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Dupouy G, Dong Y, Herzog E, Chabouté ME, Berr A. Nuclear envelope dynamics in connection to chromatin remodeling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:963-981. [PMID: 37067011 DOI: 10.1111/tpj.16246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/29/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
The nucleus is a central organelle of eukaryotic cells undergoing dynamic structural changes during cellular fundamental processes such as proliferation and differentiation. These changes rely on the integration of developmental and stress signals at the nuclear envelope (NE), orchestrating responses at the nucleo-cytoplasmic interface for efficient genomic functions such as DNA transcription, replication and repair. While in animals, correlation has already been established between NE dynamics and chromatin remodeling using last-generation tools and cutting-edge technologies, this topic is just emerging in plants, especially in response to mechanical cues. This review summarizes recent data obtained in this field with more emphasis on the mechanical stress response. It also highlights similarities/differences between animal and plant cells at multiples scales, from the structural organization of the nucleo-cytoplasmic continuum to the functional impacts of NE dynamics.
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Affiliation(s)
- Gilles Dupouy
- Institut de Biologie Moléculaire des Plantes du CNRS- Université de Strasbourg, 12 rue du Général Zimmer,, F-67084, Strasbourg, France
| | - Yihan Dong
- Institut de Biologie Moléculaire des Plantes du CNRS- Université de Strasbourg, 12 rue du Général Zimmer,, F-67084, Strasbourg, France
| | - Etienne Herzog
- Institut de Biologie Moléculaire des Plantes du CNRS- Université de Strasbourg, 12 rue du Général Zimmer,, F-67084, Strasbourg, France
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes du CNRS- Université de Strasbourg, 12 rue du Général Zimmer,, F-67084, Strasbourg, France
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes du CNRS- Université de Strasbourg, 12 rue du Général Zimmer,, F-67084, Strasbourg, France
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2
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Seem K, Kaur S, Kumar S, Mohapatra T. Epigenome editing for targeted DNA (de)methylation: a new perspective in modulating gene expression. Crit Rev Biochem Mol Biol 2024; 59:69-98. [PMID: 38440883 DOI: 10.1080/10409238.2024.2320659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024]
Abstract
Traditionally, it has been believed that inheritance is driven as phenotypic variations resulting from changes in DNA sequence. However, this paradigm has been challenged and redefined in the contemporary era of epigenetics. The changes in DNA methylation, histone modification, non-coding RNA biogenesis, and chromatin remodeling play crucial roles in genomic functions and regulation of gene expression. More importantly, some of these changes are inherited to the next generations as a part of epigenetic memory and play significant roles in gene expression. The sum total of all changes in DNA bases, histone proteins, and ncRNA biogenesis constitutes the epigenome. Continuous progress in deciphering epigenetic regulations and the existence of heritable epigenetic/epiallelic variations associated with trait of interest enables to deploy epigenome editing tools to modulate gene expression. DNA methylation marks can be utilized in epigenome editing for the manipulation of gene expression. Initially, genome/epigenome editing technologies relied on zinc-finger protein or transcriptional activator-like effector protein. However, the discovery of clustered regulatory interspaced short palindromic repeats CRISPR)/deadCRISPR-associated protein 9 (dCas9) enabled epigenome editing to be more specific/efficient for targeted DNA (de)methylation. One of the major concerns has been the off-target effects, wherein epigenome editing may unintentionally modify gene/regulatory element which may cause unintended change/harmful effects. Moreover, epigenome editing of germline cell raises several ethical/safety issues. This review focuses on the recent developments in epigenome editing tools/techniques, technological limitations, and future perspectives of this emerging technology in therapeutics for human diseases as well as plant improvement to achieve sustainable developmental goals.
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Affiliation(s)
- Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
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3
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Abdulraheem MI, Xiong Y, Moshood AY, Cadenas-Pliego G, Zhang H, Hu J. Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications. PLANTS (BASEL, SWITZERLAND) 2024; 13:163. [PMID: 38256717 PMCID: PMC10820249 DOI: 10.3390/plants13020163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
Plant stress is a significant challenge that affects the development, growth, and productivity of plants and causes an adverse environmental condition that disrupts normal physiological processes and hampers plant survival. Epigenetic regulation is a crucial mechanism for plants to respond and adapt to stress. Several studies have investigated the role of DNA methylation (DM), non-coding RNAs, and histone modifications in plant stress responses. However, there are various limitations or challenges in translating the research findings into practical applications. Hence, this review delves into the recent recovery, implications, and applications of epigenetic regulation in response to plant stress. To better understand plant epigenetic regulation under stress, we reviewed recent studies published in the last 5-10 years that made significant contributions, and we analyzed the novel techniques and technologies that have advanced the field, such as next-generation sequencing and genome-wide profiling of epigenetic modifications. We emphasized the breakthrough findings that have uncovered specific genes or pathways and the potential implications of understanding plant epigenetic regulation in response to stress for agriculture, crop improvement, and environmental sustainability. Finally, we concluded that plant epigenetic regulation in response to stress holds immense significance in agriculture, and understanding its mechanisms in stress tolerance can revolutionize crop breeding and genetic engineering strategies, leading to the evolution of stress-tolerant crops and ensuring sustainable food production in the face of climate change and other environmental challenges. Future research in this field will continue to unveil the intricacies of epigenetic regulation and its potential applications in crop improvement.
