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Godwin J, Govindasamy M, Nedounsejian K, March E, Halton R, Bourbousse C, Wolff L, Fort A, Krzyszton M, López Corrales J, Swiezewski S, Barneche F, Schubert D, Farrona S. The UBP5 histone H2A deubiquitinase counteracts PRCs-mediated repression to regulate Arabidopsis development. Nat Commun 2024; 15:667. [PMID: 38253560 PMCID: PMC10803359 DOI: 10.1038/s41467-023-44546-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Polycomb Repressive Complexes (PRCs) control gene expression through the incorporation of H2Aub and H3K27me3. In recent years, there is increasing evidence of the complexity of PRCs' interaction networks and the interplay of these interactors with PRCs in epigenome reshaping, which is fundamental to understand gene regulatory mechanisms. Here, we identified UBIQUITIN SPECIFIC PROTEASE 5 (UBP5) as a chromatin player able to counteract the deposition of the two PRCs' epigenetic hallmarks in Arabidopsis thaliana. We demonstrated that UBP5 is a plant developmental regulator based on functional analyses of ubp5-CRISPR Cas9 mutant plants. UBP5 promotes H2A monoubiquitination erasure, leading to transcriptional de-repression. Furthermore, preferential association of UBP5 at PRC2 recruiting motifs and local H3K27me3 gaining in ubp5 mutant plants suggest the existence of functional interplays between UBP5 and PRC2 in regulating epigenome dynamics. In summary, acting as an antagonist of the pivotal epigenetic repressive marks H2Aub and H3K27me3, UBP5 provides novel insights to disentangle the complex regulation of PRCs' activities.
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Affiliation(s)
- James Godwin
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Mohan Govindasamy
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Kiruba Nedounsejian
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Eduardo March
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Ronan Halton
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland
| | - Clara Bourbousse
- 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
| | - Antoine Fort
- Dept. of Veterinary and Microbial Sciences, Technological University of The Shannon: Midlands, Athlone, Co., Roscommon, Ireland
| | - Michal Krzyszton
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, Warsaw, 02-106, Poland
| | - Jesús López Corrales
- Molecular Parasitology Laboratory (MPL), Centre for One Health and Ryan Institute, School of Natural Sciences, University of Galway, Galway, H91 DK59, Ireland
| | - Szymon Swiezewski
- Laboratory of Seeds Molecular Biology, Institute of Biochemistry and Biophysics, PAS, Warsaw, 02-106, Poland
| | - Fredy Barneche
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Daniel Schubert
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Sara Farrona
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, H91 TK33, Galway, Ireland.
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Godwin J, Farrona S. The Importance of Networking: Plant Polycomb Repressive Complex 2 and Its Interactors. Epigenomes 2022; 6:epigenomes6010008. [PMID: 35323212 PMCID: PMC8948837 DOI: 10.3390/epigenomes6010008] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/13/2022] Open
Abstract
Polycomb Repressive Complex 2 (PRC2) is arguably the best-known plant complex of the Polycomb Group (PcG) pathway, formed by a group of proteins that epigenetically represses gene expression. PRC2-mediated deposition of H3K27me3 has amply been studied in Arabidopsis and, more recently, data from other plant model species has also been published, allowing for an increasing knowledge of PRC2 activities and target genes. How PRC2 molecular functions are regulated and how PRC2 is recruited to discrete chromatin regions are questions that have brought more attention in recent years. A mechanism to modulate PRC2-mediated activity is through its interaction with other protein partners or accessory proteins. Current evidence for PRC2 interactors has demonstrated the complexity of its protein network and how far we are from fully understanding the impact of these interactions on the activities of PRC2 core subunits and on the formation of new PRC2 versions. This review presents a list of PRC2 interactors, emphasizing their mechanistic action upon PRC2 functions and their effects on transcriptional regulation.
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Kakoulidou I, Avramidou EV, Baránek M, Brunel-Muguet S, Farrona S, Johannes F, Kaiserli E, Lieberman-Lazarovich M, Martinelli F, Mladenov V, Testillano PS, Vassileva V, Maury S. Epigenetics for Crop Improvement in Times of Global Change. Biology (Basel) 2021; 10:766. [PMID: 34439998 PMCID: PMC8389687 DOI: 10.3390/biology10080766] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity-naturally, genetically, chemically, or environmentally induced-can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.
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Affiliation(s)
- Ioanna Kakoulidou
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-Dimitra (ELGO-DIMITRA), 11528 Athens, Greece;
| | - Miroslav Baránek
- Faculty of Horticulture, Mendeleum—Institute of Genetics, Mendel University in Brno, Valtická 334, 69144 Lednice, Czech Republic;
| | - Sophie Brunel-Muguet
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, UNICAEN, INRAE, Normandie Université, CEDEX, F-14032 Caen, France;
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, National University of Ireland (NUI) Galway, H91 TK33 Galway, Ireland;
| | - Frank Johannes
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
- Institute for Advanced Study, Technical University of Munich, Lichtenberg Str. 2a, 85748 Garching, Germany
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Michal Lieberman-Lazarovich
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel;
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Sq. Dositeja Obradovića 8, 21000 Novi Sad, Serbia;
| | - Pilar S. Testillano
- Pollen Biotechnology of Crop Plants Group, Centro de Investigaciones Biológicas Margarita Salas-(CIB-CSIC), Ramiro Maeztu 9, 28040 Madrid, Spain;
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bldg. 21, 1113 Sofia, Bulgaria;
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, EA1207 USC1328, Université d’Orléans, F-45067 Orléans, France
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Santos AP, Gaudin V, Mozgová I, Pontvianne F, Schubert D, Tek AL, Dvořáčková M, Liu C, Fransz P, Rosa S, Farrona S. Corrigendum to: Tidying-up the plant nuclear space: domains, functions, and dynamics. J Exp Bot 2021; 72:5782. [PMID: 34196709 PMCID: PMC8318252 DOI: 10.1093/jxb/erab134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Ana Paula Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Iva Mozgová
- Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, Perpignan, France
| | - Daniel Schubert
- Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Ahmet L Tek
- Agricultural Genetic Engineering Department, Niğde Ömer Halisdemir University, Niğde, Turkey
| | | | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
- Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Paul Fransz
- University of Amsterdam, Amsterdam, The Netherlands
| | - Stefanie Rosa
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, NUI Galway, Galway, Ireland
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Farrona S, Mozgová I, Archacki R, Casas-Mollano JA. Editorial: Chromatin Stability and Dynamics: Targeting and Recruitment of Chromatin Modifiers. Front Plant Sci 2021; 12:678702. [PMID: 34135931 PMCID: PMC8201073 DOI: 10.3389/fpls.2021.678702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Sara Farrona
- Plant and Agricultural Biosciences Centre-Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Iva Mozgová
- Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Rafal Archacki
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
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6
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Santos AP, Gaudin V, Mozgová I, Pontvianne F, Schubert D, Tek AL, Dvořáčková M, Liu C, Fransz P, Rosa S, Farrona S. Tidying-up the plant nuclear space: domains, functions, and dynamics. J Exp Bot 2020; 71:5160-5178. [PMID: 32556244 PMCID: PMC8604271 DOI: 10.1093/jxb/eraa282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 01/16/2020] [Accepted: 06/12/2020] [Indexed: 05/07/2023]
Abstract
Understanding how the packaging of chromatin in the nucleus is regulated and organized to guide complex cellular and developmental programmes, as well as responses to environmental cues is a major question in biology. Technological advances have allowed remarkable progress within this field over the last years. However, we still know very little about how the 3D genome organization within the cell nucleus contributes to the regulation of gene expression. The nuclear space is compartmentalized in several domains such as the nucleolus, chromocentres, telomeres, protein bodies, and the nuclear periphery without the presence of a membrane around these domains. The role of these domains and their possible impact on nuclear activities is currently under intense investigation. In this review, we discuss new data from research in plants that clarify functional links between the organization of different nuclear domains and plant genome function with an emphasis on the potential of this organization for gene regulation.
