimized for telomerase RNA, a notable example of a low-abundance RNA recently identified. Following these optimization steps, ChIRP-MS can serve as an effective screening method for identifying candidate proteins interacting with any target RNA of interest.
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Affiliation(s)
- Lucie Bozděchová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (L.B.); (K.H.); (M.F.)
| | - Anna Rudolfová
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Kateřina Hanáková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (L.B.); (K.H.); (M.F.)
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (L.B.); (K.H.); (M.F.)
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (L.B.); (K.H.); (M.F.)
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
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2
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Lyčka M, Bubeník M, Závodník M, Peska V, Fajkus P, Demko M, Fajkus J, Fojtová M. TeloBase: a community-curated database of telomere sequences across the tree of life. Nucleic Acids Res 2024; 52:D311-D321. [PMID: 37602392 PMCID: PMC10767889 DOI: 10.1093/nar/gkad672] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/27/2023] [Accepted: 08/14/2023] [Indexed: 08/22/2023] Open
Abstract
Discoveries over the recent decade have demonstrated the unexpected diversity of telomere DNA motifs in nature. However, currently available resources, 'Telomerase database' and 'Plant rDNA database', contain just fragments of all relevant literature published over decades of telomere research as they have a different primary focus and limited updates. To fill this gap, we gathered data about telomere DNA sequences from a thorough literature screen as well as by analysing publicly available NGS data, and we created TeloBase (http://cfb.ceitec.muni.cz/telobase/) as a comprehensive database of information about telomere motif diversity. TeloBase is supplemented by internal taxonomy utilizing popular on-line taxonomic resources that enables in-house data filtration and graphical visualisation of telomere DNA evolutionary dynamics in the form of heat tree plots. TeloBase avoids overreliance on administrators for future data updates by having a simple form and community-curation system for application and approval, respectively, of new telomere sequences by users, which should ensure timeliness of the database and topicality. To demonstrate TeloBase utility, we examined telomere motif diversity in species from the fungal genus Aspergillus, and discovered (TTTATTAGGG)n sequence as a putative telomere motif in the plant family Chrysobalanaceae. This was bioinformatically confirmed by analysing template regions of identified telomerase RNAs.
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Affiliation(s)
- Martin Lyčka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
| | - Michal Bubeník
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
| | - Michal Závodník
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
| | - Vratislav Peska
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Academy of Sciences of the Czech Republic, BrnoCZ-61200, Czech Republic
| | - Petr Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Academy of Sciences of the Czech Republic, BrnoCZ-61200, Czech Republic
| | - Martin Demko
- Core Facility Bioinformatics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- Faculty of Informatics, Masaryk University, BrnoCZ-62500, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Academy of Sciences of the Czech Republic, BrnoCZ-61200, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
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3
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Pírek P, Kryštofová K, Kováčová I, Kromerová A, Zachová D, Helia O, Panzarová K, Fajkus J, Zdráhal Z, Lochmanová G, Fojtová M. Unraveling Epigenetic Changes in A. thaliana Calli: Impact of HDAC Inhibitors. Plants (Basel) 2023; 12:4177. [PMID: 38140504 PMCID: PMC10747063 DOI: 10.3390/plants12244177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/29/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
The ability for plant regeneration from dedifferentiated cells opens up the possibility for molecular bioengineering to produce crops with desirable traits. Developmental and environmental signals that control cell totipotency are regulated by gene expression via dynamic chromatin remodeling. Using a mass spectrometry-based approach, we investigated epigenetic changes to the histone proteins during callus formation from roots and shoots of Arabidopsis thaliana seedlings. Increased levels of the histone H3.3 variant were found to be the major and most prominent feature of 20-day calli, associated with chromatin relaxation. The methylation status in root- and shoot-derived calli reached the same level during long-term propagation, whereas differences in acetylation levels provided a long-lasting imprint of root and shoot origin. On the other hand, epigenetic signs of origin completely disappeared during 20 days of calli propagation in the presence of histone deacetylase inhibitors (HDACi), sodium butyrate, and trichostatin A. Each HDACi affected the state of post-translational histone modifications in a specific manner; NaB-treated calli were epigenetically more similar to root-derived calli, and TSA-treated calli resembled shoot-derived calli.
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Affiliation(s)
- Pavlína Pírek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
| | - Karolína Kryštofová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Ingrid Kováčová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
| | - Anna Kromerová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Dagmar Zachová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
| | - Ondřej Helia
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Klára Panzarová
- PSI (Photon Systems Instruments), spol. s.r.o., 66424 Drásov, Czech Republic;
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; (P.P.); (K.K.); (I.K.); (D.Z.); (J.F.); (Z.Z.)
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic;
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Lyčka M, Barták M, Helia O, Kopriva S, Moravcová D, Hájek J, Fojt L, Čmelík R, Fajkus J, Fojtová M. Sulfate supplementation affects nutrient and photosynthetic status of Arabidopsis thaliana and Nicotiana tabacum differently under prolonged exposure to cadmium. J Hazard Mater 2023; 445:130527. [PMID: 36495640 DOI: 10.1016/j.jhazmat.2022.130527] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/22/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Hydroponic experiments were performed to examine the effect of prolonged sulfate limitation combined with cadmium (Cd) exposure in Arabidopsis thaliana and a potential Cd hyperaccumulator, Nicotiana tabacum. Low sulfate treatments (20 and 40 µM MgSO4) and Cd stress (4 µM CdCl2) showed adverse effects on morphology, photosynthetic and biochemical parameters and the nutritional status of both species. For example, Cd stress decreased NO3- root content under 20 µM MgSO4 to approximately 50% compared with respective controls. Interestingly, changes in many measured parameters, such as chlorophyll and carotenoid contents, the concentrations of anions, nutrients and Cd, induced by low sulfate supply, Cd exposure or a combination of both factors, were species-specific. Our data showed opposing effects of Cd exposure on Ca, Fe, Mn, Cu and Zn levels in roots of the studied plants. In A. thaliana, levels of glutathione, phytochelatins and glucosinolates demonstrated their distinct involvement in response to sub-optimal growth conditions and Cd stress. In shoot, the levels of phytochelatins and glucosinolates in the organic sulfur fraction were not dependent on sulfate supply under Cd stress. Altogether, our data showed both common and species-specific features of the complex plant response to prolonged sulfate deprivation and/or Cd exposure.
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Affiliation(s)
- Martin Lyčka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.
| | - Miloš Barták
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Ondřej Helia
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Stanislav Kopriva
- Institute for Plant Sciences, University of Cologne, 50674 Cologne, Germany; Cluster of Excellence on Plant Sciences, University of Cologne, 50674 Cologne, Germany
| | - Dana Moravcová
- Institute of Analytical Chemistry of the Czech Academy of Sciences, 602 00 Brno, Czech Republic
| | - Josef Hájek
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Lukáš Fojt
- Institute of Biophysics of the Czech Academy of Sciences, 612 00 Brno, Czech Republic
| | - Richard Čmelík
- Institute of Analytical Chemistry of the Czech Academy of Sciences, 602 00 Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic; Institute of Biophysics of the Czech Academy of Sciences, 612 00 Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
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6
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Lyčka M, Fajkus P, Jenner LP, Sýkorová E, Fojtová M, Peska V. Identification of the Sequence and the Length of Telomere DNA. Methods Mol Biol 2023; 2672:285-302. [PMID: 37335484 DOI: 10.1007/978-1-0716-3226-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Telomeres are essential nucleoprotein structures at the very ends of linear eukaryote chromosomes. They shelter the terminal genome territories against degradation and prevent the natural chromosome ends from being recognized by repair mechanisms as double-strand DNA breaks.There are two basic characteristics of telomeric DNA, its sequence and its length. The telomere sequence is important as a "landing area" for specific telomere-binding proteins, which function as signals and moderate the interactions required for correct telomere function. While the sequence forms the proper "landing surface" of telomeric DNA, its length is similarly important. Too short or exceptionally long telomere DNA cannot perform its function properly. In this chapter, methods for the investigation of these two basic telomere DNA characteristics are described, namely, telomere motif identification and telomere length measurement.
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Affiliation(s)
- Martin Lyčka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Leon P Jenner
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Eva Sýkorová
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Vratislav Peska
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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7
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Konečná KP, Kilar A, Kováčiková P, Fajkus J, Sýkorová E, Fojtová M. Compromised function of ARM, the interactor of Arabidopsis telomerase, suggests its role in stress responses. Plant Sci 2022; 325:111453. [PMID: 36087885 DOI: 10.1016/j.plantsci.2022.111453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/02/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
ARM was identified previously as an interaction partner of the telomerase protein subunit (TERT) in Arabidopsis thaliana. To investigate the interconnection between ARM and telomerase and to identify ARM cellular functions, we analyzed a set of arm mutant lines and arm/tert double mutants. Telomere length was not affected in arm single mutant plants, in contrast to double mutants. In the second generation of homozygous arm-1/tert double mutants following the heterozygous state during the double mutant construction, telomeres shortened dramatically, even below levels in tert plants displaying severe morphological defects. Intriguingly, homozygous arm-1/tert double mutants with short telomeres grew without obvious phenotypic changes for next two generations. Then, in agreement with the onset of phenotypic changes in tert, morphological defects were timed to the 5th arm-1/tert homozygous generation. RNAseq analyses of arm-1/tert and respective single mutants displayed markedly overlapping sets of differentially expressed genes in arm-1/tert double mutant and arm-1 single mutant lines, indicating a dominant effect of the ARM mutation. RNAseq data further implied ARM involvement in circadian rhythms, responses to drugs and to biotic and abiotic stimuli. In agreement with it, we observed sensitivity of arm-1 single mutant to the heat stress during germination. Altogether, our results suggest ARM involvement in crucial cellular processes without evidencing its role in the telomerase canonical function.
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Affiliation(s)
- Klára Přikrylová Konečná
- Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic; Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Agata Kilar
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petra Kováčiková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiří Fajkus
- Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic; Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Eva Sýkorová
- Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
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8
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Abstract
Reshaping of the chromatin landscape under oxidative stress is of paramount importance for mounting an effective stress response. Unbiased systemic identification and quantification of histone marks is crucial for understanding the epigenetic component of plant responses to adverse environmental conditions. We describe a detailed method for isolation of plant histones and subsequent bottom-up proteomics approach for characterization of acetylation and methylation status. By performing label-free quantitative mass spectrometry analysis, relative abundances of histone marks can be statistically compared between experimental conditions.