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Affiliation(s)
- Mukhtar Iderawumi Abdulraheem
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Yani Xiong
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Abiodun Yusuff Moshood
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Gregorio Cadenas-Pliego
- Centro de Investigación en Química Aplicada, Blvd. Enrique Reyna 140, Saltillo 25294, Mexico;
| | - Hao Zhang
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
| | - Jiandong Hu
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
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4
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Tourdot E, Mauxion JP, Gonzalez N, Chevalier C. Endoreduplication in plant organogenesis: a means to boost fruit growth. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6269-6284. [PMID: 37343125 DOI: 10.1093/jxb/erad235] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
Endoreduplication is the major source of somatic endopolyploidy in higher plants, and leads to variation in cell ploidy levels due to iterative rounds of DNA synthesis in the absence of mitosis. Despite its ubiquitous occurrence in many plant organs, tissues, and cells, the physiological meaning of endoreduplication is not fully understood, although several roles during plant development have been proposed, mostly related to cell growth, differentiation, and specialization via transcriptional and metabolic reprogramming. Here, we review recent advances in our knowledge of the molecular mechanisms and cellular characteristics of endoreduplicated cells, and provide an overview of the multi-scale effects of endoreduplication on supporting growth in plant development. In addition, the effects of endoreduplication in fruit development are discussed, since it is highly prominent during fruit organogenesis where it acts as a morphogenetic factor supporting rapid fruit growth, as illustrated by case of the model fleshy fruit, tomato (Solanum lycopersicum).
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Affiliation(s)
- Edouard Tourdot
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Jean-Philippe Mauxion
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Nathalie Gonzalez
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Christian Chevalier
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
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5
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Gallusci P, Agius DR, Moschou PN, Dobránszki J, Kaiserli E, Martinelli F. Deep inside the epigenetic memories of stressed plants. TRENDS IN PLANT SCIENCE 2023; 28:142-153. [PMID: 36404175 DOI: 10.1016/j.tplants.2022.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Recent evidence sheds light on the peculiar type of plant intelligence. Plants have developed complex molecular networks that allow them to remember, choose, and make decisions depending on the stress stimulus, although they lack a nervous system. Being sessile, plants can exploit these networks to optimize their resources cost-effectively and maximize their fitness in response to multiple environmental stresses. Even more interesting is the capability to transmit this experience to the next generation(s) through epigenetic modifications that add to the classical genetic inheritance. In this opinion article, we present concepts and perspectives regarding the capabilities of plants to sense, perceive, remember, re-elaborate, respond, and to some extent transmit to their progeny information to adapt more efficiently to climate change.
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Affiliation(s)
- Philippe Gallusci
- Ecophysiologie et Génomique Fonctionnelle de la Vigne (EGFV), University of Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d'Ornon, France
| | - Dolores R Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta; Ġ.F. Abela Junior College, Ġuzè Debono Square, Msida, Malta
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden; Department of Biology, University of Crete, Heraklion, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Judit Dobránszki
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, Hungary
| | - Eirini Kaiserli
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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6
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Johann to Berens P, Schivre G, Theune M, Peter J, Sall SO, Mutterer J, Barneche F, Bourbousse C, Molinier J. Advanced Image Analysis Methods for Automated Segmentation of Subnuclear Chromatin Domains. EPIGENOMES 2022; 6:epigenomes6040034. [PMID: 36278680 PMCID: PMC9624336 DOI: 10.3390/epigenomes6040034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/19/2022] [Accepted: 10/01/2022] [Indexed: 11/07/2022] Open
Abstract
The combination of ever-increasing microscopy resolution with cytogenetical tools allows for detailed analyses of nuclear functional partitioning. However, the need for reliable qualitative and quantitative methodologies to detect and interpret chromatin sub-nuclear organization dynamics is crucial to decipher the underlying molecular processes. Having access to properly automated tools for accurate and fast recognition of complex nuclear structures remains an important issue. Cognitive biases associated with human-based curation or decisions for object segmentation tend to introduce variability and noise into image analysis. Here, we report the development of two complementary segmentation methods, one semi-automated (iCRAQ) and one based on deep learning (Nucl.Eye.D), and their evaluation using a collection of A. thaliana nuclei with contrasted or poorly defined chromatin compartmentalization. Both methods allow for fast, robust and sensitive detection as well as for quantification of subtle nucleus features. Based on these developments, we highlight advantages of semi-automated and deep learning-based analyses applied to plant cytogenetics.