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Affiliation(s)
- Ana Paula Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova
de Lisboa, Oeiras, Portugal
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université
Paris-Saclay, Versailles, France
| | - Iva Mozgová
- Biology Centre of the Czech Academy of Sciences, České
Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České
Budějovice, Czech Republic
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de
Perpignan Via Domitia, Perpignan, France
| | - Daniel Schubert
- Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Ahmet L Tek
- Agricultural Genetic Engineering Department, Niğde Ömer Halisdemir
University, Niğde, Turkey
| | | | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of
Tübingen, Tübingen, Germany
- Institute of Biology, University of Hohenheim, Stuttgart,
Germany
| | - Paul Fransz
- University of Amsterdam, Amsterdam, The
Netherlands
| | - Stefanie Rosa
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, NUI Galway,
Galway, Ireland
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7
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Rebelo BA, Farrona S, Ventura MR, Abranches R. Canthaxanthin, a Red-Hot Carotenoid: Applications, Synthesis, and Biosynthetic Evolution. Plants (Basel) 2020; 9:E1039. [PMID: 32824217 PMCID: PMC7463686 DOI: 10.3390/plants9081039] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 01/21/2023]
Abstract
Carotenoids are a class of pigments with a biological role in light capture and antioxidant activities. High value ketocarotenoids, such as astaxanthin and canthaxanthin, are highly appealing for applications in human nutraceutical, cosmetic, and animal feed industries due to their color- and health-related properties. In this review, recent advances in metabolic engineering and synthetic biology towards the production of ketocarotenoids, in particular the red-orange canthaxanthin, are highlighted. Also reviewed and discussed are the properties of canthaxanthin, its natural producers, and various strategies for its chemical synthesis. We review the de novo synthesis of canthaxanthin and the functional β-carotene ketolase enzyme across organisms, supported by a protein-sequence-based phylogenetic analysis. Various possible modifications of the carotenoid biosynthesis pathway and the present sustainable cost-effective alternative platforms for ketocarotenoids biosynthesis are also discussed.
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Affiliation(s)
- Bárbara A. Rebelo
- Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal;
- Bioorganic Chemistry Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal;
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, NUI Galway, H19 TK33 Galway, Ireland;
| | - M. Rita Ventura
- Bioorganic Chemistry Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal;
| | - Rita Abranches
- Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal;
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Abstract
Drought stress is one of the most common stresses encountered by crops and other plants and leads to significant productivity losses. It commonly happens that drought stress occurs more than once during the plant's life cycle. Plants suffering from drought stress can adapt their life strategies to acclimate and survive in many different ways. Interestingly, some plants have evolved a stress response strategy referred to as stress memory which leads to an enhanced response the next time the stress is encountered. The acquisition of stress memory leads to a reprogrammed transcriptional response during subsequent stress and subsequent changes both at the physiological and molecular level. Recent advances in understanding chromatin dynamics have demonstrated the involvement of chromatin modifications, especially histone marks, associated with drought stress-responsive memory genes and subsequent enhanced transcriptional responses to repeated drought stress. In this chapter, we describe recent progress in this area and summarize techniques for the study of plant epigenetic responses to stress, including the roles of ABA and transcription factors in superinduced transcriptional activation during recurrent drought stress. We also review the possible use of seed priming to induce stress memory later in the plant life cycle. Finally, we discuss the potential implications of understanding the epigenetic mechanisms involved in plant stress memory for future applications in crop improvement and drought resistance.
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Affiliation(s)
- James Godwin
- Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Sara Farrona
- Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland Galway, Galway, Ireland.
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9
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Mikulski P, Hohenstatt ML, Farrona S, Smaczniak C, Stahl Y, Kaufmann K, Angenent G, Schubert D. The Chromatin-Associated Protein PWO1 Interacts with Plant Nuclear Lamin-like Components to Regulate Nuclear Size. Plant Cell 2019; 31:1141-1154. [PMID: 30914470 PMCID: PMC6533023 DOI: 10.1105/tpc.18.00663] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 02/27/2019] [Accepted: 03/22/2019] [Indexed: 05/23/2023]
Abstract
Spatial organization of chromatin contributes to gene regulation of many cellular processes and includes a connection of chromatin with the nuclear lamina (NL). The NL is a protein mesh that resides underneath the inner nuclear membrane and consists of lamins and lamina-associated proteins. Chromatin regions associated with lamins in animals are characterized mostly by constitutive heterochromatin, but association with facultative heterochromatin mediated by Polycomb-group (PcG) proteins has been reported as well. In contrast with animals, plant NL components are largely not conserved and NL association with chromatin is poorly explored. Here, we present the connection between the lamin-like protein, CROWDED NUCLEI1 (CRWN1), and the chromatin- and PcG-associated component, PROLINE-TRYPTOPHANE-TRYPTOPHANE-PROLINE INTERACTOR OF POLYCOMBS1, in Arabidopsis (Arabidopsis thaliana). We show that PWO1 and CRWN1 proteins associate physically with each other, act in the same pathway to maintain nuclear morphology, and control expression of a similar set of target genes. Moreover, we demonstrate that transiently expressed PWO1 proteins form foci located partially at the subnuclear periphery. Ultimately, as CRWN1 and PWO1 are plant-specific, our results argue that plants might have developed an equivalent, rather than homologous, mechanism of linking chromatin repression and NL.