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Affiliation(s)
- Hana Kuchaříková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zuzana Plšková
- Phytophthora Research Centre, Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pavel Kerchev
- Phytophthora Research Centre, Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
| | - Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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9
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Fajkus P, Kilar A, Nelson ADL, Holá M, Peška V, Goffová I, Fojtová M, Zachová D, Fulnečková J, Fajkus J. Evolution of plant telomerase RNAs: farther to the past, deeper to the roots. Nucleic Acids Res 2021; 49:7680-7694. [PMID: 34181710 PMCID: PMC8287931 DOI: 10.1093/nar/gkab545] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/01/2021] [Accepted: 06/10/2021] [Indexed: 01/10/2023] Open
Abstract
The enormous sequence heterogeneity of telomerase RNA (TR) subunits has thus far complicated their characterization in a wider phylogenetic range. Our recent finding that land plant TRs are, similarly to known ciliate TRs, transcribed by RNA polymerase III and under the control of the type-3 promoter, allowed us to design a novel strategy to characterize TRs in early diverging Viridiplantae taxa, as well as in ciliates and other Diaphoretickes lineages. Starting with the characterization of the upstream sequence element of the type 3 promoter that is conserved in a number of small nuclear RNAs, and the expected minimum TR template region as search features, we identified candidate TRs in selected Diaphoretickes genomes. Homologous TRs were then used to build covariance models to identify TRs in more distant species. Transcripts of the identified TRs were confirmed by transcriptomic data, RT-PCR and Northern hybridization. A templating role for one of our candidates was validated in Physcomitrium patens. Analysis of secondary structure demonstrated a deep conservation of motifs (pseudoknot and template boundary element) observed in all published TRs. These results elucidate the evolution of the earliest eukaryotic TRs, linking the common origin of TRs across Diaphoretickes, and underlying evolutionary transitions in telomere repeats.
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Affiliation(s)
- Petr Fajkus
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61265, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic
| | - Agata Kilar
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | | | - Marcela Holá
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague CZ-16000, Czech Republic
| | - Vratislav Peška
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61265, Czech Republic
| | - Ivana Goffová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - Dagmar Zachová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic
| | - Jana Fulnečková
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61265, Czech Republic
| | - Jiří Fajkus
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno CZ-61265, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno CZ-62500, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
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10
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Lyčka M, Peska V, Demko M, Spyroglou I, Kilar A, Fajkus J, Fojtová M. WALTER: an easy way to online evaluate telomere lengths from terminal restriction fragment analysis. BMC Bioinformatics 2021; 22:145. [PMID: 33752601 PMCID: PMC7986547 DOI: 10.1186/s12859-021-04064-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 03/07/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Telomeres, nucleoprotein structures comprising short tandem repeats and delimiting the ends of linear eukaryotic chromosomes, play an important role in the maintenance of genome stability. Therefore, the determination of the length of telomeres is of high importance for many studies. Over the last years, new methods for the analysis of the length of telomeres have been developed, including those based on PCR or analysis of NGS data. Despite that, terminal restriction fragment (TRF) method remains the gold standard to this day. However, this method lacks universally accepted and precise tool capable to analyse and statistically evaluate TRF results. RESULTS To standardize the processing of TRF results, we have developed WALTER, an online toolset allowing rapid, reproducible, and user-friendly analysis including statistical evaluation of the data. Given its web-based nature, it provides an easily accessible way to analyse TRF data without any need to install additional software. CONCLUSIONS WALTER represents a major upgrade from currently available tools for the image processing of TRF scans. This toolset enables a rapid, highly reproducible, and user-friendly evaluation of almost any TRF scan including in-house statistical evaluation of the data. WALTER platform together with user manual describing the evaluation of TRF scans in detail and presenting tips and troubleshooting, as well as test data to demo the software are available at https://www.ceitec.eu/chromatin-molecular-complexes-jiri-fajkus/rg51/tab?tabId=125#WALTER and the source code at https://github.com/mlyc93/WALTER .
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Affiliation(s)
- Martin Lyčka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Vratislav Peska
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., 612 00, Brno, Czech Republic.
| | - Martin Demko
- Core Facility Bioinformatics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Faculty of Informatics, Masaryk University, 602 00, Brno, Czech Republic
| | - Ioannis Spyroglou
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
| | - Agata Kilar
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., 612 00, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic.
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic.
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11
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Konečná K, Sováková PP, Anteková K, Fajkus J, Fojtová M. Distinct Responses of Arabidopsis Telomeres and Transposable Elements to Zebularine Exposure. Int J Mol Sci 2021; 22:ijms22010468. [PMID: 33466545 PMCID: PMC7796508 DOI: 10.3390/ijms22010468] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 12/17/2022] Open
Abstract
Involvement of epigenetic mechanisms in the regulation of telomeres and transposable elements (TEs), genomic regions with the protective and potentially detrimental function, respectively, has been frequently studied. Here, we analyzed telomere lengths in Arabidopsis thaliana plants of Columbia, Landsberg erecta and Wassilevskija ecotypes exposed repeatedly to the hypomethylation drug zebularine during germination. Shorter telomeres were detected in plants growing from seedlings germinated in the presence of zebularine with a progression in telomeric phenotype across generations, relatively high inter-individual variability, and diverse responses among ecotypes. Interestingly, the extent of telomere shortening in zebularine Columbia and Wassilevskija plants corresponded to the transcriptional activation of TEs, suggesting a correlated response of these genomic elements to the zebularine treatment. Changes in lengths of telomeres and levels of TE transcripts in leaves were not always correlated with a hypomethylation of cytosines located in these regions, indicating a cytosine methylation-independent level of their regulation. These observations, including differences among ecotypes together with distinct dynamics of the reversal of the disruption of telomere homeostasis and TEs transcriptional activation, reflect a complex involvement of epigenetic processes in the regulation of crucial genomic regions. Our results further demonstrate the ability of plant cells to cope with these changes without a critical loss of the genome stability.
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Affiliation(s)
- Klára Konečná
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Pavla Polanská Sováková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Karin Anteková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
- Correspondence: ; Tel.: +420-54949-8063
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12
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Školáková P, Badri Z, Foldynová-Trantírková S, Ryneš J, Šponer J, Fojtová M, Fajkus J, Marek R, Vorlíčková M, Mergny JL, Trantírek L. Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA. Biochim Biophys Acta Gen Subj 2020; 1864:129651. [DOI: 10.1016/j.bbagen.2020.129651] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022]
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13
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Adamusová K, Khosravi S, Fujimoto S, Houben A, Matsunaga S, Fajkus J, Fojtová M. Two combinatorial patterns of telomere histone marks in plants with canonical and non-canonical telomere repeats. Plant J 2020; 102:678-687. [PMID: 31834959 DOI: 10.1111/tpj.14653] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/21/2019] [Accepted: 11/28/2019] [Indexed: 05/24/2023]
Abstract
Telomeres, nucleoprotein structures at the ends of linear eukaryotic chromosomes, are crucial for the maintenance of genome integrity. In most plants, telomeres consist of conserved tandem repeat units comprising the TTTAGGG motif. Recently, non-canonical telomeres were described in several plants and plant taxons, including the carnivorous plant Genlisea hispidula (TTCAGG/TTTCAGG), the genus Cestrum (Solanaceae; TTTTTTAGGG), and plants from the Asparagales order with either a vertebrate-type telomere repeat TTAGGG or Allium genus-specific CTCGGTTATGGG repeat. We analyzed epigenetic modifications of telomeric histones in plants with canonical and non-canonical telomeres, and further in telomeric chromatin captured from leaves of Nicotiana benthamiana transiently transformed by telomere CRISPR-dCas9-eGFP, and of Arabidopsis thaliana stably transformed with TALE_telo C-3×GFP. Two combinatorial patterns of telomeric histone modifications were identified: (i) an Arabidopsis-like pattern (A. thaliana, G. hispidula, Genlisea nigrocaulis, Allium cepa, Narcissus pseudonarcissus, Petunia hybrida, Solanum tuberosum, Solanum lycopersicum) with telomeric histones decorated predominantly by H3K9me2; (ii) a tobacco-like pattern (Nicotiana tabacum, N. benthamiana, C. elegans) with a strong H3K27me3 signal. Our data suggest that epigenetic modifications of plant telomere-associated histones are related neither to the sequence of the telomere motif nor to the lengths of the telomeres. Nor the phylogenetic position of the species plays the role; representatives of the Solanaceae family are included in both groups. As both patterns of histone marks are compatible with fully functional telomeres in respective plants, we conclude that the described specific differences in histone marks are not critical for telomere functions.
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Affiliation(s)
- Kateřina Adamusová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic
| | - Solmaz Khosravi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Seeland, Germany
| | - Satoru Fujimoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Seeland, Germany
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic
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14
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Cai N, Fňašková M, Konečná K, Fojtová M, Fajkus J, Coomber E, Watt S, Soranzo N, Preiss M, Rektor I. No Evidence of Persistence or Inheritance of Mitochondrial DNA Copy Number in Holocaust Survivors and Their Descendants. Front Genet 2020; 11:87. [PMID: 32211017 PMCID: PMC7069217 DOI: 10.3389/fgene.2020.00087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/27/2020] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial DNA copy number has been previously shown to be elevated with severe and chronic stress, as well as stress-related pathology like Major Depressive Disorder (MDD) and post-traumatic stress disorder (PTSD). While experimental data point to likely recovery of mtDNA copy number changes after the stressful event, time needed for full recovery and whether it can be achieved are still unknown. Further, while it has been shown that stress-related mtDNA elevation affects multiple tissues, its specific consequences for oogenesis and maternal inheritance of mtDNA has never been explored. In this study, we used qPCR to quantify mtDNA copy number in 15 Holocaust survivors and 102 of their second- and third-generation descendants from the Czech Republic, many of whom suffer from PTSD, and compared them to controls in the respective generations. We found no significant difference in mtDNA copy number in the Holocaust survivors compared to controls, whether they have PTSD or not, and no significant elevation in descendants of female Holocaust survivors as compared to descendants of male survivors or controls. Our results showed no evidence of persistence or inheritance of mtDNA changes in Holocaust survivors, though that does not rule out effects in other tissues or mitigating mechanism for such changes.
