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Wójcikowska B, Chwiałkowska K, Nowak K, Citerne S, Morończyk J, Wójcik AM, Kiwior-Wesołowska A, Francikowski J, Kwaśniewski M, Gaj MD. Transcriptomic profiling reveals histone acetylation-regulated genes involved in somatic embryogenesis in Arabidopsis thaliana. BMC Genomics 2024; 25:788. [PMID: 39148037 PMCID: PMC11325840 DOI: 10.1186/s12864-024-10623-5] [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] [Received: 01/18/2024] [Accepted: 07/15/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) exemplifies the unique developmental plasticity of plant cells. The regulatory processes, including epigenetic modifications controlling embryogenic reprogramming of cell transcriptome, have just started to be revealed. RESULTS To identify the genes of histone acetylation-regulated expression in SE, we analyzed global transcriptomes of Arabidopsis explants undergoing embryogenic induction in response to treatment with histone deacetylase inhibitor, trichostatin A (TSA). The TSA-induced and auxin (2,4-dichlorophenoxyacetic acid; 2,4-D)-induced transcriptomes were compared. RNA-seq results revealed the similarities of the TSA- and auxin-induced transcriptomic responses that involve extensive deregulation, mostly repression, of the majority of genes. Within the differentially expressed genes (DEGs), we identified the master regulators (transcription factors - TFs) of SE, genes involved in biosynthesis, signaling, and polar transport of auxin and NITRILASE-encoding genes of the function in indole-3-acetic acid (IAA) biosynthesis. TSA-upregulated TF genes of essential functions in auxin-induced SE, included LEC1/LEC2, FUS3, AGL15, MYB118, PHB, PHV, PLTs, and WUS/WOXs. The TSA-induced transcriptome revealed also extensive upregulation of stress-related genes, including those related to stress hormone biosynthesis. In line with transcriptomic data, TSA-induced explants accumulated salicylic acid (SA) and abscisic acid (ABA), suggesting the role of histone acetylation (Hac) in regulating stress hormone-related responses during SE induction. Since mostly the adaxial side of cotyledon explant contributes to SE induction, we also identified organ polarity-related genes responding to TSA treatment, including AIL7/PLT7, RGE1, LBD18, 40, HB32, CBF1, and ULT2. Analysis of the relevant mutants supported the role of polarity-related genes in SE induction. CONCLUSION The study results provide a step forward in deciphering the epigenetic network controlling embryogenic transition in somatic cells of plants.
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Affiliation(s)
- Barbara Wójcikowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland.
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Katarzyna Nowak
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Sylvie Citerne
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Joanna Morończyk
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Anna Maria Wójcik
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Agnieszka Kiwior-Wesołowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Jacek Francikowski
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Mirosław Kwaśniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Małgorzata Danuta Gaj
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
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Go D, Lu B, Alizadeh M, Gazzarrini S, Song L. Voice from both sides: a molecular dialogue between transcriptional activators and repressors in seed-to-seedling transition and crop adaptation. FRONTIERS IN PLANT SCIENCE 2024; 15:1416216. [PMID: 39166233 PMCID: PMC11333834 DOI: 10.3389/fpls.2024.1416216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/20/2024] [Indexed: 08/22/2024]
Abstract
High-quality seeds provide valuable nutrients to human society and ensure successful seedling establishment. During maturation, seeds accumulate storage compounds that are required to sustain seedling growth during germination. This review focuses on the epigenetic repression of the embryonic and seed maturation programs in seedlings. We begin with an extensive overview of mutants affecting these processes, illustrating the roles of core proteins and accessory components in the epigenetic machinery by comparing mutants at both phenotypic and molecular levels. We highlight how omics assays help uncover target-specific functional specialization and coordination among various epigenetic mechanisms. Furthermore, we provide an in-depth discussion on the Seed dormancy 4 (Sdr4) transcriptional corepressor family, comparing and contrasting their regulation of seed germination in the dicotyledonous species Arabidopsis and two monocotyledonous crops, rice and wheat. Finally, we compare the similarities in the activation and repression of the embryonic and seed maturation programs through a shared set of cis-regulatory elements and discuss the challenges in applying knowledge largely gained in model species to crops.
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Affiliation(s)
- Dongeun Go
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Bailan Lu
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Milad Alizadeh
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Sonia Gazzarrini
- Department of Biological Science, University of Toronto Scarborough, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Liang Song
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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Singh VK, Ahmed S, Saini DK, Gahlaut V, Chauhan S, Khandare K, Kumar A, Sharma PK, Kumar J. Manipulating epigenetic diversity in crop plants: Techniques, challenges and opportunities. Biochim Biophys Acta Gen Subj 2024; 1868:130544. [PMID: 38104668 DOI: 10.1016/j.bbagen.2023.130544] [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: 09/18/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Epigenetic modifications act as conductors of inheritable alterations in gene expression, all while keeping the DNA sequence intact, thereby playing a pivotal role in shaping plant growth and development. This review article presents an overview of techniques employed to investigate and manipulate epigenetic diversity in crop plants, focusing on both naturally occurring and artificially induced epialleles. The significance of epigenetic modifications in facilitating adaptive responses is explored through the examination of how various biotic and abiotic stresses impact them. Further, environmental chemicals are explored for their role in inducing epigenetic changes, particularly focusing on inhibitors of DNA methylation like 5-AzaC and zebularine, as well as inhibitors of histone deacetylation including trichostatin A and sodium butyrate. The review delves into various approaches for generating epialleles, including tissue culture techniques, mutagenesis, and grafting, elucidating their potential to induce heritable epigenetic modifications in plants. In addition, the ground breaking CRISPR/Cas is emphasized for its accuracy in targeting specific epigenetic changes. This presents a potent tools for deciphering the intricacies of epigenetic mechanisms. Furthermore, the intricate relationship between epigenetic modifications and non-coding RNA expression, including siRNAs and miRNAs, is investigated. The emerging role of exo-RNAi in epigenetic regulation is also introduced, unveiling its promising potential for future applications. The article concludes by addressing the opportunities and challenges presented by these techniques, emphasizing their implications for crop improvement. Conclusively, this extensive review provides valuable insights into the intricate realm of epigenetic changes, illuminating their significance in phenotypic plasticity and their potential in advancing crop improvement.
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Affiliation(s)
| | - Shoeb Ahmed
- Ch. Charan Singh University, Meerut 250004, India
| | - Dinesh Kumar Saini
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Vijay Gahlaut
- University Centre for Research and Development, Chandigarh University, Mohali 140413, Punjab, India
| | | | - Kiran Khandare
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Ashutosh Kumar
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Pradeep Kumar Sharma
- Ch. Charan Singh University, Meerut 250004, India; Maharaja Suhel Dev State University, Azamgarh 276404, U.P., India
| | - Jitendra Kumar
- National Agri-Food Biotechnology Institute, Sector-81, Mohali 140306, Punjab, India.
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Nowak K, Wójcikowska B, Gajecka M, Elżbieciak A, Morończyk J, Wójcik AM, Żemła P, Citerne S, Kiwior-Wesołowska A, Zbieszczyk J, Gaj MD. The improvement of the in vitro plant regeneration in barley with the epigenetic modifier of histone acetylation, trichostatin A. J Appl Genet 2024; 65:13-30. [PMID: 37962803 PMCID: PMC10789698 DOI: 10.1007/s13353-023-00800-9] [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] [Received: 08/15/2023] [Revised: 10/16/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023]
Abstract
Genotype-limited plant regeneration is one of the main obstacles to the broader use of genetic transformation in barley breeding. Thus, developing new approaches that might improve responses of in vitro recalcitrant genotypes remains at the center of barley biotechnology. Here, we analyzed different barley genotypes, including "Golden Promise," a genotype commonly used in the genetic transformation, and four malting barley cultivars of poor regenerative potential. The expression of hormone-related transcription factor (TF) genes with documented roles in plant regeneration was analyzed in genotypes with various plant-regenerating capacities. The results indicated differential expression of auxin-related TF genes between the barley genotypes in both the explants and the derived cultures. In support of the role of auxin in barley regeneration, distinct differences in the accumulation of free and oxidized auxin were observed in explants and explant-derived callus cultures of barley genotypes. Following the assumption that modifying gene expression might improve plant regeneration in barley, we treated the barley explants with trichostatin A (TSA), which affects histone acetylation. The effects of TSA were genotype-dependent as TSA treatment improved plant regeneration in two barley cultivars. TSA-induced changes in plant regeneration were associated with the increased expression of auxin biosynthesis-involved TFs. The study demonstrated that explant treatment with chromatin modifiers such as TSA might provide a new and effective epigenetic approach to improving plant regeneration in recalcitrant barley genotypes.