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Affiliation(s)
- Pawel Mikulski
- Institute for Biology, Freie Universität Berlin, Berlin 14195, Germany
- Institute for Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Mareike L Hohenstatt
- Institute for Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Sara Farrona
- Institute for Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Cezary Smaczniak
- Institute for Biology, Humboldt-University Berlin, Berlin 10115, Germany
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6700 AP, The Netherlands
| | - Yvonne Stahl
- Institute for Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Kerstin Kaufmann
- Institute for Biology, Humboldt-University Berlin, Berlin 10115, Germany
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6700 AP, The Netherlands
| | - Gerco Angenent
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6700 AP, The Netherlands
| | - Daniel Schubert
- Institute for Biology, Freie Universität Berlin, Berlin 14195, Germany
- Institute for Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
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Hohenstatt ML, Mikulski P, Komarynets O, Klose C, Kycia I, Jeltsch A, Farrona S, Schubert D. PWWP-DOMAIN INTERACTOR OF POLYCOMBS1 Interacts with Polycomb-Group Proteins and Histones and Regulates Arabidopsis Flowering and Development. Plant Cell 2018; 30:117-133. [PMID: 29330200 PMCID: PMC5810566 DOI: 10.1105/tpc.17.00117] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 11/28/2017] [Accepted: 01/09/2018] [Indexed: 05/10/2023]
Abstract
Polycomb-group (PcG) proteins mediate epigenetic gene regulation by setting H3K27me3 via Polycomb Repressive Complex 2 (PRC2). In plants, it is largely unclear how PcG proteins are recruited to their target genes. Here, we identified the PWWP-DOMAIN INTERACTOR OF POLYCOMBS1 (PWO1) protein, which interacts with all three Arabidopsis thaliana PRC2 histone methyltransferases and is required for maintaining full H3 occupancy at several Arabidopsis genes. PWO1 localizes and recruits CURLY LEAF to nuclear speckles in Nicotiana benthamiana nuclei, suggesting a role in spatial organization of PcG regulation. PWO1 belongs to a gene family with three members having overlapping activities: pwo1 pwo2 pwo3 triple mutants are seedling lethal and show shoot and root meristem arrest, while pwo1 single mutants are early flowering. Interestingly, the PWWP domain of PWO1 confers binding to histones, which is reduced by a point mutation in a highly conserved residue of this domain and blocked by phosphorylation of H3S28. PWO1 carrying this mutation is not able to fully complement the pwo1 pwo2 pwo3 triple mutant, indicating the requirement of this domain for PWO1 in vivo activity. Thus, the PWO family may present a novel class of histone readers that are involved in recruiting PcG proteins to subnuclear domains and in promoting Arabidopsis development.
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Affiliation(s)
| | - Pawel Mikulski
- Institute for Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany
- Institute of Biology, Freie Universität, 14195 Berlin, Germany
| | - Olga Komarynets
- Institute for Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany
- Université de Genève, 1205 Geneva, Switzerland
| | - Constanze Klose
- Institute for Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany
| | - Ina Kycia
- Institute for Biochemistry, University of Stuttgart, 70174 Stuttgart, Germany
| | - Albert Jeltsch
- Institute for Biochemistry, University of Stuttgart, 70174 Stuttgart, Germany
| | - Sara Farrona
- Institute for Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany
- Plant and AgriBiosciences Centre, National University Ireland, Galway H91 TK33, Ireland
| | - Daniel Schubert
- Institute for Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany
- Institute of Biology, Freie Universität, 14195 Berlin, Germany
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11
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March E, Farrona S. Polycomb silencing mediated by specific DNA-binding recruiters. Nat Genet 2017; 49:1416-1417. [DOI: 10.1038/ng.3961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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March E, Farrona S. Plant Deubiquitinases and Their Role in the Control of Gene Expression Through Modification of Histones. Front Plant Sci 2017; 8:2274. [PMID: 29387079 PMCID: PMC5776116 DOI: 10.3389/fpls.2017.02274] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/29/2017] [Indexed: 05/11/2023]
Abstract
Selective degradation of proteins in the cell occurs through ubiquitination, which consists of post-translational deposition of ubiquitin on proteins to target them for degradation by proteases. However, ubiquitination does not only impact on protein stability, but promotes changes in their functions. Whereas the deposition of ubiquitin has been amply studied and discussed, the antagonistic activity, deubiquitination, is just emerging and the full model and players involved in this mechanism are far from being completely understood. Nevertheless, it is the dynamic balance between ubiquitination and deubiquitination that is essential for the development and homeostasis of organisms. In this review, we present a detailed analysis of the members of the deubiquitinase (DUB) superfamily in plants and its division in different clades. We describe current knowledge in the molecular and functional characterisation of DUB proteins, focusing primarily on Arabidopsis thaliana. In addition, the striking function of the duality between ubiquitination and deubiquitination in the control of gene expression through the modification of chromatin is discussed and, using the available information of the activities of the DUB superfamily in yeast and animals as scaffold, we propose possible scenarios for the role of these proteins in plants.
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Liu L, Farrona S, Klemme S, Turck FK. Post-fertilization expression of FLOWERING LOCUS T suppresses reproductive reversion. Front Plant Sci 2014; 5:164. [PMID: 24817870 PMCID: PMC4012189 DOI: 10.3389/fpls.2014.00164] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/07/2014] [Indexed: 05/08/2023]
Abstract
FLOWERING LOCUS T (FT) encodes a systemic signal communicating the perception of long day photoperiod from leaves to the shoot apex to induce the floral transition. Transient expression of FT in the phloem companion cells of rosette leaves for one to several days was previously shown to be sufficient to commit plants to flowering. Here we show that partial commitment results in pleiotropic inflorescence meristem reversion phenotypes. FT expression is much stronger in organs formed after the floral transition such as cauline leaves, sepals, and developing siliques. We show that expression of FT and its paralog TWIN SISTER OF FT (TSF) after the floral transition plays a role in inflorescence meristem stabilization even if plants flower very late in development. CONSTANS (CO), the major activator of FT, is not required to prevent late reproductive reversion. The requirement for FT is temporal since reproductive reversion to a vegetative state occurs only in recently formed inflorescence meristems. Unlike for the expression of FT in leaves, neither the distal putative FT enhancer nor long-day photoperiod is required for FT expression in developing siliques. Expression of FT in developing siliques and their supporting stems is sufficient to stabilize flowering during the sensitive developmental window indicating that fruit generated FT participates in inflorescence stabilization.