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Affiliation(s)
- Na Cai
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - Monika Fňašková
- Neuroscience Centre, CEITEC, Masaryk University, Brno, Czechia.,1st Neurology Department, Hospital St Anne and School of Medicine, Masaryk University, Brno, Czechia
| | - Klára Konečná
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, Czechia.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, Czechia.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, Czechia.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Eve Coomber
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Stephen Watt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Nicole Soranzo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Marek Preiss
- Neuroscience Centre, CEITEC, Masaryk University, Brno, Czechia
| | - Ivan Rektor
- Neuroscience Centre, CEITEC, Masaryk University, Brno, Czechia
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15
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Fajkus P, Peška V, Závodník M, Fojtová M, Fulnečková J, Dobias Š, Kilar A, Dvořáčková M, Zachová D, Nečasová I, Sims J, Sýkorová E, Fajkus J. Telomerase RNAs in land plants. Nucleic Acids Res 2019; 47:9842-9856. [PMID: 31392988 PMCID: PMC6765143 DOI: 10.1093/nar/gkz695] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 07/26/2019] [Accepted: 07/30/2019] [Indexed: 02/07/2023] Open
Abstract
To elucidate the molecular nature of evolutionary changes of telomeres in the plant order Asparagales, we aimed to characterize telomerase RNA subunits (TRs) in these plants. The unusually long telomere repeat unit in Allium plants (12 nt) allowed us to identify TRs in transcriptomic data of representative species of the Allium genus. Orthologous TRs were then identified in Asparagales plants harbouring telomere DNA composed of TTAGGG (human type) or TTTAGGG (Arabidopsis-type) repeats. Further, we identified TRs across the land plant phylogeny, including common model plants, crop plants, and plants with unusual telomeres. Several lines of functional testing demonstrate the templating telomerase function of the identified TRs and disprove a functionality of the only previously reported plant telomerase RNA in Arabidopsis thaliana. Importantly, our results change the existing paradigm in plant telomere biology which has been based on the existence of a relatively conserved telomerase reverse transcriptase subunit (TERT) associating with highly divergent TRs even between closely related plant taxa. The finding of a monophyletic origin of genuine TRs across land plants opens the possibility to identify TRs directly in transcriptomic or genomic data and/or predict telomere sequences synthesized according to the respective TR template region.
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Affiliation(s)
- Petr Fajkus
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno CZ-61265, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - Vratislav Peška
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno CZ-61265, Czech Republic
| | - Michal Závodník
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
| | - Miloslava Fojtová
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno CZ-61265, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
| | - Jana Fulnečková
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno CZ-61265, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - Šimon Dobias
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno CZ-61265, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - Agata Kilar
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
| | - Dagmar Zachová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
| | - Ivona Nečasová
- Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
| | - Jason Sims
- Max Perutz Labs, University of Vienna, Dr. Bohr Gasse 9, A-1030, Vienna, Austria
| | - Eva Sýkorová
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno CZ-61265, Czech Republic
| | - Jiří Fajkus
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno CZ-61265, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno CZ-62500, Czech Republic
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16
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Lochmanová G, Ihnatová I, Kuchaříková H, Brabencová S, Zachová D, Fajkus J, Zdráhal Z, Fojtová M. Different Modes of Action of Genetic and Chemical Downregulation of Histone Deacetylases with Respect to Plant Development and Histone Modifications. Int J Mol Sci 2019; 20:ijms20205093. [PMID: 31615119 PMCID: PMC6829310 DOI: 10.3390/ijms20205093] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 02/02/2023] Open
Abstract
A high degree of developmental plasticity enables plants to adapt to continuous, often unfavorable and unpredictable changes in their environment. At the molecular level, adaptive advantages for plants are primarily provided by epigenetic machinery including DNA methylation, histone modifications, and the activity of noncoding RNA molecules. Using a mass spectrometry-based proteomic approach, we examined the levels of acetylated histone peptide forms in Arabidopsis plants with a loss of function of histone deacetylase 6 (HDA6), and in plants germinated in the presence of HDA inhibitors trichostatin A (TSA) and sodium butyrate (NaB). Our analyses revealed particular lysine sites at histone sequences targeted by the HDA6 enzyme, and by TSA- and NaB-sensitive HDAs. Compared with plants exposed to drugs, more dramatic changes in the overall profiles of histone post-translational modifications were identified in hda6 mutants. However, loss of HDA6 was not sufficient by itself to induce hyperacetylation to the maximum degree, implying complementary activities of other HDAs. In contrast to hda6 mutants that did not exhibit any obvious phenotypic defects, the phenotypes of seedlings exposed to HDA inhibitors were markedly affected, showing that the effect of these drugs on early plant development is not limited to the modulation of histone acetylation levels.
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Affiliation(s)
- Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
| | - Ivana Ihnatová
- RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Hana Kuchaříková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Sylva Brabencová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Dagmar Zachová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
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17
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Konečná K, Lyčka M, Nohelová L, Petráková M, Fňašková M, Koriťáková E, Sováková PP, Brabencová S, Preiss M, Rektor I, Fajkus J, Fojtová M. Holocaust history is not reflected in telomere homeostasis in survivors and their offspring. J Psychiatr Res 2019; 117:7-14. [PMID: 31255955 DOI: 10.1016/j.jpsychires.2019.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/20/2019] [Accepted: 06/24/2019] [Indexed: 01/30/2023]
Abstract
Telomeres, nucleoprotein structures at the ends of eukaryotic chromosomes, are crucial for the maintenance of genome integrity. While the lengths of telomeres at birth are determined genetically, many factors including environmental and living conditions affect the telomere lengths during a lifespan. In this context, extreme and long-term stress has been shown to negatively impact telomeres and their protective function, with even offspring being influenced by the stress experienced by parents. Using quantitative PCR, the relative lengths of telomeres of survivors of the Holocaust during World War II and two generations of their offspring were analyzed. These data were related to those of control groups, persons of comparable age without a strong life stress experience. In contrast to previous studies of other stress-exposed groups, the relative lengths of telomeres were comparable in groups of persons exposed to Holocaust-related stress and their progenies, and in control groups. Interestingly, shorter telomeres of Holocaust survivors of the age under 12 in the year 1945 compared to Holocaust survivors of the age above 12 were detected. Our results are discussed with respect to certain exceptionality of persons having been able to cope with an extreme stress more than 70 years ago and living to a very old age.
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Affiliation(s)
- Klára Konečná
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Martin Lyčka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Lucie Nohelová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Monika Petráková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Monika Fňašková
- Brain and Mind Research, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
| | - Eva Koriťáková
- Brain and Mind Research, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic; Institute of Biostatistics and Analyses, Faculty of Medicine, Masaryk University, 625 00, Brno, Czech Republic
| | - Pavla Polanská Sováková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Sylva Brabencová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Marek Preiss
- Brain and Mind Research, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic; National Institute of Mental Health and University of New York in Prague, Czech Republic
| | - Ivan Rektor
- Brain and Mind Research, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic.
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18
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Goffová I, Vágnerová R, Peška V, Franek M, Havlová K, Holá M, Zachová D, Fojtová M, Cuming A, Kamisugi Y, Angelis KJ, Fajkus J. Roles of RAD51 and RTEL1 in telomere and rDNA stability in Physcomitrella patens. Plant J 2019; 98:1090-1105. [PMID: 30834585 DOI: 10.1111/tpj.14304] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/21/2019] [Accepted: 02/27/2019] [Indexed: 05/11/2023]
Abstract
Telomeres and ribosomal RNA genes (rDNA) are essential for cell survival and particularly sensitive to factors affecting genome stability. Here, we examine the role of RAD51 and its antagonist, RTEL1, in the moss Physcomitrella patens. In corresponding mutants, we analyse their sensitivity to DNA damage, the maintenance of telomeres and rDNA, and repair of double-stranded breaks (DSBs) induced by genotoxins with various modes of action. While the loss of RTEL1 results in rapid telomere shortening, concurrent loss of both RAD51 genes has no effect on telomere lengths. We further demonstrate here the linked arrangement of 5S and 45S rRNA genes in P. patens. The spacer between 5S and 18S rRNA genes, especially the region downstream from the transcription start site, shows conspicuous clustering of sites with a high propensity to form quadruplex (G4) structures. Copy numbers of 5S and 18S rDNA are reduced moderately in the pprtel1 mutant, and significantly in the double pprad51-1-2 mutant, with no progression during subsequent cultivation. While reductions in 45S rDNA copy numbers observed in pprtel1 and pprad51-1-2 plants apply also to 5S rDNA, changes in transcript levels are different for 45S and 5S rRNA, indicating their independent transcription by RNA polymerase I and III, respectively. The loss of SOL (Sog One-Like), a transcription factor regulating numerous genes involved in DSB repair, increases the rate of DSB repair in dividing as well as differentiated tissue, and through deactivation of G2/M cell-cycle checkpoint allows the cell-cycle progression manifested as a phenotype resistant to bleomycin.
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Affiliation(s)
- Ivana Goffová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Radka Vágnerová
- The Czech Academy of Sciences, Institute of Experimental Botany, Na Karlovce 1, CZ-16000, Prague, Czech Republic
| | - Vratislav Peška
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská 135, 612 65, Brno, Czech Republic
| | - Michal Franek
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Kateřina Havlová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Marcela Holá
- The Czech Academy of Sciences, Institute of Experimental Botany, Na Karlovce 1, CZ-16000, Prague, Czech Republic
| | - Dagmar Zachová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Miloslava Fojtová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Andrew Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Karel J Angelis
- The Czech Academy of Sciences, Institute of Experimental Botany, Na Karlovce 1, CZ-16000, Prague, Czech Republic
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská 135, 612 65, Brno, Czech Republic
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19
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Crhák T, Zachová D, Fojtová M, Sýkorová E. The region upstream of the telomerase reverse transcriptase gene is essential for in planta telomerase complementation. Plant Sci 2019; 281:41-51. [PMID: 30824060 DOI: 10.1016/j.plantsci.2019.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/29/2018] [Accepted: 01/03/2019] [Indexed: 06/09/2023]
Abstract
Telomerase is essential for the maintenance of telomeres, structures located at the ends of linear eukaryotic chromosomes that are crucial for genomic stability. Telomerase has been frequently explored in mammals because of its activity in many types of cancers, but knowledge in plants is rather sketchy despite plants representing useful models due to peculiarities in their telomeres and telomerase biology. We studied in planta complementation of telomerase in Arabidopsis thaliana mutant plants with disrupted expression of the gene encoding the telomerase protein subunit (AtTERT) and significantly shortened telomeres. We found that the upstream region of AtTERT, previously identified as a putative minimal promoter, was essential for reconstitution of telomerase function, as demonstrated by the full or partial recovery of the telomere phenotype in mutants. In contrast, transformation by the full length AtTERT gene construct resulted in more progressive telomere shortening in mutants and even in wild type plants, despite the high level of AtTERT transcript and telomerase activity detected by in vitro assay. Thus, the telomerase protein subunit putative promoter is essential for in planta telomerase reconstitution and restoration of its catalytical activity. Contributions from other factors, including those tissue-specific, for proper telomerase function are discussed.