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Affiliation(s)
- Katarzyna Nowak
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland.
| | - Barbara Wójcikowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
| | - Monika Gajecka
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
| | - Anna Elżbieciak
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
| | - Joanna Morończyk
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
| | - Anna M Wójcik
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
| | - Przemysław Żemła
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
- Toxicology Research Group, Łukasiewicz Research Network, Institute of Industrial Organic Chemistry Branch Pszczyna, Doświadczalna 27, 43-200, Pszczyna, Poland
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Agnieszka Kiwior-Wesołowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
| | - Justyna Zbieszczyk
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
| | - Małgorzata D Gaj
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
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Pagano A, Gomes C, Timmerman E, Sulima P, Przyborowski JA, Kruszka D, Impens F, Paiva JAP. Revealing the transitory and local effect of zebularine on development and on proteome dynamics of Salix purpurea. FRONTIERS IN PLANT SCIENCE 2024; 14:1304327. [PMID: 38298602 PMCID: PMC10827895 DOI: 10.3389/fpls.2023.1304327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/19/2023] [Indexed: 02/02/2024]
Abstract
Introduction DNA methylation plays major roles in the epigenetic regulation of gene expression, transposon and transcriptional silencing, and DNA repair, with implications in developmental processes and phenotypic plasticity. Relevantly for woody species, DNA methylation constitutes a regulative layer in cell wall dynamics associated with xylogenesis. The use of methyltransferase and/or demethylase inhibitors has been proven informative to shed light on the methylome dynamics behind the regulation of these processes. Methods The present work employs the cytidine analog zebularine to inhibit DNA methyltransferases and induce DNA hypomethylation in Salix purpurea plantlets grown in vitro and in soil. An integrative approach was adopted to highlight the effects of zebularine on proteomic dynamics, revealing age-specific (3 weeks of in vitro culture and 1 month of growth in soil) and tissue-specific (stem and root) effects. Results and discussion After 3 weeks of recovery from zebularine treatment, a decrease of 5-mC levels was observed in different genomic contexts in the roots of explants that were exposed to zebularine, whereas a functionally heterogeneous subset of protein entries was differentially accumulated in stem samples, including entries related to cell wall biosynthesis, tissue morphogenesis, and hormonal regulation. Significant proteomic remodeling was revealed in the development from in vitro to in-soil culture, but no significant changes in 5-mC levels were observed. The identification of tissue-specific proteomic hallmarks in combination with hypomethylating agents provides new insights into the role of DNA methylation and proteome in early plant development in willow species. Proteomic data are available via ProteomeXchange with identifier PXD045653. WGBS data are available under BioProject accession PRJNA889596.
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Affiliation(s)
- Andrea Pagano
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Carolina Gomes
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Evy Timmerman
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Paweł Sulima
- Department of Genetics, Plant Breeding and Bioresource Engineering, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Jerzy Andrzej Przyborowski
- Department of Genetics, Plant Breeding and Bioresource Engineering, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Dariusz Kruszka
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Jorge Almiro Pinto Paiva
- Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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Lepri A, Longo C, Messore A, Kazmi H, Madia VN, Di Santo R, Costi R, Vittorioso P. Plants and Small Molecules: An Up-and-Coming Synergy. PLANTS (BASEL, SWITZERLAND) 2023; 12:1729. [PMID: 37111951 PMCID: PMC10145415 DOI: 10.3390/plants12081729] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 06/19/2023]
Abstract
The emergence of Arabidopsis thaliana as a model system has led to a rapid and wide improvement in molecular genetics techniques for studying gene function and regulation. However, there are still several drawbacks that cannot be easily solved with molecular genetic approaches, such as the study of unfriendly species, which are of increasing agronomic interest but are not easily transformed, thus are not prone to many molecular techniques. Chemical genetics represents a methodology able to fill this gap. Chemical genetics lies between chemistry and biology and relies on small molecules to phenocopy genetic mutations addressing specific targets. Advances in recent decades have greatly improved both target specificity and activity, expanding the application of this approach to any biological process. As for classical genetics, chemical genetics also proceeds with a forward or reverse approach depending on the nature of the study. In this review, we addressed this topic in the study of plant photomorphogenesis, stress responses and epigenetic processes. We have dealt with some cases of repurposing compounds whose activity has been previously proven in human cells and, conversely, studies where plants have been a tool for the characterization of small molecules. In addition, we delved into the chemical synthesis and improvement of some of the compounds described.
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Affiliation(s)
- A. Lepri
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - C. Longo
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - A. Messore
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - H. Kazmi
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - V. N. Madia
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - R. Di Santo
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - R. Costi
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - P. Vittorioso
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
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Liang Y, Heyman J, Lu R, De Veylder L. Evolution of wound-activated regeneration pathways in the plant kingdom. Eur J Cell Biol 2023; 102:151291. [PMID: 36709604 DOI: 10.1016/j.ejcb.2023.151291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Regeneration serves as a self-protective mechanism that allows a tissue or organ to recover its entire form and function after suffering damage. However, the regenerative capacity varies greatly within the plant kingdom. Primitive plants frequently display an amazing regenerative ability as they have developed a complex system and strategy for long-term survival under extreme stress conditions. The regenerative ability of dicot species is highly variable, but that of monocots often exhibits extreme recalcitrance to tissue replenishment. Recent studies have revealed key factors and signals that affect cell fate during plant regeneration, some of which are conserved among the plant lineage. Among these, several members of the ETHYLENE RESPONSE FACTOR (ERF) transcription factors have been implicated in wound signaling, playing crucial roles in the regenerative mechanisms after different types of wounding. An understanding of plant regeneration may ultimately lead to an increased regenerative potential of recalcitrant species, producing more high-yielding, multi-resistant and environmentally friendly crops and ensuring the long-term development of global agriculture.
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Affiliation(s)
- Yuanke Liang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Ran Lu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium.
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Lodhi N, Singh M, Srivastava R, Sawant SV, Tuli R. Epigenetic malleability at core promoter initiates tobacco PR-1a expression post salicylic acid treatment. Mol Biol Rep 2023; 50:417-431. [PMID: 36335522 DOI: 10.1007/s11033-022-08074-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Tobacco's PR-1a gene is induced by pathogen attack or exogenous application of salicylic acid (SA). Nucleosome mapping and chromatin immunoprecipitation assay were used to delineate the histone modifications on the PR-1a promoter. However, the epigenetic modifications of the inducible promoter of the PR-1a gene are not fully understood yet. METHODS AND RESULTS Southern approach was used to scan the promoter of PR-1a to identify presence of nucleosomes, ChIP assays were performed using anti-histones antibodies of repressive chromatin by di- methylated at H3K9 and H4K20 or active chromatin by acetylated H3K9/14 and H4K16 to find epigenetic malleability of nucleosome over core promoter in uninduced or induced state post SA treatment. Class I and II mammalian histone deacetylase (HDAC) inhibitor TSA treatment was used to enhance the expression of PR-1a by facilitating the histone acetylation post SA treatment. Here, we report correlated consequences of the epigenetic modifications correspond to disassembly of the nucleosome (spans from - 102 to + 55 bp, masks TATA and transcription initiation) and repressor complex from core promoter, eventually initiates the transcription of PR-1a gene post SA treatment. While active chromatin marks di and trimethylation of H3K4, acetylation of H3K9 and H4K16 are increased which are associated to the transcription initiation of PR-1a following SA treatment. However, in uninduced state constitutive expression of a negative regulator (SNI1) of AtPR1, suppresses AtPR1 expression by six-fold in Arabidopsis thaliana. Further, we report 50-to-1000-fold increased expression of AtPR1 in uninduced lsd1 mutant plants, up to threefold increased expression of AtPR1 in uninduced histone acetyl transferases (HATs) mutant plants, SNI1 dependent negative regulation of AtPR1, all together our results suggest that inactive state of PR-1a is indeed maintained by a repressive complex. CONCLUSION The study aimed to reveal the mechanism of transcription initiation of tobacco PR-1a gene in presence or absence of SA. This is the first study that reports nucleosome and repressor complex over core promoter region maintains the inactivation of gene in uninduced state, and upon induction disassembling of both initiates the downstream gene activation process.
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Affiliation(s)
- Niraj Lodhi
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226001, India. .,Mirna Analytics, New York, NY, 19047, USA.
| | - Mala Singh
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226001, India
| | - Rakesh Srivastava
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226001, India
| | - Samir V Sawant
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226001, India
| | - Rakesh Tuli
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow, 226001, India.,University Institute of Engineering & Technology (UIET), Sector 25, Panjab University, Chandigarh, 160014, India
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Stochastic Variation in DNA Methylation Modulates Nucleosome Occupancy and Alternative Splicing in Arabidopsis thaliana. PLANTS 2022; 11:plants11091105. [PMID: 35567106 PMCID: PMC9101026 DOI: 10.3390/plants11091105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 11/17/2022]
Abstract
Plants use complex gene regulatory mechanisms to overcome diverse environmental challenges. For instance, cold stress induces rapid and massive transcriptome changes via alternative splicing (AS) to confer cold tolerance in plants. In mammals, mounting evidence suggests chromatin structure can regulate co-transcriptional AS. Recent evidence also supports co-transcriptional regulation of AS in plants, but how dynamic changes in DNA methylation and the chromatin structure influence the AS process upon cold stress remains poorly understood. In this study, we used the DNA methylation inhibitor 5-Aza-2′-Deoxycytidine (5-aza-dC) to investigate the role of stochastic variations in DNA methylation and nucleosome occupancy in modulating cold-induced AS, in Arabidopsis thaliana (Arabidopsis). Our results demonstrate that 5-aza-dC derived stochastic hypomethylation modulates nucleosome occupancy and AS profiles of genes implicated in RNA metabolism, plant hormone signal transduction, and of cold-related genes in response to cold stress. We also demonstrate that cold-induced remodelling of DNA methylation regulates genes involved in amino acid metabolism. Collectively, we demonstrate that sudden changes in DNA methylation via drug treatment can influence nucleosome occupancy levels and modulate AS in a temperature-dependent manner to regulate plant metabolism and physiological stress adaptation.