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Affiliation(s)
- Liangyu Liu
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10Cologne, Germany
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, KunmingYunnan, China
- University of Chinese Academy of SciencesBeijing, China
| | - Sara Farrona
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10Cologne, Germany
| | - Sonja Klemme
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10Cologne, Germany
| | - Franziska K. Turck
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10Cologne, Germany
- *Correspondence: Franziska K. Turck, Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, Köln, NRW, Germany e-mail:
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14
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Engelhorn J, Reimer JJ, Leuz I, Göbel U, Huettel B, Farrona S, Turck F. Development-related PcG target in the apex 4 controls leaf margin architecture in Arabidopsis thaliana. Development 2012; 139:2566-75. [PMID: 22675210 DOI: 10.1242/dev.078618] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In a reverse genetics screen based on a group of genes enriched for development-related Polycomb group targets in the apex (DPAs), we isolated DPA4 as a novel regulator of leaf margin shape. T-DNA insertion lines in the DPA4 locus display enhanced leaf margin serrations and enlarged petals, whereas overexpression of DPA4 results in smooth margins. DPA4 encodes a putative RAV (Related to ABI3/VP1) transcriptional repressor and is expressed in the lateral organ boundary region and in the sinus of leaf serrations. DPA4 expression domains overlap with those of the known leaf shape regulator CUP-SHAPED COTYLEDON 2 (CUC2) and we provide evidence that DPA4 negatively regulates CUC2 expression independently of MIR164A, an established regulator of CUC2. Taken together, the data suggest DPA4 as a newly identified player in the signalling network that controls leaf serrations in Arabidopsis thaliana.
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Affiliation(s)
- Julia Engelhorn
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, 50829 Köln, Germany
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15
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Hajheidari M, Farrona S, Huettel B, Koncz Z, Koncz C. CDKF;1 and CDKD protein kinases regulate phosphorylation of serine residues in the C-terminal domain of Arabidopsis RNA polymerase II. Plant Cell 2012; 24:1626-1642. [PMID: 22547781 PMCID: PMC3398568 DOI: 10.1105/tpc.112.096834;pmid:2254778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 04/01/2012] [Accepted: 04/11/2012] [Indexed: 05/29/2023]
Abstract
Phosphorylation of conserved Y₁S₂P₃T₄S₅P₆S₇ repeats in the C-terminal domain of largest subunit of RNA polymerase II (RNAPII CTD) plays a central role in the regulation of transcription and cotranscriptional RNA processing. Here, we show that Ser phosphorylation of Arabidopsis thaliana RNAPII CTD is governed by CYCLIN-DEPENDENT KINASE F;1 (CDKF;1), a unique plant-specific CTD S₇-kinase. CDKF;1 is required for in vivo activation of functionally redundant CYCLIN-DEPENDENT KINASE Ds (CDKDs), which are major CTD S₅-kinases that also phosphorylate in vitro the S₂ and S₇ CTD residues. Inactivation of CDKF;1 causes extreme dwarfism and sterility. Inhibition of CTD S₇-phosphorylation in germinating cdkf;1 seedlings is accompanied by 3'-polyadenylation defects of pre-microRNAs and transcripts encoding key regulators of small RNA biogenesis pathways. The cdkf;1 mutation also decreases the levels of both precursor and mature small RNAs without causing global downregulation of the protein-coding transcriptome and enhances the removal of introns that carry pre-microRNA stem-loops. A triple cdkd knockout mutant is not viable, but a combination of null and weak cdkd;3 alleles in a triple cdkd123* mutant permits semidwarf growth. Germinating cdkd123* seedlings show reduced CTD S₅-phosphorylation, accumulation of uncapped precursor microRNAs, and a parallel decrease in mature microRNA. During later development of cdkd123* seedlings, however, S₇-phosphorylation and unprocessed small RNA levels decline similarly as in the cdkf;1 mutant. Taken together, cotranscriptional processing and stability of a set of small RNAs and transcripts involved in their biogenesis are sensitive to changes in the phosphorylation of RNAPII CTD by CDKF;1 and CDKDs.
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MESH Headings
- Arabidopsis/enzymology
- Arabidopsis/genetics
- Arabidopsis/growth & development
- Arabidopsis Proteins/chemistry
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Biosynthetic Pathways/genetics
- Cyclin-Dependent Kinases/metabolism
- Down-Regulation/genetics
- Gene Expression Regulation, Plant
- Genes, Plant/genetics
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Mutation/genetics
- Nucleic Acid Hybridization
- Phosphorylation
- Phosphoserine/metabolism
- Protein Serine-Threonine Kinases/metabolism
- Protein Structure, Tertiary
- RNA Caps/metabolism
- RNA Polymerase II/chemistry
- RNA Polymerase II/metabolism
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional/genetics
- RNA Splicing/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/biosynthesis
- RNA, Plant/genetics
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Untranslated/genetics
- Transcription, Genetic
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Affiliation(s)
- Mohsen Hajheidari
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Sara Farrona
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Bruno Huettel
- Max Planck Genome Centre, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Zsuzsa Koncz
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Csaba Koncz
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Institute of Plant Biology, Biological Research Center of Hungarian Academy of Sciences, H-6723 Szeged, Hungary
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16
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Hajheidari M, Farrona S, Huettel B, Koncz Z, Koncz C. CDKF;1 and CDKD protein kinases regulate phosphorylation of serine residues in the C-terminal domain of Arabidopsis RNA polymerase II. Plant Cell 2012; 24:1626-42. [PMID: 22547781 PMCID: PMC3398568 DOI: 10.1105/tpc.112.096834] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 04/01/2012] [Accepted: 04/11/2012] [Indexed: 05/19/2023]
Abstract
Phosphorylation of conserved Y₁S₂P₃T₄S₅P₆S₇ repeats in the C-terminal domain of largest subunit of RNA polymerase II (RNAPII CTD) plays a central role in the regulation of transcription and cotranscriptional RNA processing. Here, we show that Ser phosphorylation of Arabidopsis thaliana RNAPII CTD is governed by CYCLIN-DEPENDENT KINASE F;1 (CDKF;1), a unique plant-specific CTD S₇-kinase. CDKF;1 is required for in vivo activation of functionally redundant CYCLIN-DEPENDENT KINASE Ds (CDKDs), which are major CTD S₅-kinases that also phosphorylate in vitro the S₂ and S₇ CTD residues. Inactivation of CDKF;1 causes extreme dwarfism and sterility. Inhibition of CTD S₇-phosphorylation in germinating cdkf;1 seedlings is accompanied by 3'-polyadenylation defects of pre-microRNAs and transcripts encoding key regulators of small RNA biogenesis pathways. The cdkf;1 mutation also decreases the levels of both precursor and mature small RNAs without causing global downregulation of the protein-coding transcriptome and enhances the removal of introns that carry pre-microRNA stem-loops. A triple cdkd knockout mutant is not viable, but a combination of null and weak cdkd;3 alleles in a triple cdkd123* mutant permits semidwarf growth. Germinating cdkd123* seedlings show reduced CTD S₅-phosphorylation, accumulation of uncapped precursor microRNAs, and a parallel decrease in mature microRNA. During later development of cdkd123* seedlings, however, S₇-phosphorylation and unprocessed small RNA levels decline similarly as in the cdkf;1 mutant. Taken together, cotranscriptional processing and stability of a set of small RNAs and transcripts involved in their biogenesis are sensitive to changes in the phosphorylation of RNAPII CTD by CDKF;1 and CDKDs.