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Affiliation(s)
| | - Geoffrey Schivre
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Inserm, Université PSL, 75230 Paris, France
- Université Paris-Saclay, 91190 Orsay, France
| | - Marius Theune
- FB 10 / Molekulare Pflanzenphysiologie, Bioenergetik in Photoautotrophen, Universität Kassel, 34127 Kassel, Germany
| | - Jackson Peter
- Institut de Biologie Moléculaire des Plantes du CNRS, 67000 Strasbourg, France
| | | | - Jérôme Mutterer
- Institut de Biologie Moléculaire des Plantes du CNRS, 67000 Strasbourg, France
| | - Fredy Barneche
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Inserm, Université PSL, 75230 Paris, France
| | - Clara Bourbousse
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Inserm, Université PSL, 75230 Paris, France
- Correspondence: (C.B.); (J.M.)
| | - Jean Molinier
- Institut de Biologie Moléculaire des Plantes du CNRS, 67000 Strasbourg, France
- Correspondence: (C.B.); (J.M.)
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7
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Transcriptome Analysis and Intraspecific Variation in Spanish Fir ( Abies pinsapo Boiss.). Int J Mol Sci 2022; 23:ijms23169351. [PMID: 36012612 PMCID: PMC9409315 DOI: 10.3390/ijms23169351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/10/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Spanish fir (Abies pinsapo Boiss.) is an endemic, endangered tree that has been scarcely investigated at the molecular level. In this work, the transcriptome of Spanish fir was assembled, providing a large catalog of expressed genes (22,769), within which a high proportion were full-length transcripts (12,545). This resource is valuable for functional genomics studies and genome annotation in this relict conifer species. Two intraspecific variations of A. pinsapo can be found within its largest population at the Sierra de las Nieves National Park: one with standard green needles and another with bluish-green needles. To elucidate the causes of both phenotypes, we studied different physiological and molecular markers and transcriptome profiles in the needles. "Green" trees showed higher electron transport efficiency and enhanced levels of chlorophyll, protein, and total nitrogen in the needles. In contrast, needles from "bluish" trees exhibited higher contents of carotenoids and cellulose. These results agreed with the differential transcriptomic profiles, suggesting an imbalance in the nitrogen status of "bluish" trees. Additionally, gene expression analyses suggested that these differences could be associated with different epigenomic profiles. Taken together, the reported data provide new transcriptome resources and a better understanding of the natural variation in this tree species, which can help improve guidelines for its conservation and the implementation of adaptive management strategies under climatic change.
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Pasternak T, Kircher S, Pérez-Pérez JM, Palme K. A simple pipeline for cell cycle kinetic studies in the root apical meristem. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4683-4695. [PMID: 35312781 DOI: 10.1093/jxb/erac123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Root system architecture ultimately depends on precise signaling between different cells and tissues in the root apical meristem (RAM) and integration with environmental cues. This study describes a simple pipeline to simultaneously determine cellular parameters, nucleus geometry, and cell cycle kinetics in the RAM. The method uses marker-free techniques for nucleus and cell boundary detection, and 5-ethynyl-2'-deoxyuridine (EdU) staining for DNA replication quantification. Based on this approach, we characterized differences in cell volume, nucleus volume, and nucleus shape across different domains of the Arabidopsis RAM. We found that DNA replication patterns were cell layer and region dependent. G2 phase duration, which varied from 3.5 h in the pericycle to more than 4.5 h in the epidermis, was found to be associated with some features of nucleus geometry. Endocycle duration was determined as the time required to achieve 100% EdU-positive cells in the elongation zone and, as such, it was estimated to be in the region of 5 h for the epidermis and cortex. This experimental pipeline could be used to precisely map cell cycle duration in the RAM of mutants and in response to environmental stress in several plant species without the need for introgressing molecular cell cycle markers.