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10
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Bačovský V, Čegan R, Tihlaříková E, Neděla V, Hudzieczek V, Smrža L, Janíček T, Beneš V, Hobza R. Chemical genetics in Silene latifolia elucidate regulatory pathways involved in gynoecium development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2354-2368. [PMID: 35045170 DOI: 10.1093/jxb/erab538] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Dioecious plants possess diverse sex determination systems and unique mechanisms of reproductive organ development; however, little is known about how sex-linked genes shape the expression of regulatory cascades that lead to developmental differences between sexes. In Silene latifolia, a dioecious plant with stable dimorphism in floral traits, early experiments suggested that female-regulator genes act on the factors that determine the boundaries of the flower whorls. To identify these regulators, we sequenced the transcriptome of male flowers with fully developed gynoecia, induced by rapid demethylation in the parental generation. Eight candidates were found to have a positive role in gynoecium promotion, floral organ size, and whorl boundary, and affect the expression of class B MADS-box flower genes. To complement our transcriptome analysis, we closely examined the floral organs in their native state using field emission environmental scanning electron microscopy, and examined the differences between females and androhermaphrodites in their placenta and ovule organization. Our results reveal the regulatory pathways potentially involved in sex-specific flower development in the classical model of dioecy, S. latifolia. These pathways include previously hypothesized and unknown female-regulator genes that act on the factors that determine the flower boundaries, and a negative regulator of anther development, SUPERMAN-like (SlSUP).
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Affiliation(s)
- Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Radim Čegan
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Eva Tihlaříková
- Environmental Electron Microscopy Group, Institute of Scientific Instruments of the Czech Academy of Sciences, Kralovopolska 147, 612 64 Brno, Czech Republic
| | - Vilém Neděla
- Environmental Electron Microscopy Group, Institute of Scientific Instruments of the Czech Academy of Sciences, Kralovopolska 147, 612 64 Brno, Czech Republic
| | - Vojtěch Hudzieczek
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Lubomír Smrža
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Tomáš Janíček
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Vladimír Beneš
- EMBL Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, D-69117 Heidelberg, Germany
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
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11
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Hirai R, Wang S, Demura T, Ohtani M. Histone Deacetylation Controls Xylem Vessel Cell Differentiation via Transcriptional Regulation of a Transcription Repressor Complex OFP1/4-MYB75-KNAT7-BLH6. FRONTIERS IN PLANT SCIENCE 2022; 12:825810. [PMID: 35154217 PMCID: PMC8829346 DOI: 10.3389/fpls.2021.825810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Xylem vessels are indispensable tissues in vascular plants that transport water and minerals. The differentiation of xylem vessel cells is characterized by secondary cell wall deposition and programmed cell death. These processes are initiated by a specific set of transcription factors, called VASCULAR-RELATED NAC-DOMAIN (VND) family proteins, through the direct and/or indirectly induction of genes required for secondary cell wall deposition and programmed cell death. In this study, we explored novel regulatory factors for xylem vessel cell differentiation in Arabidopsis thaliana. We tested the effects of cellular stress inducers on VND7-induced differentiation of xylem vessel cells with the VND7-VP16-GR system, in which VND7 activity is post-translationally induced by dexamethasone application. We established that the histone deacetylase (HDAC) inhibitors trichostatin A (TSA) and sirtinol inhibited VND7-induced xylem vessel cell differentiation. The inhibitory effects of TSA and sirtinol treatment were detected only when they were added at the same time as the dexamethasone application, suggesting that TSA and sirtinol mainly influence the early stages of xylem vessel cell differentiation. Expression analysis revealed that these HDAC inhibitors downregulated VND7-downstream genes, including both direct and indirect targets of transcriptional activation. Notably, the HDAC inhibitors upregulated the transcript levels of negative regulators of xylem vessel cells, OVATE FAMILY PROTEIN1 (OFP1), OFP4, and MYB75, which are known to form a protein complex with BEL1-LIKE HOMEODOMAIN6 (BLH6) to repress gene transcription. The KDB system, another in vitro induction system of ectopic xylem vessel cells, demonstrated that TSA and sirtinol also inhibited ectopic formation of xylem vessel cells, and this inhibition was partially suppressed in knat7-1, bhl6-1, knat7-1 bhl6-1, and quintuple ofp1 ofp2 ofp3 ofp4 ofp5 mutants. Thus, the negative effects of HDAC inhibitors on xylem vessel cell differentiation are mediated, at least partly, by the abnormal upregulation of the transcriptional repressor complex OFP1/4-MYB75-KNAT7-BLH6. Collectively, our findings suggest that active regulation of histone deacetylation by HDACs is involved in xylem vessel cell differentiation via the OFP1/4-MYB75-KNAT7-BLH6 complex.
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Affiliation(s)
- Risaku Hirai
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shumin Wang
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Center for Digital Green-Innovation, Nara Institute of Science and Technology, Ikoma, Japan
| | - Misato Ohtani
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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12
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Yang J, Gu D, Wu S, Zhou X, Chen J, Liao Y, Zeng L, Yang Z. Feasible strategies for studying the involvement of DNA methylation and histone acetylation in the stress-induced formation of quality-related metabolites in tea (Camellia sinensis). HORTICULTURE RESEARCH 2021; 8:253. [PMID: 34848699 PMCID: PMC8632975 DOI: 10.1038/s41438-021-00679-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/19/2021] [Accepted: 08/17/2021] [Indexed: 05/26/2023]
Abstract
Tea plants are subjected to multiple stresses during growth, development, and postharvest processing, which affects levels of secondary metabolites in leaves and influences tea functional properties and quality. Most studies on secondary metabolism in tea have focused on gene, protein, and metabolite levels, whereas upstream regulatory mechanisms remain unclear. In this review, we exemplify DNA methylation and histone acetylation, summarize the important regulatory effects that epigenetic modifications have on plant secondary metabolism, and discuss feasible research strategies to elucidate the underlying specific epigenetic mechanisms of secondary metabolism regulation in tea. This information will help researchers investigate the epigenetic regulation of secondary metabolism in tea, providing key epigenetic data that can be used for future tea genetic breeding.
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Affiliation(s)
- Jie Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
| | - Dachuan Gu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
| | - Shuhua Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Xiaochen Zhou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Jiaming Chen
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Yinyin Liao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
| | - Lanting Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
| | - Ziyin Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China.
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13
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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: 23] [Impact Index Per Article: 7.7] [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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14
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Bie XM, Dong L, Li XH, Wang H, Gao XQ, Li XG. Trichostatin A and sodium butyrate promotes plant regeneration in common wheat. PLANT SIGNALING & BEHAVIOR 2020; 15:1820681. [PMID: 32962515 PMCID: PMC7671042 DOI: 10.1080/15592324.2020.1820681] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Histone acetylation modification plays a vital role in plant cell division and differentiation. However, the function on wheat mature embryo culture has not been reported. Here, we used the mature embryo of wheat genotypes including CB037, Fielder, and Chinese Spring (CS) as materials to analyze the effects of different concentrations of trichostatin A (TSA) and sodium butyrate (SB) on plant regeneration efficiency. The results showed that, compared with the control group, the induction rates of embryogenic callus and green shoot were significantly increased with the addition of 0.5 µM TSA, while they were reduced under treatment of 2.5 µM TSA on wheat mature embryo. With the respective addition of 200 µM and 1000 µM SB, regeneration frequency of three genotypes was enhanced, especially in Fielder, which reached significant difference compared with the control group. Unfortunately, 0.5 µM TSA and 200 µM SB combination had no apparent effect on wheat regeneration frequency. The results indicated that TSA and SB increase plant regeneration in common wheat. In addition, TSA had a common effect and SB had different effect among genotypes on wheat regeneration frequency. The mechanism of action needs further investigation.
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Affiliation(s)
- Xiao Min Bie
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai′an, Shandong, China
- CONTACT Xiao Min Bie
| | - Luhao Dong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai′an, Shandong, China
| | - Xiao Hui Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai′an, Shandong, China
| | - He Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai′an, Shandong, China
| | - Xi-Qi Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai′an, Shandong, China
| | - Xing Guo Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai′an, Shandong, China
- Xing Guo Li State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai′an, Shandong271018, China
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15
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Steadman CR, Banerjee S, Kunde YA, Sanders CK, Marrone BL, Twary SN. Inhibition of DNA Methylation in Picochlorum soloecismus Alters Algae Productivity. Front Genet 2020; 11:560444. [PMID: 33193644 PMCID: PMC7593850 DOI: 10.3389/fgene.2020.560444] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/03/2020] [Indexed: 12/28/2022] Open
Abstract
Eukaryotic organisms regulate the organization, structure, and accessibility of their genomes through chromatin remodeling that can be inherited as epigenetic modifications. These DNA and histone protein modifications are ultimately responsible for an organism's molecular adaptation to the environment, resulting in distinctive phenotypes. Epigenetic manipulation of algae holds yet untapped potential for the optimization of biofuel production and bioproduct formation; however, epigenetic machinery and modes-of-action have not been well characterized in algae. We sought to determine the extent to which the biofuel platform species Picochlorum soloecismus utilizes DNA methylation to regulate its genome. We found candidate genes with domains for DNA methylation in the P. soloecismus genome. Whole-genome bisulfite sequencing revealed DNA methylation in all three cytosine contexts (CpG, CHH, and CHG). While global DNA methylation is low overall (∼1.15%), it occurs in appreciable quantities (12.1%) in CpG dinucleotides in a bimodal distribution in all genomic contexts, though terminators contain the greatest number of CpG sites per kilobase. The P. soloecismus genome becomes hypomethylated during the growth cycle in response to nitrogen starvation. Algae cultures were treated daily across the growth cycle with 20 μM 5-aza-2'-deoxycytidine (5AZA) to inhibit propagation of DNA methylation in daughter cells. 5AZA treatment significantly increased optical density and forward and side scatter of cells across the growth cycle (16 days). This increase in cell size and complexity correlated with a significant increase (∼66%) in lipid accumulation. Site specific CpG DNA methylation was significantly altered with 5AZA treatment over the time course, though nitrogen starvation itself induced significant hypomethylation in CpG contexts. Genes involved in several biological processes, including fatty acid synthesis, had altered methylation ratios in response to 5AZA; we hypothesize that these changes are potentially responsible for the phenotype of early induction of carbon storage as lipids. This is the first report to utilize epigenetic manipulation strategies to alter algal physiology and phenotype. Collectively, these data suggest these strategies can be utilized to fine-tune metabolic responses, alter growth, and enhance environmental adaption of microalgae for desired outcomes.