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MESH Headings
- Arabidopsis/enzymology
- Arabidopsis/genetics
- Arabidopsis/growth & development
- Arabidopsis Proteins/chemistry
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Biosynthetic Pathways/genetics
- Cyclin-Dependent Kinases/metabolism
- Down-Regulation/genetics
- Gene Expression Regulation, Plant
- Genes, Plant/genetics
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Mutation/genetics
- Nucleic Acid Hybridization
- Phosphorylation
- Phosphoserine/metabolism
- Protein Serine-Threonine Kinases/metabolism
- Protein Structure, Tertiary
- RNA Caps/metabolism
- RNA Polymerase II/chemistry
- RNA Polymerase II/metabolism
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional/genetics
- RNA Splicing/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/biosynthesis
- RNA, Plant/genetics
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Untranslated/genetics
- Transcription, Genetic
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Affiliation(s)
- Mohsen Hajheidari
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Sara Farrona
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Bruno Huettel
- Max Planck Genome Centre, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Zsuzsa Koncz
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Csaba Koncz
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Institute of Plant Biology, Biological Research Center of Hungarian Academy of Sciences, H-6723 Szeged, Hungary
- Address correspondence to
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17
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Farrona S, Thorpe FL, Engelhorn J, Adrian J, Dong X, Sarid-Krebs L, Goodrich J, Turck F. Tissue-specific expression of FLOWERING LOCUS T in Arabidopsis is maintained independently of polycomb group protein repression. Plant Cell 2011; 23:3204-14. [PMID: 21917549 PMCID: PMC3203448 DOI: 10.1105/tpc.111.087809] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The Polycomb Group (PcG) pathway represses transcription through a mechanism conserved among plants and animals. PcG-mediated repression can determine spatial territories of gene expression, but it remains unclear whether PcG-mediated repression is a regulatory requirement for all targets. Here, we show the role of PcG proteins in the spatial regulation of FLOWERING LOCUS T (FT), a main activator of flowering in Arabidopsis thaliana exclusively expressed in the vasculature. Strikingly, the loss of PcG repression causes down-regulation of FT. In addition, our results show how the effect of PcG-mediated regulation differs for target genes and that, for FT expression, it relies primarily on tissue differentiation.
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Affiliation(s)
- Sara Farrona
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Frazer L. Thorpe
- Institute for Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
| | - Julia Engelhorn
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Jessika Adrian
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Xue Dong
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Liron Sarid-Krebs
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Justin Goodrich
- Institute for Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
| | - Franziska Turck
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Address correspondence to
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18
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Farrona S, Hurtado L, March-Díaz R, Schmitz RJ, Florencio FJ, Turck F, Amasino RM, Reyes JC. Brahma is required for proper expression of the floral repressor FLC in Arabidopsis. PLoS One 2011; 6:e17997. [PMID: 21445315 PMCID: PMC3061888 DOI: 10.1371/journal.pone.0017997] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 02/22/2011] [Indexed: 01/07/2023] Open
Abstract
Background BRAHMA (BRM) is a member of a family of ATPases of the SWI/SNF chromatin remodeling complexes from Arabidopsis. BRM has been previously shown to be crucial for vegetative and reproductive development. Methodology/Principal Findings Here we carry out a detailed analysis of the flowering phenotype of brm mutant plants which reveals that, in addition to repressing the flowering promoting genes CONSTANS (CO), FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1), BRM also represses expression of the general flowering repressor FLOWERING LOCUS C (FLC). Thus, in brm mutant plants FLC expression is elevated, and FLC chromatin exhibits increased levels of histone H3 lysine 4 tri-methylation and decreased levels of H3 lysine 27 tri-methylation, indicating that BRM imposes a repressive chromatin configuration at the FLC locus. However, brm mutants display a normal vernalization response, indicating that BRM is not involved in vernalization-mediated FLC repression. Analysis of double mutants suggests that BRM is partially redundant with the autonomous pathway. Analysis of genetic interactions between BRM and the histone H2A.Z deposition machinery demonstrates that brm mutations overcome a requirement of H2A.Z for FLC activation suggesting that in the absence of BRM, a constitutively open chromatin conformation renders H2A.Z dispensable. Conclusions/Significance BRM is critical for phase transition in Arabidopsis. Thus, BRM represses expression of the flowering promoting genes CO, FT and SOC1 and of the flowering repressor FLC. Our results indicate that BRM controls expression of FLC by creating a repressive chromatin configuration of the locus.
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Affiliation(s)
- Sara Farrona
- Max Planck Institute for Plant Breeding, Cologne, Germany.