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Affiliation(s)
- Tomáš Crhák
- The Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic; Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Dagmar Zachová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Eva Sýkorová
- The Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic.
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20
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Sováková PP, Magdolenová A, Konečná K, Rájecká V, Fajkus J, Fojtová M. Telomere elongation upon transfer to callus culture reflects the reprogramming of telomere stability control in Arabidopsis. Plant Mol Biol 2018; 98:81-99. [PMID: 30128721 DOI: 10.1007/s11103-018-0765-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/12/2018] [Indexed: 05/23/2023]
Abstract
KEY MESSAGE Standard pathways involved in the regulation of telomere stability do not contribute to gradual telomere elongation observed in the course of A. thaliana calli propagation. Genetic and epigenetic changes accompanying the culturing of plant cells have frequently been reported. Here we aimed to characterize the telomere homeostasis during long term callus propagation. While in Arabidopsis thaliana calli gradual telomere elongation was observed, telomeres were stable in Nicotiana tabacum and N. sylvestris cultures. Telomere elongation during callus propagation is thus not a general feature of plant cells. The long telomere phenotype in Arabidopsis calli was correlated neither with changes in telomerase activity nor with activation of alternative mechanisms of telomere elongation. The dynamics of telomere length changes was maintained in mutant calli with loss of function of important epigenetic modifiers but compromised in the presence of epigenetically active drug zebularine. To examine whether the cell culture-induced disruption of telomere homeostasis is associated with the modulated structure of chromosome ends, epigenetic properties of telomere chromatin were analysed. Albeit distinct changes in epigenetic modifications of telomere histones were observed, these were broadly stochastic. Our results show that contrary to animal cells, the structure and function of plant telomeres is not determined significantly by the epigenetic character of telomere chromatin. Set of differentially transcribed genes was identified in calli, but considering the known telomere- or telomerase-related functions of respective proteins, none of these changes per se was apparently related to the elongated telomere phenotype. Based on our data, we propose that the disruption in telomere homeostasis in Arabidopsis calli arises from the interplay of multiple factors, as a part of reprogramming of plant cells to long-term culture conditions.
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Affiliation(s)
- Pavla Polanská Sováková
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Alžbeta Magdolenová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Prague, Czech Republic
| | - Klára Konečná
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Veronika Rájecká
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., 612 65, Brno, Czech Republic
| | - Miloslava Fojtová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic.
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21
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Ledvinová D, Mikulášek K, Kuchaříková H, Brabencová S, Fojtová M, Zdráhal Z, Lochmanová G. Filter-Aided Sample Preparation Procedure for Mass Spectrometric Analysis of Plant Histones. Front Plant Sci 2018; 9:1373. [PMID: 30283482 PMCID: PMC6156276 DOI: 10.3389/fpls.2018.01373] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/29/2018] [Indexed: 05/21/2023]
Abstract
Characterization of histone post-translational modifications (PTMs) is still challenging, and robust histone sample preparation is essential for convincing evaluation of PTMs by mass spectrometry. An effective protocol for extracting plant histone proteins must also avoid excessive co-extraction of the numerous potential interfering compounds, including those related to secondary metabolism. Currently, the co-existence of histone marks is addressed mostly by shotgun proteomic analysis following chemical derivatization of histone lysine residues. Here, we report a straightforward approach for plant histone sample preparation for mass spectrometry, based on filter-aided sample preparation coupled with histone propionylation. The approach offers savings in sample handling and preparation time, enables removal of interfering compounds from the sample, and does not require either precipitation or dialysis of histone extract. We show the comparison of two protocol variants for derivatization of histone proteins, in-solution propionylation in the vial and propionylation on the filter unit. For both protocols, we obtained identical abundances of post-translationally modified histone peptides. Although shorter time is required for histone protein labeling on the filter unit, in-solution derivatization slightly outweighed filter-based variant by lower data variability. Nevertheless, both protocol variants appear to be efficient and convenient approach for preparation of plant histones for mass spectrometric analysis.
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Affiliation(s)
- Dominika Ledvinová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Kamil Mikulášek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hana Kuchaříková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Sylva Brabencová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- *Correspondence: Gabriela Lochmanová, ;
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22
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Jurečková JF, Sýkorová E, Hafidh S, Honys D, Fajkus J, Fojtová M. Tissue-specific expression of telomerase reverse transcriptase gene variants in Nicotiana tabacum. Planta 2017; 245:549-561. [PMID: 27900472 DOI: 10.1007/s00425-016-2624-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/23/2016] [Indexed: 06/06/2023]
Abstract
MAIN CONCLUSION In tobacco, three sequence variants of the TERT gene have been described. We revealed unbalanced levels of TERT variant transcripts in vegetative tobacco tissues and enhanced TERT transcription and telomerase activity in reproductive tissues. Telomerase is a ribonucleoprotein complex responsible for the maintenance of telomeres, structures delimiting ends of linear eukaryotic chromosomes. In the Nicotiana tabacum (tobacco) allotetraploid plant, three sequence variants (paralogs) of the gene coding for the telomerase reverse transcriptase subunit (TERT) have been described, two of them derived from the maternal N. sylvestris genome (TERT_Cs, TERT_D) and one originated from the N. tomentosiformis paternal genome (TERT_Ct). In this work, we analyzed the transcription of TERT variants in correlation with telomerase activity in tobacco tissues. High and approximately comparable levels of TERT_Ct and TERT_Cs transcripts were detected in seedlings, roots, flower buds and leaves, while the transcript of the TERT_D variant was markedly underrepresented. Similarly, in N. sylvestris tissues, TERT_Cs transcript significantly predominated. A specific pattern of TERT transcripts was found in samples of tobacco pollen with the TERT_Cs variant clearly dominating particularly at the early stage of pollen development. Detailed analysis of TERT_C variants representation in functionally distinct fractions of pollen transcriptome revealed their prevalence in large ribonucleoprotein particles encompassing translationally silent mRNA; only a minority of TERT_Ct and TERT_Cs transcripts were localized in actively translated polysomes. Histones of the TERT_C chromatin were decorated predominantly with the euchromatin-specific epigenetic modification in both telomerase-positive and telomerase-negative tobacco tissues. We conclude that the existence and transcription pattern of tobacco TERT paralogs represents an interesting phenomenon and our results indicate its functional significance. Nicotiana species have again proved to be appropriate and useful model plants in telomere biology studies.
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Affiliation(s)
- Jana Fišerová Jurečková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Eva Sýkorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Said Hafidh
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic v.v.i., Rozvojová 263, 165 02, Prague, Czech Republic
| | - David Honys
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic v.v.i., Rozvojová 263, 165 02, Prague, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
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23
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Brabencová S, Ihnatová I, Potěšil D, Fojtová M, Fajkus J, Zdráhal Z, Lochmanová G. Variations of Histone Modification Patterns: Contributions of Inter-plant Variability and Technical Factors. Front Plant Sci 2017; 8:2084. [PMID: 29270186 PMCID: PMC5725443 DOI: 10.3389/fpls.2017.02084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/22/2017] [Indexed: 05/07/2023]
Abstract
Inter-individual variability of conspecific plants is governed by differences in their genetically determined growth and development traits, environmental conditions, and adaptive responses under epigenetic control involving histone post-translational modifications. The apparent variability in histone modifications among plants might be increased by technical variation introduced in sample processing during epigenetic analyses. Thus, to detect true variations in epigenetic histone patterns associated with given factors, the basal variability among samples that is not associated with them must be estimated. To improve knowledge of relative contribution of biological and technical variation, mass spectrometry was used to examine histone modification patterns (acetylation and methylation) among Arabidopsis thaliana plants of ecotypes Columbia 0 (Col-0) and Wassilewskija (Ws) homogenized by two techniques (grinding in a cryomill or with a mortar and pestle). We found little difference in histone modification profiles between the ecotypes. However, in comparison of the biological and technical components of variability, we found consistently higher inter-individual variability in histone mark levels among Ws plants than among Col-0 plants (grown from seeds collected either from single plants or sets of plants). Thus, more replicates of Ws would be needed for rigorous analysis of epigenetic marks. Regarding technical variability, the cryomill introduced detectably more heterogeneity in the data than the mortar and pestle treatment, but mass spectrometric analyses had minor apparent effects. Our study shows that it is essential to consider inter-sample variance and estimate suitable numbers of biological replicates for statistical analysis for each studied organism when investigating changes in epigenetic histone profiles.
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Affiliation(s)
- Sylva Brabencová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Ivana Ihnatová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- *Correspondence: Gabriela Lochmanová,
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24
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Pontvianne F, Carpentier MC, Durut N, Pavlištová V, Jaške K, Schořová Š, Parrinello H, Rohmer M, Pikaard CS, Fojtová M, Fajkus J, Sáez-Vásquez J. Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome. Cell Rep 2016; 16:1574-1587. [PMID: 27477271 PMCID: PMC5279810 DOI: 10.1016/j.celrep.2016.07.016] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/24/2016] [Accepted: 07/03/2016] [Indexed: 11/27/2022] Open
Abstract
The nucleolus is the site of rRNA gene transcription, rRNA processing, and ribosome biogenesis. However, the nucleolus also plays additional roles in the cell. We isolated nucleoli using fluorescence-activated cell sorting (FACS) and identified nucleolus-associated chromatin domains (NADs) by deep sequencing, comparing wild-type plants and null mutants for the nucleolar protein NUCLEOLIN 1 (NUC1). NADs are primarily genomic regions with heterochromatic signatures and include transposable elements (TEs), sub-telomeric regions, and mostly inactive protein-coding genes. However, NADs also include active rRNA genes and the entire short arm of chromosome 4 adjacent to them. In nuc1 null mutants, which alter rRNA gene expression and overall nucleolar structure, NADs are altered, telomere association with the nucleolus is decreased, and telomeres become shorter. Collectively, our studies reveal roles for NUC1 and the nucleolus in the spatial organization of chromosomes as well as telomere maintenance.