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Affiliation(s)
- Christina R Steadman
- Los Alamos National Laboratory, Bioenergy and Biome Sciences, Los Alamos, NM, United States
| | - Shounak Banerjee
- Los Alamos National Laboratory, Bioenergy and Biome Sciences, Los Alamos, NM, United States
| | - Yuliya A Kunde
- Los Alamos National Laboratory, Bioenergy and Biome Sciences, Los Alamos, NM, United States
| | - Claire K Sanders
- Los Alamos National Laboratory, Bioenergy and Biome Sciences, Los Alamos, NM, United States
| | - Babetta L Marrone
- Los Alamos National Laboratory, Bioenergy and Biome Sciences, Los Alamos, NM, United States
| | - Scott N Twary
- Los Alamos National Laboratory, Bioenergy and Biome Sciences, Los Alamos, NM, United States
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16
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Lee MH, Lee J, Choi SH, Jie EY, Jeong JC, Kim CY, Kim SW. The Effect of Sodium Butyrate on Adventitious Shoot Formation Varies among the Plant Species and the Explant Types. Int J Mol Sci 2020; 21:E8451. [PMID: 33182800 PMCID: PMC7696800 DOI: 10.3390/ijms21228451] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/24/2022] Open
Abstract
Histone acetylation plays an important role in plant growth and development. Here, we investigated the effect of sodium butyrate (NaB), a histone deacetylase inhibitor, on adventitious shoot formation from protoplast-derived calli and cotyledon explants of tobacco (Nicotiana benthamiana) and tomato (Solanum lycopersicum). The frequency of adventitious shoot formation from protoplast-derived calli was higher in shoot induction medium (SIM) containing NaB than in the control. However, the frequency of adventitious shoot formation from cotyledon explants of tobacco under the 0.1 mM NaB treatment was similar to that in the control, but it decreased with increasing NaB concentration. Unlike in tobacco, NaB decreased adventitious shoot formation in tomato explants in a concentration-dependent manner, but it did not have any effect on adventitious shoot formation in calli. NaB inhibited or delayed the expression of D-type cyclin (CYCD3-1) and shoot-regeneration regulatory gene WUSCHEL (WUS) in cotyledon explants of tobacco and tomato. However, compared to that in control SIM, the expression of WUS was promoted more rapidly in tobacco calli cultured in NaB-containing SIM, but the expression of CYCD3-1 was inhibited. In conclusion, the effect of NaB on adventitious shoot formation and expression of CYCD3-1 and WUS genes depended on the plant species and whether the effects were tested on explants or protoplast-derived calli.
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Affiliation(s)
| | | | | | | | | | | | - Suk Weon Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Korea; (M.H.L.); (J.L.); (S.H.C.); (E.Y.J.); (J.C.J.); (C.Y.K.)
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17
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Pagano A, L'Andolina C, Sabatini ME, de Sousa Araújo S, Balestrazzi A, Macovei A. Sodium butyrate induces genotoxic stress in function of photoperiod variations and differentially modulates the expression of genes involved in chromatin modification and DNA repair in Petunia hybrida seedlings. PLANTA 2020; 251:102. [PMID: 32350684 DOI: 10.1007/s00425-020-03392-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Sodium butyrate applied to Petunia hybrida seeds under a long-day photoperiod has a negative impact (reduced seedling length, decreased production of photosynthetic pigments, and accumulation of DNA damage) on early seedling development, whereas its administration under dark/light conditions (complete dark conditions for 5 days followed by exposure to long-day photoperiod for 5 days) bypasses some of the adverse effects. Genotoxic stress impairs plant development. To circumvent DNA damage, plants activate DNA repair pathways in concert with chromatin dynamics. These are essential during seed germination and seedling establishment, and may be influenced by photoperiod variations. To assess this interplay, an experimental design was developed in Petunia hybrida, a relevant horticultural crop and model species. Seeds were treated with different doses of sodium butyrate (NaB, 1 mM and 5 mM) as a stress agent applied under different light/dark conditions throughout a time period of 10 days. Phenotypic (germination percentage and speed, seedling length, and photosynthetic pigments) and molecular (DNA damage and gene expression profiles) analyses were performed to monitor the response to the imposed conditions. Seed germination was not affected by the treatments. Seedling development was hampered by increasing NaB concentrations applied under a long-day photoperiod (L) as reflected by the decreased seedling length accompanied by increased DNA damage. When seedlings were grown under dark conditions for 5 days and then exposed to long-day photoperiod for the remaining 5 days (D/L), the damaging effects of NaB were circumvented. NaB exposure under L conditions resulted in enhanced expression of HAT/HDAC (HISTONE ACETYLTRANSFERASES/HISTONE DEACTEYLASES) genes along with repression of genes involved in DNA repair. Differently, under D/L conditions, the expression of DNA repair genes was increased by NaB treatment and this was associated with lower levels of DNA damage. The observed DNA damage and gene expression profiles suggest the involvement of chromatin modification- and DNA repair-associated pathways in response to NaB and dark/light exposure during seedling development.
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Affiliation(s)
- Andrea Pagano
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Corrado L'Andolina
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Maria Elisa Sabatini
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
- Viral Control of Cellular Pathways and Biology of Tumorigenesis Unit, European Institute of Oncology (IFOM-IEO), via Adamello 16, 20139, Milano, Italy
| | - Susana de Sousa Araújo
- Instituto de Tecnologia Química E Biológica António Xavier (ITQB-NOVA), Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Alma Balestrazzi
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy.
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18
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Nowicka A, Tokarz B, Zwyrtková J, Dvořák Tomaštíková E, Procházková K, Ercan U, Finke A, Rozhon W, Poppenberger B, Otmar M, Niezgodzki I, Krečmerová M, Schubert I, Pecinka A. Comparative analysis of epigenetic inhibitors reveals different degrees of interference with transcriptional gene silencing and induction of DNA damage. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:68-84. [PMID: 31733119 DOI: 10.1111/tpj.14612] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/25/2019] [Accepted: 10/29/2019] [Indexed: 06/10/2023]
Abstract
Repetitive DNA sequences and some genes are epigenetically repressed by transcriptional gene silencing (TGS). When genetic mutants are not available or problematic to use, TGS can be suppressed by chemical inhibitors. However, informed use of epigenetic inhibitors is partially hampered by the absence of any systematic comparison. In addition, there is emerging evidence that epigenetic inhibitors cause genomic instability, but the nature of this damage and its repair remain unclear. To bridge these gaps, we compared the effects of 5-azacytidine (AC), 2'-deoxy-5-azacytidine (DAC), zebularine and 3-deazaneplanocin A (DZNep) on TGS and DNA damage repair. The most effective inhibitor of TGS was DAC, followed by DZNep, zebularine and AC. We confirmed that all inhibitors induce DNA damage and suggest that this damage is repaired by multiple pathways with a critical role of homologous recombination and of the SMC5/6 complex. A strong positive link between the degree of cytidine analog-induced DNA demethylation and the amount of DNA damage suggests that DNA damage is an integral part of cytidine analog-induced DNA demethylation. This helps us to understand the function of DNA methylation in plants and opens the possibility of using epigenetic inhibitors in biotechnology.
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Affiliation(s)
- Anna Nowicka
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
- Max Planck Institute for Plant Breeding Research (MPIPZ), DE-50829, Cologne, Germany
- The Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Niezapominajek 21, PL-30 239, Krakow, Poland
| | - Barbara Tokarz
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
- Unit of Botany and Plant Physiology, Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Al. 29 Listopada 54, PL-31 425, Krakow, Poland
| | - Jana Zwyrtková
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
| | - Eva Dvořák Tomaštíková
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
| | - Klára Procházková
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
| | - Ugur Ercan
- Max Planck Institute for Plant Breeding Research (MPIPZ), DE-50829, Cologne, Germany
| | - Andreas Finke
- Max Planck Institute for Plant Breeding Research (MPIPZ), DE-50829, Cologne, Germany
| | - Wilfried Rozhon
- Biotechnology of Horticultural Crops, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Liesel-Beckmann-Straße 1, DE-85354, Freising, Germany
| | - Brigitte Poppenberger
- Biotechnology of Horticultural Crops, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Liesel-Beckmann-Straße 1, DE-85354, Freising, Germany
| | - Miroslav Otmar
- Institute of Organic Chemistry and Biochemistry, CZ-166 10, Praha 6, Czech Republic
| | - Igor Niezgodzki
- Biogeosystem Modelling Group, ING PAN - Institute of Geological Sciences Polish Academy of Sciences, Research Center in Krakow, Senacka 1, PL-31 002, Krakow, Poland
| | - Marcela Krečmerová
- Institute of Organic Chemistry and Biochemistry, CZ-166 10, Praha 6, Czech Republic
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, Stadt Seeland, DE-06466, Gatersleben, OT, Germany
| | - Ales Pecinka
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
- Max Planck Institute for Plant Breeding Research (MPIPZ), DE-50829, Cologne, Germany
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Experimental DNA Demethylation Associates with Changes in Growth and Gene Expression of Oak Tree Seedlings. G3-GENES GENOMES GENETICS 2020; 10:1019-1028. [PMID: 31941723 PMCID: PMC7056980 DOI: 10.1534/g3.119.400770] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Epigenetic modifications such as DNA methylation, where methyl groups are added to cytosine base pairs, have the potential to impact phenotypic variation and gene expression, and could influence plant response to changing environments. One way to test this impact is through the application of chemical demethylation agents, such as 5-Azacytidine, which inhibit DNA methylation and lead to a partial reduction in DNA methylation across the genome. In this study, we treated 5-month-old seedlings of the tree, Quercus lobata, with foliar application of 5-Azacytidine to test whether a reduction in genome-wide methylation would cause differential gene expression and change phenotypic development. First, we demonstrate that demethylation treatment led to 3–6% absolute reductions and 6.7–43.2% relative reductions in genome-wide methylation across CG, CHG, and CHH sequence contexts, with CHH showing the strongest relative reduction. Seedlings treated with 5-Azacytidine showed a substantial reduction in new growth, which was less than half that of control seedlings. We tested whether this result could be due to impact of the treatment on the soil microbiome and found minimal differences in the soil microbiome between two groups, although with limited sample size. We found no significant differences in leaf fluctuating asymmetry (i.e., deviations from bilateral symmetry), which has been found in other studies. Nonetheless, treated seedlings showed differential expression of a total of 23 genes. Overall, this study provides initial evidence that DNA methylation is involved in gene expression and phenotypic variation in seedlings and suggests that removal of DNA methylation affects plant development.