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Affiliation(s)
- Taras Pasternak
- Faculty for Biology, Institute of Biology II/Molecular Plant Physiology, Germany
- Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - Stefan Kircher
- Faculty for Biology, Institute of Biology II/Molecular Plant Physiology, Germany
| | | | - Klaus Palme
- Faculty for Biology, Institute of Biology II/Molecular Plant Physiology, Germany
- Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, China
- ScreenSYS GmbH, Engesserstr. 4, 79108 Freiburg, Germany
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9
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A review on CRISPR/Cas-based epigenetic regulation in plants. Int J Biol Macromol 2022; 219:1261-1271. [DOI: 10.1016/j.ijbiomac.2022.08.182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/13/2022] [Accepted: 08/29/2022] [Indexed: 01/09/2023]
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10
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Yang F, Pecinka A. Multiple Roles of SMC5/6 Complex during Plant Sexual Reproduction. Int J Mol Sci 2022; 23:ijms23094503. [PMID: 35562893 PMCID: PMC9099584 DOI: 10.3390/ijms23094503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 12/01/2022] Open
Abstract
Chromatin-based processes are essential for cellular functions. Structural maintenance of chromosomes (SMCs) are evolutionarily conserved molecular machines that organize chromosomes throughout the cell cycle, mediate chromosome compaction, promote DNA repair, or control sister chromatid attachment. The SMC5/6 complex is known for its pivotal role during the maintenance of genome stability. However, a dozen recent plant studies expanded the repertoire of SMC5/6 complex functions to the entire plant sexual reproductive phase. The SMC5/6 complex is essential in meiosis, where its activity must be precisely regulated to allow for normal meiocyte development. Initially, it is attenuated by the recombinase RAD51 to allow for efficient strand invasion by the meiosis-specific recombinase DMC1. At later stages, it is essential for the normal ratio of interfering and non-interfering crossovers, detoxifying aberrant joint molecules, preventing chromosome fragmentation, and ensuring normal chromosome/sister chromatid segregation. The latter meiotic defects lead to the production of diploid male gametes in Arabidopsis SMC5/6 complex mutants, increased seed abortion, and production of triploid offspring. The SMC5/6 complex is directly involved in controlling normal embryo and endosperm cell divisions, and pioneer studies show that the SMC5/6 complex is also important for seed development and normal plant growth in cereals.
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Affiliation(s)
- Fen Yang
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany (IEB), Czech Academy of Sciences, 77900 Olomouc, Czech Republic;
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, 77900 Olomouc, Czech Republic
| | - Ales Pecinka
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany (IEB), Czech Academy of Sciences, 77900 Olomouc, Czech Republic;
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, 77900 Olomouc, Czech Republic
- Correspondence:
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11
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Tatout C, Mougeot G, Parry G, Baroux C, Pradillo M, Evans D. The INDEPTH (Impact of Nuclear Domains on Gene Expression and Plant Traits) Academy: a community resource for plant science. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1926-1933. [PMID: 35090020 PMCID: PMC8982392 DOI: 10.1093/jxb/erac005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
This Community Resource paper introduces the range of materials developed by the INDEPTH (Impact of Nuclear Domains on Gene Expression and Plant Traits) COST Action made available through the INDEPTH Academy. Recent rapid growth in understanding of the significance of epigenetic controls in plant and crop science has led to a need for shared, high-quality resources, standardization of protocols, and repositories for open access data. The INDEPTH Academy provides a range of masterclass tutorials, standardized protocols, and teaching webinars, together with a rapidly developing repository to support imaging and spatial analysis of the nucleus and deep learning for automated analysis. These resources were developed partly as a response to the COVID-19 pandemic, but also driven by needs and opportunities identified by the INDEPTH community of ~200 researchers in 80 laboratories from 32 countries. This community report outlines the resources produced and how they will be extended beyond the INDEPTH project, but also aims to encourage the wider community to engage with epigenetics and nuclear structure by accessing these resources.
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Affiliation(s)
- Christophe Tatout
- Université Clermont Auvergne, CNRS, INSERM, GReD Clermont-Ferrand, France
| | - Guillaume Mougeot
- Université Clermont Auvergne, CNRS, INSERM, GReD Clermont-Ferrand, France
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Geraint Parry
- GARNet, Department of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
- Arabidopsis Events UK, 13 Mayhurst Ave, Woking GU22 8DE, UK
| | - Célia Baroux
- Zürich-Basel Plant Science Center, Department for Plant and Microbial Biology, University of Zürich, Switzerland
| | - Mónica Pradillo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - David Evans
- Department of Biological and Molecular Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
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12
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Kuo P, Darbyshire A, Lambing C. Super-resolution Chromatin Visualization Using a Combined Method of Fluorescence In Situ Hybridization and Structured Illumination Microscopy in Solanum lycopersicum. Methods Mol Biol 2022; 2484:85-92. [PMID: 35461446 DOI: 10.1007/978-1-0716-2253-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chromatin organization influences gene and transposon expression, and regulates various cellular processes. Higher order chromatin structure has been widely studied using genomic approaches and microscopy image analyses. Chromosome conformation capture and sequencing the junction of DNA fragments enables the study of both chromatin interaction and chromosome folding. However, certain cell types are embedded in other cell types which complicate the process of studying them using high-throughput genomic approaches. To overcome this limitation, high-resolution microscopy techniques are now available to investigate chromatin organization in single cells. In this chapter, we provide a detailed protocol to prepare chromosome spreading from tomato nuclei, to label genomic loci by fluorescence in situ hybridization, and to visualize these locations at high resolution with Structured Illumination microscopy.