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Affiliation(s)
- Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France; Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France; Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
| | - Marie-Christine Carpentier
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France; Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
| | - Nathalie Durut
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France; Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
| | - Veronika Pavlištová
- Central European Institute of Technology and Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Karin Jaške
- Central European Institute of Technology and Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Šárka Schořová
- Central European Institute of Technology and Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | | | | | - Craig S Pikaard
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA; Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA
| | - Miloslava Fojtová
- Central European Institute of Technology and Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Jiří Fajkus
- Central European Institute of Technology and Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France; Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860 Perpignan, France
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25
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Tran TD, Cao HX, Jovtchev G, Neumann P, Novák P, Fojtová M, Vu GTH, Macas J, Fajkus J, Schubert I, Fuchs J. Centromere and telomere sequence alterations reflect the rapid genome evolution within the carnivorous plant genus Genlisea. Plant J 2015; 84:1087-99. [PMID: 26485466 DOI: 10.1111/tpj.13058] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 10/07/2015] [Accepted: 10/15/2015] [Indexed: 05/25/2023]
Abstract
Linear chromosomes of eukaryotic organisms invariably possess centromeres and telomeres to ensure proper chromosome segregation during nuclear divisions and to protect the chromosome ends from deterioration and fusion, respectively. While centromeric sequences may differ between species, with arrays of tandemly repeated sequences and retrotransposons being the most abundant sequence types in plant centromeres, telomeric sequences are usually highly conserved among plants and other organisms. The genome size of the carnivorous genus Genlisea (Lentibulariaceae) is highly variable. Here we study evolutionary sequence plasticity of these chromosomal domains at an intrageneric level. We show that Genlisea nigrocaulis (1C = 86 Mbp; 2n = 40) and G. hispidula (1C = 1550 Mbp; 2n = 40) differ as to their DNA composition at centromeres and telomeres. G. nigrocaulis and its close relative G. pygmaea revealed mainly 161 bp tandem repeats, while G. hispidula and its close relative G. subglabra displayed a combination of four retroelements at centromeric positions. G. nigrocaulis and G. pygmaea chromosome ends are characterized by the Arabidopsis-type telomeric repeats (TTTAGGG); G. hispidula and G. subglabra instead revealed two intermingled sequence variants (TTCAGG and TTTCAGG). These differences in centromeric and, surprisingly, also in telomeric DNA sequences, uncovered between groups with on average a > 9-fold genome size difference, emphasize the fast genome evolution within this genus. Such intrageneric evolutionary alteration of telomeric repeats with cytosine in the guanine-rich strand, not yet known for plants, might impact the epigenetic telomere chromatin modification.
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Affiliation(s)
- Trung D Tran
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Hieu X Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Gabriele Jovtchev
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Pavel Neumann
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branišovská 31/1160, 37005, České Budějovice, Czech Republic
| | - Petr Novák
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branišovská 31/1160, 37005, České Budějovice, Czech Republic
| | - Miloslava Fojtová
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Giang T H Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Jiří Macas
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branišovská 31/1160, 37005, České Budějovice, Czech Republic
| | - Jiří Fajkus
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 61265, Brno, Czech Republic
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
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26
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Dvořáčková M, Fojtová M, Fajkus J. Chromatin dynamics of plant telomeres and ribosomal genes. Plant J 2015; 83:18-37. [PMID: 25752316 DOI: 10.1111/tpj.12822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/03/2015] [Accepted: 03/03/2015] [Indexed: 05/03/2023]
Abstract
Telomeres and genes encoding 45S ribosomal RNA (rDNA) are frequently located adjacent to each other on eukaryotic chromosomes. Although their primary roles are different, they show striking similarities with respect to their features and additional functions. Both genome domains have remarkably dynamic chromatin structures. Both are hypersensitive to dysfunctional histone chaperones, responding at the genomic and epigenomic levels. Both generate non-coding transcripts that, in addition to their epigenetic roles, may induce gross chromosomal rearrangements. Both give rise to chromosomal fragile sites, as their replication is intrinsically problematic. However, at the same time, both are essential for maintenance of genomic stability and integrity. Here we discuss the structural and functional inter-connectivity of telomeres and rDNA, with a focus on recent results obtained in plants.
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Affiliation(s)
- Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Kamenice 5, 62500, Brno, Czech Republic
- Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Kamenice 5, 62500, Brno, Czech Republic
- Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Kamenice 5, 62500, Brno, Czech Republic
- Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
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27
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Jankowska M, Fuchs J, Klocke E, Fojtová M, Polanská P, Fajkus J, Schubert V, Houben A. Holokinetic centromeres and efficient telomere healing enable rapid karyotype evolution. Chromosoma 2015; 124:519-28. [PMID: 26062516 DOI: 10.1007/s00412-015-0524-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 11/24/2022]
Abstract
Species with holocentric chromosomes are often characterized by a rapid karyotype evolution. In contrast to species with monocentric chromosomes where acentric fragments are lost during cell division, breakage of holocentric chromosomes creates fragments with normal centromere activity. To decipher the mechanism that allows holocentric species an accelerated karyotype evolution via chromosome breakage, we analyzed the chromosome complements of irradiated Luzula elegans plants. The resulting chromosomal fragments and rearranged chromosomes revealed holocentromere-typical CENH3 and histone H2AThr120ph signals as well as the same mitotic mobility like unfragmented chromosomes. Newly synthesized telomeres at break points become detectable 3 weeks after irradiation. The presence of active telomerase suggests a telomerase-based mechanism of chromosome healing. A successful transmission of holocentric chromosome fragments across different generations was found for most offspring of irradiated plants. Hence, a combination of holokinetic centromere activity and the fast formation of new telomeres at break points enables holocentric species a rapid karyotype evolution involving chromosome fissions and rearrangements.
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Affiliation(s)
- Maja Jankowska
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Correnstrasse 3, D-06466, Stadt Seeland, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Correnstrasse 3, D-06466, Stadt Seeland, Germany
| | - Evelyn Klocke
- Julius Kühn-Institute, Institute for Breeding Research on Horticultural Crops, Erwin-Baur-Straße 27, D-06484, Quedlinburg, Germany
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, CZ-625 00, Brno, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00, Brno, Czech Republic
| | - Pavla Polanská
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, CZ-625 00, Brno, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, CZ-625 00, Brno, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00, Brno, Czech Republic
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Correnstrasse 3, D-06466, Stadt Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Correnstrasse 3, D-06466, Stadt Seeland, Germany.
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28
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Peška V, Fajkus P, Fojtová M, Dvořáčková M, Hapala J, Dvořáček V, Polanská P, Leitch AR, Sýkorová E, Fajkus J. Characterisation of an unusual telomere motif (TTTTTTAGGG)n in the plant Cestrum elegans (Solanaceae), a species with a large genome. Plant J 2015; 82:644-54. [PMID: 25828846 DOI: 10.1111/tpj.12839] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/20/2015] [Accepted: 03/23/2015] [Indexed: 05/26/2023]
Abstract
The characterization of unusual telomere sequence sheds light on patterns of telomere evolution, maintenance and function. Plant species from the closely related genera Cestrum, Vestia and Sessea (family Solanaceae) lack known plant telomeric sequences. Here we characterize the telomere of Cestrum elegans, work that was a challenge because of its large genome size and few chromosomes (1C 9.76 pg; n = 8). We developed an approach that combines BAL31 digestion, which digests DNA from the ends and chromosome breaks, with next-generation sequencing (NGS), to generate data analysed in RepeatExplorer, designed for de novo repeats identification and quantification. We identify an unique repeat motif (TTTTTTAGGG)n in C. elegans, occurring in ca. 30 400 copies per haploid genome, averaging ca. 1900 copies per telomere, and synthesized by telomerase. We demonstrate that the motif is synthesized by telomerase. The occurrence of an unusual eukaryote (TTTTTTAGGG)n telomeric motif in C. elegans represents a switch in motif from the 'typical' angiosperm telomere (TTTAGGG)n . That switch may have happened with the divergence of Cestrum, Sessea and Vestia. The shift in motif when it arose would have had profound effects on telomere activity. Thus our finding provides a unique handle to study how telomerase and telomeres responded to genetic change, studies that will shed more light on telomere function.
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Affiliation(s)
- Vratislav Peška
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265, Brno, Czech Republic
- Faculty of Science, and CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Petr Fajkus
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265, Brno, Czech Republic
- Faculty of Science, and CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Miloslava Fojtová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265, Brno, Czech Republic
- Faculty of Science, and CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Martina Dvořáčková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265, Brno, Czech Republic
- Faculty of Science, and CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Jan Hapala
- Faculty of Science, and CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Vojtěch Dvořáček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265, Brno, Czech Republic
| | - Pavla Polanská
- Faculty of Science, and CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Eva Sýkorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265, Brno, Czech Republic
- Faculty of Science, and CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Jiří Fajkus
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265, Brno, Czech Republic
- Faculty of Science, and CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
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29
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Fojtová M, Sýkorová E, Najdekrová L, Polanská P, Zachová D, Vagnerová R, Angelis KJ, Fajkus J. Telomere dynamics in the lower plant Physcomitrella patens. Plant Mol Biol 2015; 87:591-601. [PMID: 25701469 DOI: 10.1007/s11103-015-0299-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 02/16/2015] [Indexed: 06/04/2023]
Abstract
A comparative approach in biology is needed to assess the universality of rules governing this discipline. In plant telomere research, most of the key principles were established based on studies in only single model plant, Arabidopsis thaliana. These principles include the absence of telomere shortening during plant development and the corresponding activity of telomerase in dividing (meristem) plant cells. Here we examine these principles in Physcomitrella patens as a representative of lower plants. To follow telomerase expression, we first characterize the gene coding for the telomerase reverse transcriptase subunit PpTERT in P. patens, for which only incomplete prediction has been available so far. In protonema cultures of P. patens, growing by filament apical cell division, the proportion of apical (dividing) cells was quantified and telomere length, telomerase expression and activity were determined. Our results show telomere stability and demonstrate proportionality of telomerase activity and expression with the number of apical cells. In addition, we analyze telomere maintenance in mre11, rad50, nbs1, ku70 and lig4 mutants of P. patens and compare the impact of these mutations in double-strand-break (DSB) repair pathways with earlier observations in corresponding A. thaliana mutants. Telomere phenotypes are absent and DSB repair kinetics is not affected in P. patens mutants for DSB factors involved in non-homologous end joining (NHEJ). This is compliant with the overall dominance of homologous recombination over NHEJ pathways in the moss, contrary to the inverse situation in flowering plants.