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Badia MB, Maurino VG, Pavlovic T, Arias CL, Pagani MA, Andreo CS, Saigo M, Drincovich MF, Gerrard Wheeler MC. Loss of function of Arabidopsis NADP-malic enzyme 1 results in enhanced tolerance to aluminum stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:653-665. [PMID: 31626366 DOI: 10.1111/tpj.14571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 09/10/2019] [Accepted: 09/19/2019] [Indexed: 05/29/2023]
Abstract
In acidic soils, aluminum (Al) toxicity is a significant limitation to crop production worldwide. Given its Al-binding capacity, malate allows internal as well as external detoxification strategies to cope with Al stress, but little is known about the metabolic processes involved in this response. Here, we analyzed the relevance of NADP-dependent malic enzyme (NADP-ME), which catalyzes the oxidative decarboxylation of malate, in Al tolerance. Plants lacking NADP-ME1 (nadp-me1) display reduced inhibition of root elongation along Al treatment compared with the wild type (wt). Moreover, wt roots exposed to Al show a drastic decrease in NADP-ME1 transcript levels. Although malate levels in seedlings and root exudates are similar in nadp-me1 and wt, a significant increase in intracellular malate is observed in roots of nadp-me1 after long exposure to Al. The nadp-me1 plants also show a lower H2 O2 content in root apices treated with Al and no inhibition of root elongation when exposed to glutamate, an amino acid implicated in Al signaling. Proteomic studies showed several differentially expressed proteins involved in signal transduction, primary metabolism and protection against biotic and other abiotic stimuli and redox processes in nadp-me1, which may participate directly or indirectly in Al tolerance. The results indicate that NADP-ME1 is involved in adjusting the malate levels in the root apex, and its loss results in an increased content of this organic acid. Furthermore, the results suggest that NADP-ME1 affects signaling processes, such as the generation of reactive oxygen species and those that involve glutamate, which could lead to inhibition of root growth.
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Affiliation(s)
- Mariana Beatriz Badia
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Verónica Graciela Maurino
- Institute of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich-Heine-Universität, Universitätsstrasse 1, 40225, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Tatiana Pavlovic
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Cintia Lucía Arias
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - María Ayelén Pagani
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Carlos Santiago Andreo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Mariana Saigo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - María Fabiana Drincovich
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Mariel Claudia Gerrard Wheeler
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
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21
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Agustí M, Mesejo C, Muñoz-Fambuena N, Vera-Sirera F, de Lucas M, Martínez-Fuentes A, Reig C, Iglesias DJ, Primo-Millo E, Blázquez MA. Fruit-dependent epigenetic regulation of flowering in Citrus. THE NEW PHYTOLOGIST 2020; 225:376-384. [PMID: 31273802 DOI: 10.1111/nph.16044] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/26/2019] [Indexed: 06/09/2023]
Abstract
In many perennial plants, seasonal flowering is primarily controlled by environmental conditions, but in certain polycarpic plants, environmental signals are locally gated by the presence of developing fruits initiated in the previous season through an unknown mechanism. Polycarpy is defined as the ability of plants to undergo several rounds of reproduction during their lifetime, alternating vegetative and reproductive meristems in the same individual. To understand how fruits regulate flowering in polycarpic plants, we focused on alternate bearing in Citrus trees that had been experimentally established as fully flowering or nonflowering. We found that the presence of the fruit causes epigenetic changes correlating with the induction of the CcMADS19 floral repressor, which prevents the activation of the floral promoter CiFT2 even in the presence of the floral inductive signals. By contrast, newly emerging shoots display an opposite epigenetic scenario associated with CcMADS19 repression, thereby allowing the activation of CiFT2 the following cold season.
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Affiliation(s)
- Manuel Agustí
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Carlos Mesejo
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Natalia Muñoz-Fambuena
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Francisco Vera-Sirera
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, 46022, Valencia, Spain
| | - Miguel de Lucas
- Department of Biosciences, Durham University, Stockton Rd, Durham, DH1 3LE, UK
| | - Amparo Martínez-Fuentes
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Carmina Reig
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Domingo J Iglesias
- Centro de Citricultura y Producción Vegetal, IVIA-GV, 46113, Moncada, Valencia, Spain
| | - Eduardo Primo-Millo
- Centro de Citricultura y Producción Vegetal, IVIA-GV, 46113, Moncada, Valencia, Spain
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, 46022, Valencia, Spain
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22
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He D, Xia B, Zhou Q, Wang L, Huang X. Rare earth elements regulate the endocytosis and DNA methylation in root cells of Arabidopsis thaliana. CHEMOSPHERE 2019; 227:522-532. [PMID: 31004819 DOI: 10.1016/j.chemosphere.2019.04.076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/30/2019] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
With increasing application of rare earth elements (REEs), the resulting environmental safety has attracted extensive attention. When REEs act on plant leaves, REEs can initiate endocytosis in leaf cells, causing more REEs enter plant cells and then severe damage to plants. But when REEs directly act on plant roots, whether and how REEs affect the endocytosis in root cells remain unknown. Here, we characterized effects of lanthanum [La(III)], a REE with high accumulation in environment, on the endocytosis in root cells of Arabidopsis thaliana, and revealed effect mechanism from the perspective of DNA methylation. We found that La(III) enhanced the endocytosis in root cells and the extent of enhancement depended on the dose and time of La(III) exposure: 160 μM > 80 μM >30 μM (12 h); 80 μM > 30 μM >160 μM (24 h); 24 h > 12 h. La(III)-enhanced endocytosis in root cells resulted from DNA methylation, which was closely related to the expression level of genes encoding DNA methylases/demethylases: CMT3, DRM2 and DNMT2 for 12 h, MET1, CMT1, CMT2, CMT3, DRM2, DNMT2, ROS1, DME, DML2, DML5a, and DML5b for 24 h. Conversely, enhanced endocytosis also promoted the expression level of genes encoding DNA methylases/demethylases. Our findings provide references for understanding the mechanisms by which REEs impact plants.
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Affiliation(s)
- Ding He
- State Key Laboratory of Food Science and Technology, Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, 214122, China
| | - Binxin Xia
- State Key Laboratory of Food Science and Technology, Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, 214122, China
| | - Qing Zhou
- State Key Laboratory of Food Science and Technology, Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, 214122, China
| | - Lihong Wang
- State Key Laboratory of Food Science and Technology, Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, 214122, China.
| | - Xiaohua Huang
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China.
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23
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Luan X, Liu S, Ke S, Dai H, Xie XM, Hsieh TF, Zhang XQ. Epigenetic modification of ESP, encoding a putative long noncoding RNA, affects panicle architecture in rice. RICE (NEW YORK, N.Y.) 2019; 12:20. [PMID: 30945026 PMCID: PMC6447638 DOI: 10.1186/s12284-019-0282-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/27/2019] [Indexed: 05/22/2023]
Abstract
Epigenetic variants broaden phenotypic diversity in eukaryotes. Epialleles may also provide a new genetic source for crop breeding, but very few epialleles related to agricultural traits have been identified in rice. Here, we identified Epi-sp, a gain-of-function epiallele of the rice ESP (Epigenetic Short Panicle, Os01g0356951), which encodes a putative long noncoding RNA. The Epi-sp plants show a dense and short panicle phenotype, an agronomically important phenotypes that is inherited in a semidominant manner. We did not find any nucleotide sequence variation in ESP. Instead, we found hypomethylation in the transcriptional termination region (TTR) of ESP gene, which caused ectopic expression of ESP in Epi-sp plants. Bisulfite analysis revealed that the methylation status of 26 CGs and 13 CHGs within a continuous 313-bp region is essential for the regulation of ESP expression. Thus, our work identified a unique rice epiallele and demonstrated that epigenetic modification of ESP is associated with the regulation of panicle architecture in rice.