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Affiliation(s)
- Pallas Kuo
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
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13
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Lenykó-Thegze A, Fábián A, Mihók E, Makai D, Cseh A, Sepsi A. Pericentromeric chromatin reorganisation follows the initiation of recombination and coincides with early events of synapsis in cereals. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1585-1602. [PMID: 34171148 DOI: 10.1111/tpj.15391] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/04/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
The reciprocal exchange of genetic information between homologous chromosomes during meiotic recombination is essential to secure balanced chromosome segregation and to promote genetic diversity. The chromosomal position and frequency of reciprocal genetic exchange shapes the efficiency of breeding programmes and influences crop improvement under a changing climate. In large genome cereals, such as wheat and barley, crossovers are consistently restricted to subtelomeric chromosomal regions, thus preventing favourable allele combinations being formed within a considerable proportion of the genome, including interstitial and pericentromeric chromatin. Understanding the key elements driving crossover designation is therefore essential to broaden the regions available for crossovers. Here, we followed early meiotic chromatin dynamism in cereals through the visualisation of a homologous barley chromosome arm pair stably transferred into the wheat genetic background. By capturing the dynamics of a single chromosome arm at the same time as detecting the undergoing events of meiotic recombination and synapsis, we showed that subtelomeric chromatin of homologues synchronously transitions to an open chromatin structure during recombination initiation. By contrast, pericentromeric and interstitial regions preserved their closed chromatin organisation and become unpackaged only later, concomitant with initiation of recombinatorial repair and the initial assembly of the synaptonemal complex. Our results raise the possibility that the closed pericentromeric chromatin structure in cereals may influence the fate decision during recombination initiation, as well as the spatial development of synapsis, and may also explain the suppression of crossover events in the proximity of the centromeres.
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Affiliation(s)
- Andrea Lenykó-Thegze
- Department of Biological Resources, Eötvös Loránd Research Network, Centre for Agricultural Research, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Attila Fábián
- Department of Biological Resources, Eötvös Loránd Research Network, Centre for Agricultural Research, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Edit Mihók
- Department of Biological Resources, Eötvös Loránd Research Network, Centre for Agricultural Research, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Diána Makai
- Department of Biological Resources, Eötvös Loránd Research Network, Centre for Agricultural Research, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - András Cseh
- Department of Molecular Breeding, Eötvös Loránd Research Network, Centre for Agricultural Research, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Adél Sepsi
- Department of Biological Resources, Eötvös Loránd Research Network, Centre for Agricultural Research, Brunszvik u. 2, Martonvásár, 2462, Hungary
- Department of Applied Biotechnology and Food Science (ABÉT), BME, Budapest University of Technology and Economics, Műegyetem rkp. 3-9, Budapest, 1111, Hungary
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14
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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 2021; 10:766. [PMID: 34439998 PMCID: PMC8389687 DOI: 10.3390/biology10080766] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [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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15
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Giudice G, Moffa L, Varotto S, Cardone MF, Bergamini C, De Lorenzis G, Velasco R, Nerva L, Chitarra W. Novel and emerging biotechnological crop protection approaches. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1495-1510. [PMID: 33945200 PMCID: PMC8384607 DOI: 10.1111/pbi.13605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/01/2021] [Accepted: 04/13/2021] [Indexed: 05/05/2023]
Abstract
Traditional breeding or genetically modified organisms (GMOs) have for a long time been the sole approaches to effectively cope with biotic and abiotic stresses and implement the quality traits of crops. However, emerging diseases as well as unpredictable climate changes affecting agriculture over the entire globe force scientists to find alternative solutions required to quickly overcome seasonal crises. In this review, we first focus on cisgenesis and genome editing as challenging biotechnological approaches for breeding crops more tolerant to biotic and abiotic stresses. In addition, we take into consideration a toolbox of new techniques based on applications of RNA interference and epigenome modifications, which can be adopted for improving plant resilience. Recent advances in these biotechnological applications are mainly reported for non-model plants and woody crops in particular. Indeed, the characterization of RNAi machinery in plants is fundamental to transform available information into biologically or biotechnologically applicable knowledge. Finally, here we discuss how these innovative and environmentally friendly techniques combined with traditional breeding can sustain a modern agriculture and be of potential contribution to climate change mitigation.