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Affiliation(s)
- Miloslava Fojtová
- Faculty of Science and CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
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30
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31
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Majerová E, Mandáková T, Vu GTH, Fajkus J, Lysak MA, Fojtová M. Chromatin features of plant telomeric sequences at terminal vs. internal positions. Front Plant Sci 2014; 5:593. [PMID: 25408695 PMCID: PMC4219495 DOI: 10.3389/fpls.2014.00593] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 10/11/2014] [Indexed: 05/19/2023]
Abstract
Epigenetic mechanisms are involved in regulation of crucial cellular processes in eukaryotic organisms. Data on the epigenetic features of plant telomeres and their epigenetic regulation were published mostly for Arabidopsis thaliana, in which the presence of interstitial telomeric repeats (ITRs) may interfere with genuine telomeres in most analyses. Here, we studied the epigenetic landscape and transcription of telomeres and ITRs in Nicotiana tabacum with long telomeres and no detectable ITRs, and in Ballantinia antipoda with large blocks of pericentromeric ITRs and relatively short telomeres. Chromatin of genuine telomeres displayed heterochromatic as well as euchromatic marks, while ITRs were just heterochromatic. Methylated cytosines were present at telomeres and ITRs, but showed a bias with more methylation toward distal telomere positions and different blocks of B. antipoda ITRs methylated to different levels. Telomeric transcripts TERRA (G-rich) and ARRET (C-rich) were identified in both plants and their levels varied among tissues with a maximum in blossoms. Plants with substantially different proportions of internally and terminally located telomeric repeats are instrumental in clarifying the chromatin status of telomeric repeats at distinct chromosome locations.
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Affiliation(s)
- Eva Majerová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology and Faculty of Science, Masaryk UniversityBrno, Czech Republic
| | - Terezie Mandáková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology and Faculty of Science, Masaryk UniversityBrno, Czech Republic
| | - Giang T. H. Vu
- Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology and Faculty of Science, Masaryk UniversityBrno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i.Brno, Czech Republic
| | - Martin A. Lysak
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology and Faculty of Science, Masaryk UniversityBrno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology and Faculty of Science, Masaryk UniversityBrno, Czech Republic
- *Correspondence: Miloslava Fojtová, Central European Institute of Technology and Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic e-mail:
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32
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Ogrocká A, Polanská P, Majerová E, Janeba Z, Fajkus J, Fojtová M. Compromised telomere maintenance in hypomethylated Arabidopsis thaliana plants. Nucleic Acids Res 2013; 42:2919-31. [PMID: 24334955 PMCID: PMC3950684 DOI: 10.1093/nar/gkt1285] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Telomeres, nucleoprotein structures at the ends of linear eukaryotic chromosomes, are important for the maintenance of genomic stability. Telomeres were considered as typical heterochromatic regions, but in light of recent results, this view should be reconsidered. Asymmetrically located cytosines in plant telomeric DNA repeats may be substrates for a DNA methyltransferase enzyme and indeed, it was shown that these repeats are methylated. Here, we analyse the methylation of telomeric cytosines and the length of telomeres in Arabidopsis thaliana methylation mutants (met 1-3 and ddm 1-8), and in their wild-type siblings that were germinated in the presence of hypomethylation drugs. Our results show that cytosine methylation in telomeric repeats depends on the activity of MET1 and DDM1 enzymes. Significantly shortened telomeres occur in later generations of methylation mutants as well as in plants germinated in the presence of hypomethylation drugs, and this phenotype is stably transmitted to the next plant generation. A possible role of compromised in vivo telomerase action in the observed telomere shortening is hypothesized based on telomere analysis of hypomethylated telomerase knockout plants. Results are discussed in connection with previous data in this field obtained using different model systems.
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Affiliation(s)
- Anna Ogrocká
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10, Prague, Czech Republic and Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
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33
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Zachová D, Fojtová M, Dvořáčková M, Mozgová I, Lermontova I, Peška V, Schubert I, Fajkus J, Sýkorová E. Structure-function relationships during transgenic telomerase expression in Arabidopsis. Physiol Plant 2013; 149:114-26. [PMID: 23278240 DOI: 10.1111/ppl.12021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 12/13/2012] [Accepted: 12/14/2012] [Indexed: 05/11/2023]
Abstract
Although telomerase (EC 2.7.7.49) is important for genome stability and totipotency of plant cells, the principles of its regulation are not well understood. Therefore, we studied subcellular localization and function of the full-length and truncated variants of the catalytic subunit of Arabidopsis thaliana telomerase, AtTERT, in planta. Our results show that multiple sites in AtTERT may serve as nuclear localization signals, as all the studied individual domains of the AtTERT were targeted to the nucleus and/or the nucleolus. Although the introduced genomic or cDNA AtTERT transgenes display expression at transcript and protein levels, they are not able to fully complement the lack of telomerase functions in tert -/- mutants. The failure to reconstitute telomerase function in planta suggests a more complex telomerase regulation in plant cells than would be expected based on results of similar experiments in mammalian model systems.
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Affiliation(s)
- Dagmar Zachová
- Faculty of Science and Central European Institute of Technology, Masaryk University, CZ-61137, Brno, Czech Republic
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34
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Sýkorová E, Fojtová M, Peška V. A polymerase chain reaction-based approach for evaluation of telomere-associated sequences and interstitial telomeric sequences. Anal Biochem 2013; 439:8-10. [PMID: 23583821 DOI: 10.1016/j.ab.2013.03.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/18/2013] [Accepted: 03/21/2013] [Indexed: 11/27/2022]
Abstract
Telomere minisatellites could be present in both terminal and internal chromosomal regions. We monitored the progress of BAL-31 nuclease digestion on Arabidopsis thaliana genomic DNA prepared by standard isolation techniques to verify its cleavage at terminal and internal genomic regions. A subtelomeric position of candidate sequences was validated using conventional polymerase chain reaction (PCR), combining the C-strand-specific telomeric primer with a subtelomeric reverse primer, and confirmed by quantitative PCR (qPCR) using sequence-specific primer pairs on DNA samples after BAL-31 digestion. qPCR amplification showed a gradual decrease in subtelomeric sequence signals, in contrast to interstitial telomeric sequences from pericentromere and control sequences.
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Affiliation(s)
- Eva Sýkorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65 Brno, Czech Republic.
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35
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Ševčíková T, Bišová K, Fojtová M, Lukešová A, Hrčková K, Sýkorová E. Completion of cell division is associated with maximum telomerase activity in naturally synchronized cultures of the green alga Desmodesmus quadricauda. FEBS Lett 2013; 587:743-8. [PMID: 23395610 DOI: 10.1016/j.febslet.2013.01.058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 01/17/2013] [Accepted: 01/23/2013] [Indexed: 10/27/2022]
Abstract
Telomerase maintains the ends of eukaryotic chromosomes, and its activity is an important parameter correlating with the proliferative capacity of cells. We have investigated cell cycle-specific changes in telomerase activity using cultures of Desmodesmus quadricauda, a model alga naturally synchronized by light/dark entrainment. A quantitative telomerase assay revealed high activity in algal cultures, with slight changes during the light period. Significantly increased telomerase activity was observed at the end of the dark phase, when cell division was complete. In contrast to other models, a natural separation between nuclear and cellular division typical for the cell cycle in D. quadricauda made this observation possible.
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Affiliation(s)
- Tereza Ševčíková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, vvi, 612 65 Brno, Czech Republic
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Legartová S, Jugová A, Stixová L, Kozubek S, Fojtová M, Zdráhal Z, Lochmanová G, Bártová E. Epigenetic aspects of HP1 exchange kinetics in apoptotic chromatin. Biochimie 2012; 95:167-79. [PMID: 23023195 DOI: 10.1016/j.biochi.2012.09.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 09/10/2012] [Indexed: 10/27/2022]
Abstract
Apoptotic bodies are the most condensed form of chromatin. In general, chromatin structure and function are mostly dictated by histone post-translational modifications. Thus, we have analyzed the histone signature in apoptotic cells, characterized by pronounced chromatin condensation. Here, H2B mono-acetylation, and H3K9 and H4 acetylation was significantly decreased in apoptotic cells, which maintained a high level of H3K9 methylation. This phenotype was independent of p53 function and distinct levels of anti-apoptotic Bcl2 protein. Interestingly, after etoposide treatment of leukemia and multiple myeloma cells, H3K9 and H4 hypoacetylation was accompanied by increased H3K9me2, but not H3K9me1 or H3K9me3. In adherent mouse fibroblasts, a high level of H3K9me3 and histone deacetylation in apoptotic bodies was likely responsible for the pronounced (∼40%) recovery of GFP-HP1α and GFP-HP1β after photobleaching. HP1 mobility in apoptotic cells appeared to be unique because limited exchange after photobleaching was observed for other epigenetically important proteins, including GFP-JMJD2b histone demethylase (∼10% fluorescence recovery) or Polycomb group-related GFP-BMI1 protein (∼20% fluorescence recovery). These findings imply a novel fact that only certain subset of proteins in apoptotic bodies is dynamic.
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Affiliation(s)
- Soňa Legartová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
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Ogrocká A, Sýkorová E, Fajkus J, Fojtová M. Developmental silencing of the AtTERT gene is associated with increased H3K27me3 loading and maintenance of its euchromatic environment. J Exp Bot 2012; 63:4233-41. [PMID: 22511802 PMCID: PMC3398451 DOI: 10.1093/jxb/ers107] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Telomerase, an enzyme responsible for the maintenance of linear chromosome ends, is precisely regulated during plant development. In animals, involvement of the epigenetic state of the telomerase reverse transcriptase (TERT) gene in the complex regulation of telomerase activity has been reported. To reveal whether epigenetic mechanisms participate in the regulation of plant telomerase, the relationship between telomerase activity in tissues of Arabidopsis thaliana and DNA methylation and histone modifications in the A. thaliana TERT (AtTERT) upstream region was studied. As expected, a gradual decrease of telomerase activity during leaf maturation was observed. A different pattern with a more progressive loss of telomerase activity and AtTERT transcription during leaf development was revealed in MET1 gene-knockout mutants. Analysis of DNA methylation in the AtTERT upstream region showed low levels of methylated cytosines without notable differences between telomerase-positive and telomerase-negative wild-type tissues. Surprisingly, a high level of CG methylation was found in the AtTERT coding region, although this type of methylation is a characteristic attribute of constitutively expressed genes. Analysis of chromatin modifications in the AtTERT upstream region and in exon 5 showed increased loading of the H3K27me3 mark in the telomerase-negative mature leaf compared to telomerase-positive seedlings, whereas H3K4me3, H3K9Ac, and H3K9me2 were approximately at the same level. Consistently, the chromatin structure of the AtTERT gene was maintained. These results are discussed in the context of the general involvement of epigenetic mechanisms in the regulation of gene expression and with respect to similar studies performed in animal models.