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Affiliation(s)
- Xin Luan
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Shuchun Liu
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Shanwen Ke
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Hang Dai
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Xin-Ming Xie
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Tzung-Fu Hsieh
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081 USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695 USA
| | - Xiang-Qian Zhang
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
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24
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Wójcikowska B, Botor M, Morończyk J, Wójcik AM, Nodzyński T, Karcz J, Gaj MD. Trichostatin A Triggers an Embryogenic Transition in Arabidopsis Explants via an Auxin-Related Pathway. FRONTIERS IN PLANT SCIENCE 2018; 9:1353. [PMID: 30271420 PMCID: PMC6146766 DOI: 10.3389/fpls.2018.01353] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 08/28/2018] [Indexed: 05/23/2023]
Abstract
Auxin is an important regulator of plant ontogenies including embryo development and the exogenous application of this phytohormone has been found to be necessary for the induction of the embryogenic response in plant explants that have been cultured in vitro. However, in the present study, we show that treatment of Arabidopsis explants with trichostatin A (TSA), which is a chemical inhibitor of histone deacetylases, induces somatic embryogenesis (SE) without the exogenous application of auxin. We found that the TSA-treated explants generated somatic embryos that developed efficiently on the adaxial side of the cotyledons, which are the parts of an explant that are involved in auxin-induced SE. A substantial reduction in the activity of histone deacetylase (HDAC) was observed in the TSA-treated explants, thus confirming a histone acetylation-related mechanism of the TSA-promoted embryogenic response. Unexpectedly, the embryogenic effect of TSA was lower on the auxin-supplemented media and this finding further suggests an auxin-related mechanism of TSA-induced SE. Congruently, we found a significantly increased content of indolic compounds, which is indicative of IAA and an enhanced DR5::GUS signal in the TSA-treated explants. In line with these results, two of the YUCCA genes (YUC1 and YUC10), which are involved in auxin biosynthesis, were found to be distinctly up-regulated during TSA-induced SE and their expression was colocalised with the explant sites that are involved in SE. Beside auxin, ROS were extensively accumulated in response to TSA, thereby indicating that a stress-response is involved in TSA-triggered SE. Relevantly, we showed that the genes encoding the transcription factors (TFs) that have a regulatory function in auxin biosynthesis including LEC1, LEC2, BBM, and stress responses (MYB118) were highly up-regulated in the TSA-treated explants. Collectively, the results provide several pieces of evidence about the similarities between the molecular pathways of SE induction that are triggered by TSA and 2,4-D that involve the activation of the auxin-responsive TF genes that have a regulatory function in auxin biosynthesis and stress responses. The study suggests the involvement of histone acetylation in the auxin-mediated release of the embryogenic program of development in the somatic cells of Arabidopsis.
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Affiliation(s)
| | - Malwina Botor
- Department of Molecular Biology and Genetics, Medical University of SilesiaKatowice, Poland
| | - Joanna Morończyk
- Department of Genetics, University of Silesia in KatowiceKatowice, Poland
| | - Anna Maria Wójcik
- Department of Genetics, University of Silesia in KatowiceKatowice, Poland
| | - Tomasz Nodzyński
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU – Central European Institute of Technology, Masaryk UniversityBrno, Czechia
| | - Jagna Karcz
- Scanning Electron Microscopy Laboratory, University of Silesia in KatowiceKatowice, Poland
| | - Małgorzata D. Gaj
- Department of Genetics, University of Silesia in KatowiceKatowice, Poland
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25
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A naturally occurring epiallele associates with leaf senescence and local climate adaptation in Arabidopsis accessions. Nat Commun 2018; 9:460. [PMID: 29386641 PMCID: PMC5792623 DOI: 10.1038/s41467-018-02839-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 01/03/2018] [Indexed: 11/09/2022] Open
Abstract
Epigenetic variation has been proposed to facilitate adaptation to changing environments, but evidence that natural epialleles contribute to adaptive evolution has been lacking. Here we identify a retrotransposon, named “NMR19” (naturally occurring DNA methylation variation region 19), whose methylation and genomic location vary among Arabidopsis thaliana accessions. We classify NMR19 as NMR19-4 and NMR19-16 based on its location, and uncover NMR19-4 as an epiallele that controls leaf senescence by regulating the expression of PHEOPHYTIN PHEOPHORBIDE HYDROLASE (PPH). We find that the DNA methylation status of NMR19-4 is stably inherited and independent of genetic variation. In addition, further analysis indicates that DNA methylation of NMR19-4 correlates with local climates, implying that NMR19-4 is an environmentally associated epiallele. In summary, we discover a novel epiallele, and provide mechanistic insights into its origin and potential function in local climate adaptation. Epigenetic variation underlies various aspects of phenotypic diversity of plants. Here, He et al show a naturally occurring epiallele controls Arabidopsis leaf senescence by regulating the expression of PHEOPHYTIN PHEOPHORBIDE HYDROLASE (PPH), and is associated with local climate adaptation.
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26
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Zheng YS, Lu YQ, Meng YY, Zhang RZ, Zhang H, Sun JM, Wang MM, Li LH, Li RY. Identification of interacting proteins of the TaFVE protein involved in spike development in bread wheat. Proteomics 2017; 17. [PMID: 28225203 DOI: 10.1002/pmic.201600331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 01/24/2017] [Accepted: 02/20/2017] [Indexed: 02/06/2023]
Abstract
WD-40 repeat-containing protein MSI4 (FVE)/MSI4 plays important roles in determining flowering time in Arabidopsis. However, its function is unexplored in wheat. In the present study, coimmunoprecipitation and nanoscale liquid chromatography coupled to MS/MS were used to identify FVE in wheat (TaFVE)-interacting or associated proteins. Altogether 89 differentially expressed proteins showed the same downregulated expression trends as TaFVE in wheat line 5660M. Among them, 62 proteins were further predicted to be involved in the interaction network of TaFVE and 11 proteins have been shown to be potential TaFVE interactors based on curated databases and experimentally determined in other species by the STRING. Both yeast two-hybrid assay and bimolecular fluorescence complementation assay showed that histone deacetylase 6 and histone deacetylase 15 directly interacted with TaFVE. Multiple chromatin-remodelling proteins and polycomb group proteins were also identified and predicted to interact with TaFVE. These results showed that TaFVE directly interacted with multiple proteins to form multiple complexes to regulate spike developmental process, e.g. histone deacetylate, chromatin-remodelling and polycomb repressive complex 2 complexes. In addition, multiple flower development regulation factors (e.g. flowering locus K homology domain, flowering time control protein FPA, FY, flowering time control protein FCA, APETALA 1) involved in floral transition were also identified in the present study. Taken together, these results further elucidate the regulatory functions of TaFVE and help reveal the genetic mechanisms underlying wheat spike differentiation.
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Affiliation(s)
- Yong-Sheng Zheng
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Yu-Qing Lu
- Institute of Crop Sciences, National Key Facilities for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Ying-Ying Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Rong-Zhi Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Han Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Jia-Mei Sun
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Mu-Mu Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Li-Hui Li
- Institute of Crop Sciences, National Key Facilities for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Ru-Yu Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
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27
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Song Y, Liu L, Li G, An L, Tian L. Trichostatin A and 5-Aza-2'-Deoxycytidine influence the expression of cold-induced genes in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2017; 12:e1389828. [PMID: 29027833 PMCID: PMC5703259 DOI: 10.1080/15592324.2017.1389828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The expression of cold-induced genes is critical for plants to survive under freezing stress. However, the underlying mechanisms for the decision of when, where, and which genes to express are unclear when a plant meets a sudden temperature drop. Previous studies have demonstrated epigenetics to play a central role in the regulation of gene expression in plant responses to environmental stress. DNA methylation and histone deacetylation are the two most important epigenetic modifications. This study was conducted to investigate the effects of inhibiting DNA methylation and histone deacetylation on gene expression, and to explore the potential role of epigenetics in plant responses to cold stress. The results revealed that histone deacetylase inhibitors (trichostatin A) and DNA methylation inhibitors (5-Aza-2'-deoxycytosine) treatment enhanced cold tolerance. DNA microarray analysis and the gene ontology method revealed 76 cold-induced differently expressed genes in Arabidopsis thaliana seedlings that were treated to 0°C for 24 h following Trichostatin A and 5-Aza-2'-Deoxycytidine. Furthermore, analyses of metabolic pathways and transcription factors of 3305 differentially expressed genes were performed. Each four metabolic pathways were significantly affected (p < 0.01) by Trichostatin A and 5-Aza-2'-Deoxycytidine. Finally, 10 genes were randomly selected and verified via qPCR analysis. Our study indicated that Trichostatin A and 5-Aza-2'-Deoxycytidine can improve the plant cold resistance and influence the expression of the cold-induced gene in A. thaliana. This result will advance our understanding of plant freezing responses and may provide a helpful strategy for cold tolerance improvement in crops.