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Affiliation(s)
- Gaetano Giudice
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
- Department of Agricultural and Environmental Sciences ‐ Production, Landscape, Agroenergy (DiSAA)University of MilanoMilanoItaly
| | - Loredana Moffa
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A)University of UdineUdineItaly
| | - Serena Varotto
- Department of Agronomy Animals Food Natural Resources and Environment (DAFNAE)University of PadovaLegnaroPDItaly
| | - Maria Francesca Cardone
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)TuriBAItaly
| | - Carlo Bergamini
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)TuriBAItaly
| | - Gabriella De Lorenzis
- Department of Agricultural and Environmental Sciences ‐ Production, Landscape, Agroenergy (DiSAA)University of MilanoMilanoItaly
| | - Riccardo Velasco
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
| | - Luca Nerva
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)TorinoItaly
| | - Walter Chitarra
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)ConeglianoTVItaly
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)TorinoItaly
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16
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Dalakouras A, Vlachostergios D. Epigenetic approaches to crop breeding: current status and perspectives. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5356-5371. [PMID: 34017985 DOI: 10.1093/jxb/erab227] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/18/2021] [Indexed: 05/10/2023]
Abstract
In order to tackle the cumulative adverse effects of global climate change, reduced farmland, and heightened needs of an ever-increasing world population, modern agriculture is in urgent search of solutions that can ensure world food security and sustainable development. Classical crop breeding is still a powerful method to obtain crops with valued agronomical traits, but its potential is gradually being compromised by the menacing decline of genetic variation. Resorting to the epigenome as a source of variation could serve as a promising alternative. Here, we discuss current status of epigenetics-mediated crop breeding (epibreeding), highlight its advances and limitations, outline currently available methodologies, and propose novel RNA-based strategies to modify the epigenome in a gene-specific and transgene-free manner.
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Affiliation(s)
- Athanasios Dalakouras
- Institute of Industrial and Forage Crops, HAO-DEMETER, 41335 Larissa, Greece
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, 57001 Thessaloniki, Greece
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17
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Evans DE, Mermet S, Tatout C. Advancing knowledge of the plant nuclear periphery and its application for crop science. Nucleus 2021; 11:347-363. [PMID: 33295233 PMCID: PMC7746251 DOI: 10.1080/19491034.2020.1838697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In this review, we explore recent advances in knowledge of the structure and dynamics of the plant nuclear envelope. As a paradigm, we focused our attention on the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex, a structurally conserved bridging complex comprising SUN domain proteins in the inner nuclear membrane and KASH domain proteins in the outer nuclear membrane. Studies have revealed that this bridging complex has multiple functions with structural roles in positioning the nucleus within the cell, conveying signals across the membrane and organizing chromatin in the 3D nuclear space with impact on gene transcription. We also provide an up-to-date survey in nuclear dynamics research achieved so far in the model plant Arabidopsis thaliana that highlights its potential impact on several key plant functions such as growth, seed maturation and germination, reproduction and response to biotic and abiotic stress. Finally, we bring evidences that most of the constituents of the LINC Complex and associated components are, with some specificities, conserved in monocot and dicot crop species and are displaying very similar functions to those described for Arabidopsis. This leads us to suggest that a better knowledge of this system and a better account of its potential applications will in the future enhance the resilience and productivity of crop plants.
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Affiliation(s)
- David E Evans
- Department of Biological and Medical Sciences, Oxford Brookes University , Oxford, UK
| | - Sarah Mermet
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France
| | - Christophe Tatout
- GReD, CNRS, INSERM, Université Clermont Auvergne , Clermont-Ferrand, France
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18
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Markus C, Pecinka A, Merotto A. Insights into the Role of Transcriptional Gene Silencing in Response to Herbicide-Treatments in Arabidopsis thaliana. Int J Mol Sci 2021; 22:3314. [PMID: 33804990 PMCID: PMC8037345 DOI: 10.3390/ijms22073314] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 11/24/2022] Open
Abstract
Herbicide resistance is broadly recognized as the adaptive evolution of weed populations to the intense selection pressure imposed by the herbicide applications. Here, we tested whether transcriptional gene silencing (TGS) and RNA-directed DNA Methylation (RdDM) pathways modulate resistance to commonly applied herbicides. Using Arabidopsis thaliana wild-type plants exposed to sublethal doses of glyphosate, imazethapyr, and 2,4-D, we found a partial loss of TGS and increased susceptibility to herbicides in six out of 11 tested TGS/RdDM mutants. Mutation in REPRESSOR OF SILENCING 1 (ROS1), that plays an important role in DNA demethylation, leading to strongly increased susceptibility to all applied herbicides, and imazethapyr in particular. Transcriptomic analysis of the imazethapyr-treated wild type and ros1 plants revealed a relation of the herbicide upregulated genes to chemical stimulus, secondary metabolism, stress condition, flavonoid biosynthesis, and epigenetic processes. Hypersensitivity to imazethapyr of the flavonoid biosynthesis component TRANSPARENT TESTA 4 (TT4) mutant plants strongly suggests that ROS1-dependent accumulation of flavonoids is an important mechanism for herbicide stress response in A. thaliana. In summary, our study shows that herbicide treatment affects transcriptional gene silencing pathways and that misregulation of these pathways makes Arabidopsis plants more sensitive to herbicide treatment.