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Affiliation(s)
- Anna Ogrocká
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Eva Sýkorová
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 65, 612 65 Brno, Czech Republic
| | - Jiří Fajkus
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 65, 612 65 Brno, Czech Republic
| | - Miloslava Fojtová
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- To whom correspondence should be addressed. E-mail:
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Sýkorová E, Fulnečková J, Mokroš P, Fajkus J, Fojtová M, Peška V. Three TERT genes in Nicotiana tabacum. Chromosome Res 2012; 20:381-94. [PMID: 22543812 DOI: 10.1007/s10577-012-9282-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 03/15/2012] [Accepted: 03/29/2012] [Indexed: 01/15/2023]
Abstract
Telomerase is essential for proper functioning of telomeres in eukaryotes. We cloned and characterised genes for the protein subunit of telomerase (TERT) in the allotetraploid Nicotiana tabacum (tobacco) and its diploid progenitor species Nicotiana sylvestris and Nicotiana tomentosiformis with the aim of determining if allopolyploidy (hybridisation and genome duplication) influences TERT activity and divergence. Two of the three sequence variants present in the tobacco genome (NtTERT-C/s and NtTERT-D) revealed similarity to two sequence variants found in N. sylvestris and another variant (NtTERT-C/t) was similar to TERT of N. tomentosiformis. Variants of N. sylvestris origin showed less similarity to each other (80.5 % in the genomic region; 90.1 % in the coding sequence) than that between the NtTERT-C/s and NtTERT-C/t variants (93.6 and 97.2 %, respectively). The NtTERT-D variant was truncated at the 5' end, and indels indicated that it was a pseudogene. All tobacco variants were transcribed and alternatively spliced sequences were detected. Analysis of gene arrangements uncovered a novel exon in the N-terminal domain of TERT variants, a feature that is likely to be commonly found in Solanaceae species. In addition, species-specific duplications were observed within exon 5. The putative function, copy number and evolutionary origin of these NtTERT sequence variants are discussed.
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Affiliation(s)
- Eva Sýkorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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Fojtová M, Peška V, Dobšáková Z, Mozgová I, Fajkus J, Sýkorová E. Molecular analysis of T-DNA insertion mutants identified putative regulatory elements in the AtTERT gene. J Exp Bot 2011; 62:5531-45. [PMID: 21865176 PMCID: PMC3223050 DOI: 10.1093/jxb/err235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Analysis of plants bearing a T-DNA insertion is a potent tool of modern molecular biology, providing valuable information about the function and involvement of genes in metabolic pathways. A collection of 12 Arabidopsis thaliana lines with T-DNA insertions in the gene coding for the catalytic subunit of telomerase (AtTERT) and in adjacent regions was screened for telomerase activity [telomere repeat amplification protocol (TRAP) assay], telomere length (terminal restriction fragments), and AtTERT transcription (quantitative reverse transcription-PCR). Lines with the insertion located upstream of the start codon displayed unchanged telomere stability and telomerase activity, defining a putative minimal AtTERT promoter and the presence of a regulatory element linked to increased transcription in the line SALK_048471. Lines bearing a T-DNA insertion inside the protein-coding region showed telomere shortening and lack of telomerase activity. Transcription in most of these lines was unchanged upstream of the T-DNA insertion, while it was notably decreased downstream. The expression profile varied markedly in mutant lines harbouring insertions at the 5' end of AtTERT which showed increased transcription and abolished tissue specificity. Moreover, the line FLAG_385G01 (T-DNA insertion inside intron 1) revealed the presence of a highly abundant downstream transcript with normal splicing but without active telomerase. The role of regulatory elements found along the AtTERT gene is discussed in respect to natural telomerase expression and putative intron-mediated enhancement.
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Affiliation(s)
- Miloslava Fojtová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265 Brno, Czech Republic
- Department of Functional Genomics and Proteomics, Faculty of Science and CEITEC - Central European Institute of Technology, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Vratislav Peška
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265 Brno, Czech Republic
- Department of Functional Genomics and Proteomics, Faculty of Science and CEITEC - Central European Institute of Technology, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Zuzana Dobšáková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265 Brno, Czech Republic
- To whom correspondence should be addressed. E-mail:
| | - Iva Mozgová
- Department of Functional Genomics and Proteomics, Faculty of Science and CEITEC - Central European Institute of Technology, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Jiří Fajkus
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265 Brno, Czech Republic
- Department of Functional Genomics and Proteomics, Faculty of Science and CEITEC - Central European Institute of Technology, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Eva Sýkorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265 Brno, Czech Republic
- Department of Functional Genomics and Proteomics, Faculty of Science and CEITEC - Central European Institute of Technology, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
- To whom correspondence should be addressed. E-mail:
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Majerová E, Fojtová M, Mozgová I, Bittová M, Fajkus J. Hypomethylating drugs efficiently decrease cytosine methylation in telomeric DNA and activate telomerase without affecting telomere lengths in tobacco cells. Plant Mol Biol 2011; 77:371-80. [PMID: 21866390 DOI: 10.1007/s11103-011-9816-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 08/11/2011] [Indexed: 05/23/2023]
Abstract
Telomere homeostasis is regulated at multiple levels, including the local chromatin structure of telomeres and subtelomeres. Recent reports demonstrated that a decrease in repressive chromatin marks, such as levels of cytosine methylation in subtelomeric regions, results in telomere elongation in mouse cells. Here we show that a considerable fraction of cytosines is methylated not only in subtelomeric, but also in telomeric DNA of tobacco BY-2 cells. Drug-induced hypomethylation (demonstrated at subtelomeric, telomeric, and global DNA levels) results in activation of telomerase. However, in contrast to mouse cells, the decrease in 5-methylcytosine levels and upregulation of telomerase do not result in any changes of telomere lengths. These results demonstrate the involvement of epigenetic mechanisms in the multilevel process of regulation of telomerase activity in plant cells and, at the same time, they indicate that changes in telomerase activity can be overridden by other factors governing telomere length stability.
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Affiliation(s)
- Eva Majerová
- Department of Functional Genomics and Proteomics, Faculty of Science and Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, Czech Republic
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Crhák Khaitová L, Fojtová M, Křížová K, Lunerová J, Fulneček J, Depicker A, Kovařík A. Paramutation of tobacco transgenes by small RNA-mediated transcriptional gene silencing. Epigenetics 2011; 6:650-60. [PMID: 21521939 PMCID: PMC3121974 DOI: 10.4161/epi.6.5.15764] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 04/06/2011] [Indexed: 02/03/2023] Open
Abstract
It has been well established that trans-acting small RNAs guide promoter methylation leading to its inactivation and gene silencing at the transcriptional level (TGS). Here we addressed the question of the influence of the locus structure and epigenetic modifications of the target locus on its susceptibility for being paramutated by trans-acting small RNA molecules. Silencing was induced by crossing a 35S promoter silencer locus 271 with two different 35S-driven transgene loci, locus 2 containing a highly expressed single copy gene and locus 1 containing an inverted posttranscriptionally silenced (PTGS) repeat of this gene. Three generations of exposure to RNA signals from the 271 locus were required to complete silencing and methylation of the 35S promoter within locus 2. Segregating methylated locus 2 epialleles were obtained only from the third generation of hybrids, and this methylation was not correlated with silencing. Strikingly, only one generation was required for the PTGS locus 1 to acquire complete TGS and 35S promoter methylation. In this case, paramutated locus 1 epialleles bearing methylated and inactive 35S promoters segregated already from the first generation of hybrids. The results support the hypothesis that PTGS loci containing a palindrome structure and methylation in the coding region are more sensitive to paramutation by small RNAs and exhibit a strong tendency to formation of meiotically transmissible TGS epialleles. These features contrast with a non-methylated single copy transgenic locus that required several generations of contact with RNA silencing molecules to become imprinted in a stable epiallele.
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Affiliation(s)
- Lucie Crhák Khaitová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; Brno, Czech Republic
| | - Miloslava Fojtová
- Department of Functional Genomics and Proteomics; Institute of Experimental Biology; Faculty of Science; Masaryk University; Brno, Czech Republic
| | - Kateřina Křížová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; Brno, Czech Republic
| | - Jana Lunerová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; Brno, Czech Republic
| | - Jaroslav Fulneček
- Institute of Biophysics; Academy of Sciences of the Czech Republic; Brno, Czech Republic
| | - Anna Depicker
- Department of Plant Systems Biology; VIB; Department of Plant Biotechnology and Genetics; Ghent University; Ghent, Belgium
| | - Aleš Kovařík
- Institute of Biophysics; Academy of Sciences of the Czech Republic; Brno, Czech Republic
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Pivoňková H, Horáková P, Fojtová M, Fojta M. Direct Voltammetric Analysis of DNA Modified with Enzymatically Incorporated 7-Deazapurines. Anal Chem 2010; 82:6807-13. [DOI: 10.1021/ac100757v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hana Pivoňková
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic, Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic
| | - Petra Horáková
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic, Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic
| | - Miloslava Fojtová
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic, Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic, Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic
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Uhlírová R, Horáková AH, Galiová G, Legartová S, Matula P, Fojtová M, Varecha M, Amrichová J, Vondrácek J, Kozubek S, Bártová E. SUV39h- and A-type lamin-dependent telomere nuclear rearrangement. J Cell Biochem 2010; 109:915-26. [PMID: 20069564 DOI: 10.1002/jcb.22466] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Telomeres are specialized chromatin structures that are situated at the end of linear chromosomes and play an important role in cell senescence and immortalization. Here, we investigated whether changes in histone signature influence the nuclear arrangement and positioning of telomeres. Analysis of mouse embryonic fibroblasts revealed that telomeres were organized into specific clusters that partially associated with centromeric clusters. This nuclear arrangement was influenced by deficiency of the histone methyltransferase SUV39h, LMNA deficiency, and the histone deacetylase inhibitor Trichostatin A (TSA). Similarly, nuclear radial distributions of telomeric clusters were preferentially influenced by TSA, which caused relocation of telomeres closer to the nuclear center. Telomeres also co-localized with promyelocytic leukemia bodies (PML). This association was increased by SUV39h deficiency and decreased by LMNA deficiency. These differences could be explained by differing levels of the telomerase subunit, TERT, in SUV39h- and LMNA-deficient fibroblasts. Taken together, our data show that SUV39h and A-type lamins likely play a key role in telomere maintenance and telomere nuclear architecture.