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Affiliation(s)
- Yuan Song
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Gansu Province, Lanzhou, China
- CONTACT Lining Tian ; Yuan Song Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, The South of Tianshui Road 222#, Lanzhou City, China Lanzhou 730000
| | - Lijun Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Gansu Province, Lanzhou, China
| | - Gaopeng Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Gansu Province, Lanzhou, China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Gansu Province, Lanzhou, China
| | - Lining Tian
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, Canada, N5V4T3
- CONTACT Lining Tian ; Yuan Song Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, The South of Tianshui Road 222#, Lanzhou City, China Lanzhou 730000
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28
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Jiang F, Ryabova D, Diedhiou J, Hucl P, Randhawa H, Marillia EF, Foroud NA, Eudes F, Kathiria P. Trichostatin A increases embryo and green plant regeneration in wheat. PLANT CELL REPORTS 2017; 36:1701-1706. [PMID: 28752355 DOI: 10.1007/s00299-017-2183-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/13/2017] [Indexed: 05/19/2023]
Abstract
Chemical agents such as trichostatin A (TSA) can assist in optimization of doubled haploidy for rapid improvements in wheat germplasm and addressing recalcitrance issues in cell culture responses. In wheat, plant regeneration through microspore culture is an integral part of doubled haploid (DH) production. However, low response to tissue culture and genotype specificity are two major constraints in the broad deployment of this breeding tool. Recently, the structure of chromatin was shown to be linked with cell transitions during tissue culture. Specifically, repression of genes that are required for cell morphogenesis, through acetylation of histones, may play an important role in this process. Reduction of histone acetylation by chemical inhibition may increase tissue culture efficiency. Here, the role of trichostatin A (TSA) in inducing microspore-derived embryos was investigated in wheat. The optimal dose of TSA was determined for wheat cultivars and subsequently validated in F1 hybrids. A significant increase in the efficiency of DH production was observed in both cultivated varieties and F1 hybrids. Thus, the inclusion of TSA in DH protocols for wheat breeding programs is advocated.
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Affiliation(s)
| | - Daria Ryabova
- Agriculture and Agri-Food Canada, Lethbridge, Canada
| | | | - Pierre Hucl
- Crop Development Centre, University of Saskatchewan, Saskatoon, Canada
| | | | | | - Nora A Foroud
- Agriculture and Agri-Food Canada, Lethbridge, Canada
| | | | - Palak Kathiria
- Agriculture and Agri-Food Canada, Lethbridge, Canada.
- National Research Council Canada, Saskatoon, Canada.
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29
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Santos AP, Ferreira LJ, Oliveira MM. Concerted Flexibility of Chromatin Structure, Methylome, and Histone Modifications along with Plant Stress Responses. BIOLOGY 2017; 6:biology6010003. [PMID: 28275209 PMCID: PMC5371996 DOI: 10.3390/biology6010003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/05/2017] [Accepted: 01/10/2017] [Indexed: 12/12/2022]
Abstract
The spatial organization of chromosome structure within the interphase nucleus, as well as the patterns of methylome and histone modifications, represent intersecting layers that influence genome accessibility and function. This review is focused on the plastic nature of chromatin structure and epigenetic marks in association to stress situations. The use of chemical compounds (epigenetic drugs) or T-DNA-mediated mutagenesis affecting epigenetic regulators (epi-mutants) are discussed as being important tools for studying the impact of deregulated epigenetic backgrounds on gene function and phenotype. The inheritability of epigenetic marks and chromatin configurations along successive generations are interpreted as a way for plants to “communicate” past experiences of stress sensing. A mechanistic understanding of chromatin and epigenetics plasticity in plant response to stress, including tissue- and genotype-specific epigenetic patterns, may help to reveal the epigenetics contributions for genome and phenotype regulation.
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Affiliation(s)
- Ana Paula Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit. Av. da República, 2780-157 Oeiras, Portugal.
| | - Liliana J Ferreira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit. Av. da República, 2780-157 Oeiras, Portugal.
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit. Av. da República, 2780-157 Oeiras, Portugal.
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30
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Kawanabe T, Ishikura S, Miyaji N, Sasaki T, Wu LM, Itabashi E, Takada S, Shimizu M, Takasaki-Yasuda T, Osabe K, Peacock WJ, Dennis ES, Fujimoto R. Role of DNA methylation in hybrid vigor in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2016; 113:E6704-E6711. [PMID: 27791039 PMCID: PMC5087013 DOI: 10.1073/pnas.1613372113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Hybrid vigor or heterosis refers to the superior performance of F1 hybrid plants over their parents. Heterosis is particularly important in the production systems of major crops. Recent studies have suggested that epigenetic regulation such as DNA methylation is involved in heterosis, but the molecular mechanism of heterosis is still unclear. To address the epigenetic contribution to heterosis in Arabidopsis thaliana, we used mutant genes that have roles in DNA methylation. Hybrids between C24 and Columbia-0 (Col) without RNA polymerase IV (Pol IV) or methyltransferase I (MET1) function did not reduce the level of biomass heterosis (as evaluated by rosette diameter). Hybrids with a mutation in decrease in dna methylation 1 (ddm1) showed a decreased heterosis level. Vegetative heterosis in the ddm1 mutant hybrid was reduced but not eliminated; a complete reduction could result if there was a change in methylation at all loci critical for generating the level of heterosis, whereas if only a proportion of the loci have methylation changes there may only be a partial reduction in heterosis.
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Affiliation(s)
- Takahiro Kawanabe
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Sonoko Ishikura
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Naomi Miyaji
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Taku Sasaki
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Li Min Wu
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT 2601, Australia
| | - Etsuko Itabashi
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Satoko Takada
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, 22-174-4, Narita, Kitakami, Iwate, 024-0003, Japan
| | - Takeshi Takasaki-Yasuda
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Kenji Osabe
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - W James Peacock
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT 2601, Australia; University of Technology, Sydney, Broadway, NSW 2007, Australia;
| | - Elizabeth S Dennis
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT 2601, Australia; University of Technology, Sydney, Broadway, NSW 2007, Australia
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Saitama, 332-0012 Japan
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Deng Z, Liu X, Jin J, Xu H, Gao Q, Wang Y, Zhao J. Histone Deacetylase Inhibitor Trichostatin a Promotes the Apoptosis of Osteosarcoma Cells through p53 Signaling Pathway Activation. Int J Biol Sci 2016; 12:1298-1308. [PMID: 27877082 PMCID: PMC5118776 DOI: 10.7150/ijbs.16569] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/20/2016] [Indexed: 01/13/2023] Open
Abstract
Purpose: The purpose of this study was to investigate the profile of histone deacetylase (HDAC) activity and expression in osteosarcoma cells and tissues from osteosarcoma patients and to examine the mechanism by which a histone deacetylase (HDAC) inhibitor, Trichostatin A (TSA), promotes the apoptosis of osteosarcoma cells. Methods: HDAC activity and histone acetyltransferase (HAT) activity were determined in nuclear extracts of MG63 cells, hFOB 1.19 cells and tissues from 6 patients with primary osteosarcoma. The protein expression of Class I HDACs (1, 2, 3 and 8) and the activation of the p53 signaling pathway were examined by Western blot. Cell growth and apoptosis were determined by 3-(4, 5-dimethyl-2-thiazolyl)-2H-tetrazolium bromide (MTT) assay and flow cytometry, respectively. Results: Nuclear HDAC activity and class I HDAC expression were significantly higher in MG63 cells than in hFOB 1.19 cells, and a similar trend was observed in the human osteosarcoma tissues compared with the paired adjacent non-cancerous tissues. TSA significantly inhibited the growth of MG63 cells and promoted apoptosis in a dose-dependent manner through p53 signaling pathway activation. Conclusion: Class I HDACs play a central role in the pathogenesis of osteosarcoma, and HDAC inhibitors may thus have promise as new therapeutic agents against osteosarcoma.
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Affiliation(s)
- Zhantao Deng
- Department of Orthopedics, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
- Center for Translational Medicine, Nanjing University Medical School, Nanjing, Jiangsu, PR China
- Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing, PR China
| | - Xiaozhou Liu
- Department of Orthopedics, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Jiewen Jin
- Center for Translational Medicine, Nanjing University Medical School, Nanjing, Jiangsu, PR China
- Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing, PR China
| | - Haidong Xu
- Department of Orthopedics, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Qian Gao
- Center for Translational Medicine, Nanjing University Medical School, Nanjing, Jiangsu, PR China
- Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing, PR China
| | - Yong Wang
- Center for Translational Medicine, Nanjing University Medical School, Nanjing, Jiangsu, PR China
- Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing, PR China
| | - Jianning Zhao
- Department of Orthopedics, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
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A Comparative Analysis of 5-Azacytidine- and Zebularine-Induced DNA Demethylation. G3-GENES GENOMES GENETICS 2016; 6:2773-80. [PMID: 27402357 PMCID: PMC5015934 DOI: 10.1534/g3.116.030262] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The nonmethylable cytosine analogs, 5-azacytidine and zebularine, are widely used to inhibit DNA methyltransferase activity and reduce genomic DNA methylation. In this study, whole-genome bisulfite sequencing is used to construct maps of DNA methylation with single base pair resolution in Arabidopsis thaliana seedlings treated with each demethylating agent. We find that both inhibitor treatments result in nearly indistinguishable patterns of genome-wide DNA methylation and that 5-azacytidine had a slightly greater demethylating effect at higher concentrations across the genome. Transcriptome analyses revealed a substantial number of upregulated genes, with an overrepresentation of transposable element genes, in particular CACTA-like elements. This demonstrates that chemical demethylating agents have a disproportionately large effect on loci that are otherwise silenced by DNA methylation.