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Adrian J, Farrona S, Reimer JJ, Albani MC, Coupland G, Turck F. cis-Regulatory elements and chromatin state coordinately control temporal and spatial expression of FLOWERING LOCUS T in Arabidopsis. Plant Cell 2010; 22:1425-40. [PMID: 20472817 PMCID: PMC2899882 DOI: 10.1105/tpc.110.074682] [Citation(s) in RCA: 222] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 04/16/2010] [Accepted: 05/03/2010] [Indexed: 05/17/2023]
Abstract
Flowering time of summer annual Arabidopsis thaliana accessions is largely determined by the timing of FLOWERING LOCUS T (FT) expression in the leaf vasculature. To understand the complex interplay between activating and repressive inputs controlling flowering through FT, cis-regulatory sequences of FT were identified in this study. A proximal and an approximately 5-kb upstream promoter region containing highly conserved sequence blocks were found to be essential for FT activation by CONSTANS (CO). Chromatin-associated protein complexes add another layer to FT regulation. In plants constitutively overexpressing CO, changes in chromatin status, such as a decrease in binding of LIKE HETEROCHROMATIN PROTEIN1 (LHP1) and increased acetylation of H3K9 and K14, were observed throughout the FT locus, although these changes appear to be a consequence of FT upregulation and not a prerequisite for activation. Binding of LHP1 was required to repress enhancer elements located between the CO-controlled regions. By contrast, the distal and proximal promoter sequences required for FT activation coincide with locally LHP1 and H3K27me3 depleted chromatin, indicating that chromatin status facilitates the accessibility of transcription factors to FT. Therefore, distant regulatory regions are required for FT transcription, reflecting the complexity of its control and differences in chromatin status delimit functionally important cis-regulatory regions.
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20
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Aichinger E, Villar CBR, Farrona S, Reyes JC, Hennig L, Köhler C. CHD3 proteins and polycomb group proteins antagonistically determine cell identity in Arabidopsis. PLoS Genet 2009; 5:e1000605. [PMID: 19680533 PMCID: PMC2718830 DOI: 10.1371/journal.pgen.1000605] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [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: 04/22/2009] [Accepted: 07/16/2009] [Indexed: 11/19/2022] Open
Abstract
Dynamic regulation of chromatin structure is of fundamental importance for modulating genomic activities in higher eukaryotes. The opposing activities of Polycomb group (PcG) and trithorax group (trxG) proteins are part of a chromatin-based cellular memory system ensuring the correct expression of specific transcriptional programs at defined developmental stages. The default silencing activity of PcG proteins is counteracted by trxG proteins that activate PcG target genes and prevent PcG mediated silencing activities. Therefore, the timely expression and regulation of PcG proteins and counteracting trxG proteins is likely to be of fundamental importance for establishing cell identity. Here, we report that the chromodomain/helicase/DNA–binding domain CHD3 proteins PICKLE (PKL) and PICKLE RELATED2 (PKR2) have trxG-like functions in plants and are required for the expression of many genes that are repressed by PcG proteins. The pkl mutant could partly suppress the leaf and flower phenotype of the PcG mutant curly leaf, supporting the idea that CHD3 proteins and PcG proteins antagonistically determine cell identity in plants. The direct targets of PKL in roots include the PcG genes SWINGER and EMBRYONIC FLOWER2 that encode subunits of Polycomb repressive complexes responsible for trimethylating histone H3 at lysine 27 (H3K27me3). Similar to mutants lacking PcG proteins, lack of PKL and PKR2 caused reduced H3K27me3 levels and, therefore, increased expression of a set of PcG protein target genes in roots. Thus, PKL and PKR2 are directly required for activation of PcG protein target genes and in roots are also indirectly required for repression of PcG protein target genes. Reduced PcG protein activity can lead to cell de-differentiation and callus-like tissue formation in pkl pkr2 mutants. Thus, in contrast to mammals, where PcG proteins are required to maintain pluripotency and to prevent cell differentiation, in plants PcG proteins are required to promote cell differentiation by suppressing embryonic development. In higher eukaryotes only a small proportion of genomic information is required in any specific cell type at a given developmental stage. The intricate decision whether a gene should be active or repressed is made by the counteractive activities of trithorax group (trxG) and Polycomb group (PcG) proteins that form part of a chromatin-based cellular memory system. Here we show that the CHD3 proteins PICKLE and PICKLE RELATED2 (PKR2) have trxG-like functions in plants and activate PcG protein target genes. Lack of PKL function can partially suppress PcG mutant leaf and flower phenotypes, supporting the idea that CHD3 proteins and PcG proteins act antagonistically during plant development. We identified PcG genes among the direct PKL/PKR2 targets in roots and demonstrated that lack of pkl pkr2 results in reduced PcG protein activities, leading to similar root phenotypes in pkl pkr2 and PcG protein mutants. Previous studies have implicated PKL as a transcriptional repressor, but we provide evidence that CHD3 proteins such as PKL and PKR2 act as transcriptional activators in plants and assume trxG-like function to counteract PcG protein–mediated gene repression.
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Affiliation(s)
- Ernst Aichinger
- Department of Biology and Zurich-Basel Plant Science Center, Swiss Federal Institute of Technology, ETH Centre, Zurich, Switzerland
| | - Corina B. R. Villar
- Department of Biology and Zurich-Basel Plant Science Center, Swiss Federal Institute of Technology, ETH Centre, Zurich, Switzerland
| | - Sara Farrona
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | - José C. Reyes
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | - Lars Hennig
- Department of Biology and Zurich-Basel Plant Science Center, Swiss Federal Institute of Technology, ETH Centre, Zurich, Switzerland
| | - Claudia Köhler
- Department of Biology and Zurich-Basel Plant Science Center, Swiss Federal Institute of Technology, ETH Centre, Zurich, Switzerland
- * E-mail:
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Farrona S, Hurtado L, Reyes JC. A Nucleosome Interaction Module Is Required for Normal Function of Arabidopsis thaliana BRAHMA. J Mol Biol 2007; 373:240-50. [PMID: 17825834 DOI: 10.1016/j.jmb.2007.07.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [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: 04/26/2007] [Revised: 07/06/2007] [Accepted: 07/10/2007] [Indexed: 11/20/2022]
Abstract
The BRAHMA (BRM) gene encodes the SNF2-type ATPase of the putative Arabidopsis thaliana SWI/SNF chromatin remodelling complex. This family of ATPases is characterized by the presence of a conserved catalytic domain and an arrangement of auxiliary domains, whose functions in the remodelling activity remains unclear. Here, we characterize, at the molecular and functional level, the carboxy-terminal part of Arabidopsis BRM. We have found three DNA-binding regions that bind various free DNA and nucleosomal probes with different specificity. One of these regions contains an AT-hook motif. The carboxy terminus also contains a bromodomain able to bind histones H3 and H4. We propose that this array of domains constitute a nucleosome interaction module that helps BRM to interact with its substrate. We also characterize an Arabidopsis mutant that expresses a BRM protein lacking the last 454 amino acid residues (BRM-DeltaC), encompassing the bromodomain and two of the three DNA-binding activities identified. This mutant displays an intermediate phenotype between those of the wild-type and a null allele mutant, suggesting that the nucleosome interaction module is required for the normal function of BRM but it is not essential for the remodelling activity of BRM-containing SWI/SNF complexes.