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Affiliation(s)
- Radka Uhlírová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-612 65 Brno, Czech Republic
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Humpoliková-Adámková L, Kovařík J, Dušek L, Lauerová L, Boudný V, Fait V, Fojtová M, Krejčí E, Kovařík A. Interferon-alpha treatment may negatively influence disease progression in melanoma patients by hyperactivation of STAT3 protein. Eur J Cancer 2009; 45:1315-1323. [PMID: 19232485 DOI: 10.1016/j.ejca.2009.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 01/13/2009] [Indexed: 02/01/2023]
Abstract
Interferon-alpha (IFN-alpha) is an important drug used in anti-melanoma therapy. However, metastases eventually reappear in almost 60% of melanoma patients, who have received adjuvant cytokine therapy suggesting that IFN-alpha can paradoxically promote disease progression in some cases, at least. In this study, we have investigated the possibility that a growth-promoting STAT3 protein might be activated by interferon-alpha in melanoma cells. We examined 24 primary cultures established from node metastases of melanoma patients who were monitored in a 5-year clinical follow-up. The patients differed in the course of disease and survival end-points. Using Western blot analyses, we show that interferon-alpha stimulated STAT3 phosphorylation at tyrosine (Y705) residue in 17% of cases. These over-reactive cell populations originated from patients who had the shortest disease-free intervals. A significant correlation was obtained between the length of survival end-points and a lack of STAT3 activation by IFN-alpha. No STAT3 induction was observed in normal melanocytes. The STAT1 activation at tyrosine (Y701) occurred at a similar frequency as that of STAT3 (17%) albeit in different patients, no clear correlation with the clinical status could be made. The interferon-alpha/beta receptors (IRFARs) were expressed irrespective to the signal transducers and activators of transcription (STATs) inducibility suggesting that signalling defects occur downstream from IRFAR. We propose that in some cases the application of IFN-alpha could increase the probability of disease progression via overactive STAT3. The tests for STAT3 inducibility prior to cytokine immunotherapy in the clinic are therefore warranted.
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Affiliation(s)
- L Humpoliková-Adámková
- Department of Experimental Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - J Kovařík
- Department of Experimental Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - L Dušek
- Institute of Biostatistics and Analyses, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
| | - L Lauerová
- Department of Experimental Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - V Boudný
- Department of Experimental Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - V Fait
- Department of Experimental Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - M Fojtová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612 65 Brno, Czech Republic
| | - E Krejčí
- Department of Experimental Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - A Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612 65 Brno, Czech Republic.
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Lunerová-Bedrichová J, Bleys A, Fojtová M, Khaitová L, Depicker A, Kovarík A. Trans-generation inheritance of methylation patterns in a tobacco transgene following a post-transcriptional silencing event. Plant J 2008; 54:1049-62. [PMID: 18315537 DOI: 10.1111/j.1365-313x.2008.03475.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We have studied the inheritance of the epigenetic state of tobacco transgenes whose expression was post-transcriptionally silenced by an invertedly repeated silencer locus. We show that, in hybrids, the coding region of the target neomycin phosphotransferase (nptII) gene was almost exclusively methylated at CG configurations, and dense non-CG methylation occurred in the 3' untranslated region. Homologous sequences in the silencer locus were heavily methylated at both CG and non-CG motifs. After segregation of the silencer locus, the CG methylation but not the non-CG methylation of the target genes was transmitted to the progeny. In the segregants, we observed an overall increase of CG methylation in the target genes, associated with a re-distribution from the 3' end of the coding region towards the middle. This pattern was inherited with some fluctuation for at least two additional generations in the absence of a detectable T-DNA-derived small RNA fraction. Thus CG methylation is not cleared during meiosis and may be inherited over generations without RNA signals being present. These epi-allelic variants re-expressed the reporter gene immediately after segregation of the trigger, showing that relatively dense CG methylation (approximately 60-80%) imprinted on most of the coding region (>500 bp) did not reduce expression compared with the parental non-methylated locus. We propose that the genic CG methylation seen in euchromatic regions of the genome may originate from ancient post-transcriptional gene silencing events as a result of adventitiously produced methylation-directing RNA molecules.
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Affiliation(s)
- Jana Lunerová-Bedrichová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., CZ-61265 Brno, Czech Republic
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Fojtová M, Bleys A, Bedřichová J, Van Houdt H, Křížová K, Depicker A, Kovařík A. The trans-silencing capacity of invertedly repeated transgenes depends on their epigenetic state in tobacco. Nucleic Acids Res 2006; 34:2280-93. [PMID: 16670434 PMCID: PMC1456325 DOI: 10.1093/nar/gkl180] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 03/13/2006] [Accepted: 03/22/2006] [Indexed: 11/13/2022] Open
Abstract
We studied the in trans-silencing capacities of a transgene locus that carried the neomycin phosphotransferase II reporter gene linked to the 35S promoter in an inverted repeat (IR). This transgene locus was originally posttranscriptionally silenced but switched to a transcriptionally silenced epiallele after in vitro tissue culture. Here, we show that both epialleles were strongly methylated in the coding region and IR center. However, by genomic sequencing, we found that the 1.0 kb region around the transcription start site was heavily methylated in symmetrical and non-symmetrical contexts in transcriptionally but not in posttranscriptionally silenced epilallele. Also, the posttranscriptionally silenced epiallele could trans-silence and trans-methylate homologous transgene loci irrespective of their genomic organization. We demonstrate that this in trans-silencing was accompanied by the production of small RNA molecules. On the other hand, the transcriptionally silenced variant could neither trans-silence nor trans-methylate homologous sequences, even after being in the same genetic background for generations and meiotic cycles. Interestingly, 5-aza-2-deoxy-cytidine-induced hypomethylation could partially restore signaling from the transcriptionally silenced epiallele. These results are consistent with the hypothesis that non-transcribed highly methylated IRs are poor silencers of homologous loci at non-allelic positions even across two generations and that transcription of the inverted sequences is essential for their trans-silencing potential.
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Affiliation(s)
- Miloslava Fojtová
- Institute of Biophysics, Academy of Sciences of the Czech RepublicCZ-612 65 Brno, Czech Republic
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent UniversityB-9052 Ghent, Belgium
| | - Annick Bleys
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent UniversityB-9052 Ghent, Belgium
| | - Jana Bedřichová
- Institute of Biophysics, Academy of Sciences of the Czech RepublicCZ-612 65 Brno, Czech Republic
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent UniversityB-9052 Ghent, Belgium
| | - Helena Van Houdt
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent UniversityB-9052 Ghent, Belgium
| | - Kateřina Křížová
- Institute of Biophysics, Academy of Sciences of the Czech RepublicCZ-612 65 Brno, Czech Republic
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent UniversityB-9052 Ghent, Belgium
| | - Anna Depicker
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent UniversityB-9052 Ghent, Belgium
| | - Aleš Kovařík
- To whom correspondence should be addressed at Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ 612 65 Brno, Czech Republic. Tel: +420 541 517 178; Fax: +420 541 211 293;
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Fojta M, Fojtová M, Havran L, Pivoňková H, Dorčák V, Šestáková I. Electrochemical monitoring of phytochelatin accumulation in Nicotiana tabacum cells exposed to sub-cytotoxic and cytotoxic levels of cadmium. Anal Chim Acta 2006. [DOI: 10.1016/j.aca.2005.10.084] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Abstract
The nuclear architecture of selected chromosomes in apoptotic nuclei of human leukemic cells K-562 and HL-60 was investigated. Etoposide and prolonged confluence were used for the induction of apoptosis. DAPI as well as TUNEL labeling of apoptotic nuclear bodies was combined with visualization of chromosomal territories by the FISH technique. Simultaneous vital staining by annexin V, propidium iodide, and Hoechst 33342 was applied to distinguish apoptotic, necrotic, and intact cell fraction of tested populations. Our FISH analyses revealed that the three-dimensional (3D) structure of apoptotic nuclei as well as the 3D structure of apoptotic bodies is preserved in formaldehyde-fixed cells. High-molecular-weight DNA fragmentation was determined in apoptotic K-562 cells in contrast to oligonucleosomal cleavage observed in apoptotic HL-60 cells. In K-562 populations, chromosomal territories were located separately either in one apoptotic body or underwent disassembly into chromosomal segments dispersed into single and/or several apoptotic bodies. The apoptotic disorganization of chromosomal territories was irregular, leading mainly to chromosomal segments of different sizes and, consequently, chromosomal disassembly was not observed at specific sites. In comparison with the control, an increased number of centromeric FISH signals were observed in prolonged confluence-treated K-562 cells induced to apoptosis. This finding can be explained either as a consequence of apoptosis or by polyploidization. Sequential staining of the same apoptotic nuclei by the FISH and TUNEL techniques revealed that chromosomal territory segmentation precedes the formation of nuclear apoptotic bodies.
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Affiliation(s)
- E Bártová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
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Fojtová M, Fulnecková J, Fajkus J, Kovarík A. Recovery of tobacco cells from cadmium stress is accompanied by DNA repair and increased telomerase activity. J Exp Bot 2002; 53:2151-8. [PMID: 12379781 DOI: 10.1093/jxb/erf080] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
It has been shown previously that apoptosis of tobacco cells induced by cadmium ions shows a relatively long lag period between exposure and cell death. This lag phase lasts for 3 d in TBY-2 cell cultures and is characterized by the maintenance of full cell viability despite extensive fragmentation of DNA into pieces of chromatin loop size. Experiments reported here demonstrate that cell death can be prevented if 50 micro M CdSO(4) is removed from the growth medium during the lag phase, suggesting that an irreversible apoptotic trigger is delivered within 24 h, between the third and fourth days of cadmium treatment. The post-cadmium recovery phase was characterized by DNA repair at the level of 50-200 kb and increased telomerase activity. Analysis of high-molecular-weight DNA by pulsed-field-gel electrophoresis revealed that the majority of DNA strand breaks was repaired within 48 h after cadmium withdrawal. Telomerase activity increased 2.5-fold in the recovery phase, but elevated levels were also found in cell extracts from apoptotic cells suggesting that telomerase might be associated with DNA repair, but it is not capable of inhibiting ongoing apoptosis. Limited exposure of TBY-2 cells to cadmium elicits non-random DNA damage of relatively high magnitude that can be repaired. It is proposed that plants might have developed a highly efficient DNA repair system to cope with transient genotoxic stress.
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Affiliation(s)
- Miloslava Fojtová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, CZ-612 65, Czech Republic
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Koukalová B, Votruba I, Fojtová M, Holý A, Kovarík A. Hypomethylation of CNG targets induced with dihydroxypropyladenine is rapidly reversed in the course of mitotic cell division in tobacco. Theor Appl Genet 2002; 105:1097-1098. [PMID: 12582938 DOI: 10.1007/s00122-002-1152-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
- B. Koukalová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
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