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Affiliation(s)
- Catarine Markus
- Department of Crop Science, Federal University of Rio Grande do Sul, Porto Alegre, RS 91540-000, Brazil;
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Institute of Experimental Botany, Czech Academy Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - Aldo Merotto
- Department of Crop Science, Federal University of Rio Grande do Sul, Porto Alegre, RS 91540-000, Brazil;
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19
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Kumar S, Mohapatra T. Dynamics of DNA Methylation and Its Functions in Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2021; 12:596236. [PMID: 34093600 PMCID: PMC8175986 DOI: 10.3389/fpls.2021.596236] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 04/19/2021] [Indexed: 05/20/2023]
Abstract
Epigenetic modifications in DNA bases and histone proteins play important roles in the regulation of gene expression and genome stability. Chemical modification of DNA base (e.g., addition of a methyl group at the fifth carbon of cytosine residue) switches on/off the gene expression during developmental process and environmental stresses. The dynamics of DNA base methylation depends mainly on the activities of the writer/eraser guided by non-coding RNA (ncRNA) and regulated by the developmental/environmental cues. De novo DNA methylation and active demethylation activities control the methylation level and regulate the gene expression. Identification of ncRNA involved in de novo DNA methylation, increased DNA methylation proteins guiding DNA demethylase, and methylation monitoring sequence that helps maintaining a balance between DNA methylation and demethylation is the recent developments that may resolve some of the enigmas. Such discoveries provide a better understanding of the dynamics/functions of DNA base methylation and epigenetic regulation of growth, development, and stress tolerance in crop plants. Identification of epigenetic pathways in animals, their existence/orthologs in plants, and functional validation might improve future strategies for epigenome editing toward climate-resilient, sustainable agriculture in this era of global climate change. The present review discusses the dynamics of DNA methylation (cytosine/adenine) in plants, its functions in regulating gene expression under abiotic/biotic stresses, developmental processes, and genome stability.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Suresh Kumar, ; , orcid.org/0000-0002-7127-3079
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20
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Castillo AM, Valero-Rubira I, Burrell MÁ, Allué S, Costar MA, Vallés MP. Trichostatin A Affects Developmental Reprogramming of Bread Wheat Microspores towards an Embryogenic Route. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1442. [PMID: 33114625 PMCID: PMC7693754 DOI: 10.3390/plants9111442] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/17/2020] [Accepted: 10/21/2020] [Indexed: 12/24/2022]
Abstract
Microspores can be developmentally reprogrammed by the application of different stress treatments to initiate an embryogenic pathway leading to the production of doubled haploid (DH) plants. Epigenetic modifications are involved in cell reprogramming and totipotency in response to stress. To increase microspore embryogenesis (ME) efficiency in bread wheat, the effect of the histone deacetylase inhibitor trichostatin A (TSA) has been examined in two cultivars of wheat with different microspore embryogenesis response. Diverse strategies were assayed using 0-0.4 µM TSA as a single induction treatment and after or simultaneously with cold or mannitol stresses. The highest efficiency was achieved when 0.4 µM TSA was applied to anthers for 5 days simultaneously with a 0.7 M mannitol treatment, producing a four times greater number of green DH plants than mannitol. Ultrastructural studies by transmission electron microscopy indicated that mannitol with TSA and mannitol treatments induced similar morphological changes in early stages of microspore reprogramming, although TSA increased the number of microspores with 'star-like' morphology and symmetric divisions. The effect of TSA on the transcript level of four ME marker genes indicated that the early signaling pathways in ME, involving the TaTDP1 and TAA1b genes, may be mediated by changes in acetylation patterns of histones and/or other proteins.