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Affiliation(s)
- S Farrona
- Centro Andaluz de Biología Molecular y Medicina Regenerativa and Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas, Américo Vespucio s/n, E-41092 Sevilla, Spain
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22
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Corbesier L, Vincent C, Jang S, Fornara F, Fan Q, Searle I, Giakountis A, Farrona S, Gissot L, Turnbull C, Coupland G. FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science 2007. [PMID: 17446353 DOI: 10.1126/science.114752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
In plants, seasonal changes in day length are perceived in leaves, which initiate long-distance signaling that induces flowering at the shoot apex. The identity of the long-distance signal has yet to be determined. In Arabidopsis, activation of FLOWERING LOCUS T (FT) transcription in leaf vascular tissue (phloem) induces flowering. We found that FT messenger RNA is required only transiently in the leaf. In addition, FT fusion proteins expressed specifically in phloem cells move to the apex and move long distances between grafted plants. Finally, we provide evidence that FT does not activate an intermediate messenger in leaves. We conclude that FT protein acts as a long-distance signal that induces Arabidopsis flowering.
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Affiliation(s)
- Laurent Corbesier
- Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, D-50829 Cologne, Germany
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23
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Corbesier L, Vincent C, Jang S, Fornara F, Fan Q, Searle I, Giakountis A, Farrona S, Gissot L, Turnbull C, Coupland G. FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science 2007; 316:1030-3. [PMID: 17446353 DOI: 10.1126/science.1141752] [Citation(s) in RCA: 1254] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
In plants, seasonal changes in day length are perceived in leaves, which initiate long-distance signaling that induces flowering at the shoot apex. The identity of the long-distance signal has yet to be determined. In Arabidopsis, activation of FLOWERING LOCUS T (FT) transcription in leaf vascular tissue (phloem) induces flowering. We found that FT messenger RNA is required only transiently in the leaf. In addition, FT fusion proteins expressed specifically in phloem cells move to the apex and move long distances between grafted plants. Finally, we provide evidence that FT does not activate an intermediate messenger in leaves. We conclude that FT protein acts as a long-distance signal that induces Arabidopsis flowering.
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Affiliation(s)
- Laurent Corbesier
- Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, D-50829 Cologne, Germany
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24
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Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, Buisine N, Gagnot S, Martienssen RA, Coupland G, Colot V. Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet 2007; 3:e86. [PMID: 17542647 PMCID: PMC1885283 DOI: 10.1371/journal.pgen.0030086] [Citation(s) in RCA: 437] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 04/17/2007] [Indexed: 01/13/2023] Open
Abstract
TERMINAL FLOWER 2/LIKE HETEROCHROMATIN PROTEIN 1 (TFL2/LHP1) is the only Arabidopsis protein with overall sequence similarity to the HETEROCHROMATIN PROTEIN 1 (HP1) family of metazoans and S. pombe. TFL2/LHP1 represses transcription of numerous genes, including the flowering-time genes FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC), as well as the floral organ identity genes AGAMOUS (AG) and APETALA 3 (AP3). These genes are also regulated by proteins of the Polycomb repressive complex 2 (PRC2), and it has been proposed that TFL2/LHP1 represents a potential stabilizing factor of PRC2 activity. Here we show by chromatin immunoprecipitation and hybridization to an Arabidopsis Chromosome 4 tiling array (ChIP-chip) that TFL2/LHP1 associates with hundreds of small domains, almost all of which correspond to genes located within euchromatin. We investigated the chromatin marks to which TFL2/LHP1 binds and show that, in vitro, TFL2/LHP1 binds to histone H3 di- or tri-methylated at lysine 9 (H3K9me2 or H3K9me3), the marks recognized by HP1, and to histone H3 trimethylated at lysine 27 (H3K27me3), the mark deposited by PRC2. However, in vivo TFL2/LHP1 association with chromatin occurs almost exclusively and co-extensively with domains marked by H3K27me3, but not H3K9me2 or -3. Moreover, the distribution of H3K27me3 is unaffected in lhp1 mutant plants, indicating that unlike PRC2 components, TFL2/LHP1 is not involved in the deposition of this mark. Rather, our data suggest that TFL2/LHP1 recognizes specifically H3K27me3 in vivo as part of a mechanism that represses the expression of many genes targeted by PRC2. Stable repression of gene expression is an important aspect of the developmental programs of higher organisms. In plants and animals, DNA is organized within chromatin, which contains at its core a set of evolutionarily conserved proteins called histones. These proteins can be modified for example by methylation or acetylation of lysines or phosphorylation of serines. Specific combinations of these histone modifications are interpreted by other chromatin proteins and thereby play essential roles in gene regulation. One such potential effector of the histone code in the flowering plant Arabidopsis is TERMINAL FLOWER 2/LIKE HETEROCHROMATIN PROTEIN 1 (TFL2/LHP1). Here we present highly detailed “epigenomic” maps that establish that TFL2/LHP1 associates with a subset of Arabidopsis genes that are marked by tri-methylation of Lysine 27 of histone H3. In plants and animals, an evolutionarily conserved complex called PRC2 deposits this mark. In Drosophila and mammals this modified histone is then read by another complex, called PRC1, to maintain the stable repression of genes. In Arabidopsis however, no PRC1 complex exists, and our results provide evidence that TFL2/LHP1 may fulfill a related function.
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Affiliation(s)
- Franziska Turck
- Abteilung Entwicklungsbiologie der Pflanzen, Max Planck Institut für Züchtungsforschung, Cologne, Germany
| | - François Roudier
- Unité de Recherche en Génomique Végétale, CNRS UMR8114, INRA UMR1165, Université d'Evry Val d'Essonne, Evry, France
| | - Sara Farrona
- Abteilung Entwicklungsbiologie der Pflanzen, Max Planck Institut für Züchtungsforschung, Cologne, Germany
| | - Marie-Laure Martin-Magniette
- Unité de Recherche en Génomique Végétale, CNRS UMR8114, INRA UMR1165, Université d'Evry Val d'Essonne, Evry, France
- Mathématiques et Informatiques Appliquées, AgroParisTech, INRA UMR518, Paris, France
| | - Elodie Guillaume
- Unité de Recherche en Génomique Végétale, CNRS UMR8114, INRA UMR1165, Université d'Evry Val d'Essonne, Evry, France
| | - Nicolas Buisine
- Unité de Recherche en Génomique Végétale, CNRS UMR8114, INRA UMR1165, Université d'Evry Val d'Essonne, Evry, France
| | - Séverine Gagnot
- Unité de Recherche en Génomique Végétale, CNRS UMR8114, INRA UMR1165, Université d'Evry Val d'Essonne, Evry, France
| | - Robert A Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - George Coupland
- Abteilung Entwicklungsbiologie der Pflanzen, Max Planck Institut für Züchtungsforschung, Cologne, Germany
- * To whom correspondence should be addressed. E-mail: (GC); (VC)
| | - Vincent Colot
- Unité de Recherche en Génomique Végétale, CNRS UMR8114, INRA UMR1165, Université d'Evry Val d'Essonne, Evry, France
- * To whom correspondence should be addressed. E-mail: (GC); (VC)
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Hurtado L, Farrona S, Reyes JC. The putative SWI/SNF complex subunit BRAHMA activates flower homeotic genes in Arabidopsis thaliana. Plant Mol Biol 2006; 62:291-304. [PMID: 16845477 DOI: 10.1007/s11103-006-9021-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Accepted: 05/16/2006] [Indexed: 05/04/2023]
Abstract
Arabidopsis thaliana BRAHMA (BRM, also called AtBRM) is a SNF2 family protein homolog of Brahma, the ATPase of the Drosophila SWI/SNF complex involved in chromatin remodeling during transcription. Here we show that, in contrast to its Drosophila counterpart, BRM is not an essential gene. Thus, homozygous BRM loss of function mutants are viable but exhibit numerous defects including dwarfism, altered leaf and root development and several reproduction defects. The analysis of the progeny of self-fertilized heterozygous brm plants and reciprocal crosses between heterozygous and wild type plants indicated that disruption of BRM reduced both male and female gametophyte transmission. This was consistent with the presence of aborted ovules in the self-fertilized heterozygous flowers that contained arrested embryos predominantly at the two terminal cells stage. Furthermore, brm homozygous mutants were completely sterile. Flowers of brm loss-of-function mutants have several developmental abnormalities, including homeotic transformations in the second and third floral whorls. In accordance with these results, brm mutants present reduced levels of APETALA2, APETALA3, PISTILLATA and NAC-LIKE, ACTIVATED BY AP3/PI. We have previously shown that BRM strongly interacts with AtSWI3C. Now we extend our interaction studies demonstrating that BRM interacts weakly with AtSWI3B but not with AtSWI3A or AtSWI3D. In agreement with these results, the phenotype described in this study for brm plants is very similar to that previously described for the AtSWI3C mutant plants, suggesting that both proteins participate in the same genetic pathway or form a molecular complex.
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Affiliation(s)
- Lidia Hurtado
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, Av. Américo Vespucio 49, E-41092 Sevilla, Spain
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26
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Abstract
Chromatin remodeling is essential for the reprogramming of transcription associated with development and cell differentiation. The SWI/SNF complex was the first chromatin remodeling complex characterized in yeast and Drosophila. In this work we have characterized an Arabidopsis thaliana homolog of Brahma, the ATPase of the Drosophila SWI/SNF complex. As its Drosophila counterpart, Arabidopsis thaliana BRAHMA (AtBRM) is a nuclear protein present in a high molecular mass complex. Furthermore, the N terminus of AtBRM interacts, in the two-hybrid system, with CHB4 (AtSWI3C), an Arabidopsis homolog of the yeast SWI/SNF complex subunit SWI3. The AtBRM gene is primarily expressed in meristems, organ primordia and tissues with active cell division. Silencing of the expression of the AtBRM gene by RNA interference demonstrated that AtBRM is required for vegetative and reproductive development. The AtBRM silenced plants exhibited a reduction in overall plant size with small and curled leafs, as well as a reduction in the size of the inflorescence meristem. In the absence of AtBRM, Arabidopsis flowers have small petals and stamens, immature anthers, homeotic transformations and reduced fertility. The AtBRM silenced plants flower earlier than wild-type plants both under inductive and non-inductive photoperiods. Furthermore, levels of CO, FT and SOC1 transcripts were up-regulated under non-inductive conditions suggesting that AtBRM is a repressor of the photoperiod-dependent flowering pathway.
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Affiliation(s)
- Sara Farrona
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Américo Vespucio s/n, E-41092 Sevilla, Spain
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27
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Abstract
Chromatin remodeling is essential for the reprogramming of transcription associated with development and cell differentiation. The SWI/SNF complex was the first chromatin remodeling complex characterized in yeast and Drosophila. In this work we have characterized an Arabidopsis thaliana homolog of Brahma, the ATPase of the Drosophila SWI/SNF complex. As its Drosophila counterpart, Arabidopsis thaliana BRAHMA (AtBRM) is a nuclear protein present in a high molecular mass complex. Furthermore, the N terminus of AtBRM interacts, in the two-hybrid system, with CHB4 (AtSWI3C), an Arabidopsis homolog of the yeast SWI/SNF complex subunit SWI3. The AtBRM gene is primarily expressed in meristems, organ primordia and tissues with active cell division. Silencing of the expression of the AtBRM gene by RNA interference demonstrated that AtBRM is required for vegetative and reproductive development. The AtBRM silenced plants exhibited a reduction in overall plant size with small and curled leafs, as well as a reduction in the size of the inflorescence meristem. In the absence of AtBRM, Arabidopsis flowers have small petals and stamens, immature anthers, homeotic transformations and reduced fertility. The AtBRM silenced plants flower earlier than wild-type plants both under inductive and non-inductive photoperiods. Furthermore, levels of CO, FT and SOC1 transcripts were up-regulated under non-inductive conditions suggesting that AtBRM is a repressor of the photoperiod-dependent flowering pathway.
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Affiliation(s)
- Sara Farrona
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Américo Vespucio s/n, E-41092 Sevilla, Spain
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