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Affiliation(s)
- Ana María Castillo
- Departamento de Genética y Producción Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Avda Montañana 1005, 50059 Zaragoza, Spain; (A.M.C.); (I.V.-R.); (S.A.); (M.A.C.)
| | - Isabel Valero-Rubira
- Departamento de Genética y Producción Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Avda Montañana 1005, 50059 Zaragoza, Spain; (A.M.C.); (I.V.-R.); (S.A.); (M.A.C.)
| | - María Ángela Burrell
- Departamento de Patología, Anatomía y Fisiología, Facultad de Ciencias, Universidad de Navarra, C/Irrunlarrea s/n, 31008 Pamplona, Spain;
| | - Sandra Allué
- Departamento de Genética y Producción Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Avda Montañana 1005, 50059 Zaragoza, Spain; (A.M.C.); (I.V.-R.); (S.A.); (M.A.C.)
| | - María Asunción Costar
- Departamento de Genética y Producción Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Avda Montañana 1005, 50059 Zaragoza, Spain; (A.M.C.); (I.V.-R.); (S.A.); (M.A.C.)
| | - María Pilar Vallés
- Departamento de Genética y Producción Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Avda Montañana 1005, 50059 Zaragoza, Spain; (A.M.C.); (I.V.-R.); (S.A.); (M.A.C.)
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21
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Hummel G, Berr A, Graindorge S, Cognat V, Ubrig E, Pflieger D, Molinier J, Drouard L. Epigenetic silencing of clustered tRNA genes in Arabidopsis. Nucleic Acids Res 2020; 48:10297-10312. [PMID: 32941623 PMCID: PMC7544208 DOI: 10.1093/nar/gkaa766] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/21/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
Beyond their key role in translation, cytosolic transfer RNAs (tRNAs) are involved in a wide range of other biological processes. Nuclear tRNA genes (tDNAs) are transcribed by the RNA polymerase III (RNAP III) and cis-elements, trans-factors as well as genomic features are known to influence their expression. In Arabidopsis, besides a predominant population of dispersed tDNAs spread along the 5 chromosomes, some clustered tDNAs have been identified. Here, we demonstrate that these tDNA clusters are transcriptionally silent and that pathways involved in the maintenance of DNA methylation play a predominant role in their repression. Moreover, we show that clustered tDNAs exhibit repressive chromatin features whilst their dispersed counterparts contain permissive euchromatic marks. This work demonstrates that both genomic and epigenomic contexts are key players in the regulation of tDNAs transcription. The conservation of most of these regulatory processes suggests that this pioneering work in Arabidopsis can provide new insights into the regulation of RNA Pol III transcription in other organisms, including vertebrates.
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Affiliation(s)
- Guillaume Hummel
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Alexandre Berr
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Stéfanie Graindorge
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Valérie Cognat
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Elodie Ubrig
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - David Pflieger
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Jean Molinier
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Laurence Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
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22
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Parry G, Pradillo M, Probst AV, Tatout C. Untangling chromatin interactions. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5115-5118. [PMID: 32803270 DOI: 10.1093/jxb/eraa334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Geraint Parry
- GARNet, School of Biosciences, Cardiff University, Cardiff, UK
| | | | - Aline V Probst
- Université Clermont Auvergne, CNRS, Inserm, GReD, Clermont-Ferrand, France
| | - Christophe Tatout
- Université Clermont Auvergne, CNRS, Inserm, GReD, Clermont-Ferrand, France
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23
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Varotto S, Tani E, Abraham E, Krugman T, Kapazoglou A, Melzer R, Radanović A, Miladinović D. Epigenetics: possible applications in climate-smart crop breeding. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5223-5236. [PMID: 32279074 PMCID: PMC7475248 DOI: 10.1093/jxb/eraa188] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/09/2020] [Indexed: 05/23/2023]
Abstract
To better adapt transiently or lastingly to stimuli from the surrounding environment, the chromatin states in plant cells vary to allow the cells to fine-tune their transcriptional profiles. Modifications of chromatin states involve a wide range of post-transcriptional histone modifications, histone variants, DNA methylation, and activity of non-coding RNAs, which can epigenetically determine specific transcriptional outputs. Recent advances in the area of '-omics' of major crops have facilitated identification of epigenetic marks and their effect on plant response to environmental stresses. As most epigenetic mechanisms are known from studies in model plants, we summarize in this review recent epigenetic studies that may be important for improvement of crop adaptation and resilience to environmental changes, ultimately leading to the generation of stable climate-smart crops. This has paved the way for exploitation of epigenetic variation in crop breeding.
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Affiliation(s)
- Serena Varotto
- Department of Agronomy, Food, Natural Resources, Animals, and the Environment, University of Padova, Agripolis, Viale dell’Università, Padova, Italy
| | - Eleni Tani
- Department of Crop Science, Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, Athens, Greece
| | - Eleni Abraham
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Demeter (HAO-Demeter), Lykovrysi, Greece
| | - Rainer Melzer
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin, Ireland
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