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Tonosaki K, Osabe K, Kawanabe T, Fujimoto R. The importance of reproductive barriers and the effect of allopolyploidization on crop breeding. BREEDING SCIENCE 2016; 66:333-49. [PMID: 27436943 PMCID: PMC4902455 DOI: 10.1270/jsbbs.15114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/25/2016] [Indexed: 05/04/2023]
Abstract
Inter-specific hybrids are a useful source for increasing genetic diversity. Some reproductive barriers before and/or after fertilization prevent production of hybrid plants by inter-specific crossing. Therefore, techniques to overcome the reproductive barrier have been developed, and have contributed to hybridization breeding. In recent studies, identification of molecules involved in plant reproduction has been studied to understand the mechanisms of reproductive barriers. Revealing the molecular mechanisms of reproductive barriers may allow us to overcome reproductive barriers in inter-specific crossing, and to efficiently produce inter-specific hybrids in cross-combinations that cannot be produced through artificial techniques. Inter-specific hybrid plants can potentially serve as an elite material for plant breeding, produced through the merging of genomes of parental species by allopolyploidization. Allopolyploidization provides some benefits, such as heterosis, increased genetic diversity and phenotypic variability, which are caused by dynamic changes of the genome and epigenome. Understanding of allopolyploidization mechanisms is important for practical utilization of inter-specific hybrids as a breeding material. This review discusses the importance of reproductive barriers and the effect of allopolyploidization in crop breeding programs.
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Affiliation(s)
- Kaoru Tonosaki
- Kihara Institute for Biological Research, Yokohama City University,
641-12 Maioka, Totsuka, Yokohama, Kanagawa 244-0813,
Japan
- Corresponding author (e-mail: )
| | - Kenji Osabe
- Okinawa Institute of Science and Technology,
1919-1 Tancha, Onna-son, Kunigami, Okinawa 904-0495,
Japan
| | - Takahiro Kawanabe
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe 657-8501,
Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe 657-8501,
Japan
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Sako K, Kim JM, Matsui A, Nakamura K, Tanaka M, Kobayashi M, Saito K, Nishino N, Kusano M, Taji T, Yoshida M, Seki M. Ky-2, a Histone Deacetylase Inhibitor, Enhances High-Salinity Stress Tolerance in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2016; 57:776-83. [PMID: 26657894 DOI: 10.1093/pcp/pcv199] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/05/2015] [Indexed: 05/20/2023]
Abstract
Adaptation to environmental stress requires genome-wide changes in gene expression. Histone modifications are involved in gene regulation, but the role of histone modifications under environmental stress is not well understood. To reveal the relationship between histone modification and environmental stress, we assessed the effects of inhibitors of histone modification enzymes during salinity stress. Treatment with Ky-2, a histone deacetylase inhibitor, enhanced high-salinity stress tolerance in Arabidopsis. We confirmed that Ky-2 possessed inhibition activity towards histone deacetylases by immunoblot analysis. To investigate how Ky-2 improved salt stress tolerance, we performed transcriptome and metabolome analysis. These data showed that the expression of salt-responsive genes and salt stress-related metabolites were increased by Ky-2 treatment under salinity stress. A mutant deficient in AtSOS1(Arabidopis thaliana SALT OVERLY SENSITIVE 1), which encodes an Na(+)/H(+)antiporter and was among the up-regulated genes, lost the salinity stress tolerance conferred by Ky-2. We confirmed that acetylation of histone H4 at AtSOS1 was increased by Ky-2 treatment. Moreover, Ky-2 treatment decreased the intracellular Na(+)accumulation under salinity stress, suggesting that enhancement of SOS1-dependent Na(+)efflux contributes to increased high-salinity stress tolerance caused by Ky-2 treatment.
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Affiliation(s)
- Kaori Sako
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Jong-Myong Kim
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Kotaro Nakamura
- Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502 Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Makoto Kobayashi
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Kazuki Saito
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8522 Japan
| | - Norikazu Nishino
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, 808-0196 Japan
| | - Miyako Kusano
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572 Japan
| | - Teruaki Taji
- Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502 Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012 Japan
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Lee K, Park OS, Jung SJ, Seo PJ. Histone deacetylation-mediated cellular dedifferentiation in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2016; 191:95-100. [PMID: 26724747 DOI: 10.1016/j.jplph.2015.12.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/24/2015] [Accepted: 12/11/2015] [Indexed: 05/20/2023]
Abstract
Chromatin structure determines the accessibility of transcriptional regulators to target DNA and contributes to regulation of gene expression. Posttranslational modifications of core histone proteins underlie the reversible changes in chromatin structure. Epigenetic regulation is closely associated with cellular differentiation. Consistently, we found that histone deacetylation is required for callus formation from leaf explants in Arabidopsis . Treatment with trichostatin A (TSA) led to defective callus formation on callus-inducing medium (CIM). Gene expression profiling revealed that a subset of HDAC genes, including HISTONE DEACETYLASE 9 (HDA9), HD-TUINS PROTEIN 1 (HDT1), HDT2, HDT4, and SIRTUIN 1 (SRT1), was significantly up-regulated in calli. In support of this, genetic mutations of HDA9 or HDT1 showed reduced capability of callus formation, probably owing to their roles in regulating auxin and embryonic and meristematic developmental signaling. Taken together, our findings suggest that histone deacetylation is intimately associated with the leaf-to-callus transition, and multiple signaling pathways are controlled by means of histone modification during cellular dedifferentiation.
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Affiliation(s)
- Kyounghee Lee
- Department of Bioactive Material Sciences and Research Center of Bioactive Materials, Chonbuk National University, Jeonju 561-756, Republic of Korea
| | - Ok-Sun Park
- Department of Chemistry and Research Institute of Physics and Chemistry, Chonbuk National University, Jeonju 561-756, Republic of Korea
| | - Su-Jin Jung
- Department of Chemistry and Research Institute of Physics and Chemistry, Chonbuk National University, Jeonju 561-756, Republic of Korea
| | - Pil Joon Seo
- Department of Bioactive Material Sciences and Research Center of Bioactive Materials, Chonbuk National University, Jeonju 561-756, Republic of Korea; Department of Chemistry and Research Institute of Physics and Chemistry, Chonbuk National University, Jeonju 561-756, Republic of Korea.
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Zhang X, Sun J, Cao X, Song X. Epigenetic Mutation of RAV6 Affects Leaf Angle and Seed Size in Rice. PLANT PHYSIOLOGY 2015; 169:2118-28. [PMID: 26351308 PMCID: PMC4634063 DOI: 10.1104/pp.15.00836] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 09/06/2015] [Indexed: 05/18/2023]
Abstract
Heritable epigenetic variants of genes, termed epialleles, can broaden genetic and phenotypic diversity in eukaryotes. Epialleles may also provide a new source of beneficial traits for crop breeding, but very few epialleles related to agricultural traits have been identified in crops. Here, we identified Epi-rav6, a gain-of-function epiallele of rice (Oryza sativa) RELATED TO ABSCISIC ACID INSENSITIVE3 (ABI3)/VIVIPAROUS1 (VP1) 6 (RAV6), which encodes a B3 DNA-binding domain-containing protein. The Epi-rav6 plants show larger lamina inclination and smaller grain size; these agronomically important phenotypes are inherited in a semidominant manner. We did not find nucleotide sequence variation of RAV6. Instead, we found hypomethylation in the promoter region of RAV6, which caused ectopic expression of RAV6 in Epi-rav6 plants. Bisulfite analysis revealed that cytosine methylation of four CG and two CNG loci within a continuous 96-bp region plays essential roles in regulating RAV6 expression; this region contains a conserved miniature inverted repeat transposable element transposon insertion in cultivated rice genomes. Overexpression of RAV6 in the wild type phenocopied the Epi-rav6 phenotype. The brassinosteroid (BR) receptor BR INSENSITIVE1 and BR biosynthetic genes EBISU DWARF, DWARF11, and BR-DEFICIENT DWARF1 were ectopically expressed in Epi-rav6 plants. Also, treatment with a BR biosynthesis inhibitor restored the leaf angle defects of Epi-rav6 plants. This indicates that RAV6 affects rice leaf angle by modulating BR homeostasis and demonstrates an essential regulatory role of epigenetic modification on a key gene controlling important agricultural traits. Thus, our work identifies a unique rice epiallele, which may represent a common phenomenon in complex crop genomes.
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Affiliation(s)
- Xiangqian Zhang
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China (X.Z.);State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (J.S., X.C., X.S.); andCollaborative Innovation Center of Genetics and Development, Shanghai 200433, China (X.C.)
| | - Jing Sun
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China (X.Z.);State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (J.S., X.C., X.S.); andCollaborative Innovation Center of Genetics and Development, Shanghai 200433, China (X.C.)
| | - Xiaofeng Cao
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China (X.Z.);State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (J.S., X.C., X.S.); andCollaborative Innovation Center of Genetics and Development, Shanghai 200433, China (X.C.)
| | - Xianwei Song
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China (X.Z.);State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (J.S., X.C., X.S.); andCollaborative Innovation Center of Genetics and Development, Shanghai 200433, China (X.C.)
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Song Y, Liu L, Feng Y, Wei Y, Yue X, He W, Zhang H, An L. Chilling- and Freezing-Induced Alterations in Cytosine Methylation and Its Association with the Cold Tolerance of an Alpine Subnival Plant, Chorispora bungeana. PLoS One 2015; 10:e0135485. [PMID: 26270551 PMCID: PMC4535906 DOI: 10.1371/journal.pone.0135485] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 07/23/2015] [Indexed: 12/24/2022] Open
Abstract
Chilling (0–18°C) and freezing (<0°C) are two distinct types of cold stresses. Epigenetic regulation can play an important role in plant adaptation to abiotic stresses. However, it is not yet clear whether and how epigenetic modification (i.e., DNA methylation) mediates the adaptation to cold stresses in nature (e.g., in alpine regions). Especially, whether the adaptation to chilling and freezing is involved in differential epigenetic regulations in plants is largely unknown. Chorispora bungeana is an alpine subnival plant that is distributed in the freeze-thaw tundra in Asia, where chilling and freezing frequently fluctuate daily (24 h). To disentangle how C. bungeana copes with these intricate cold stresses through epigenetic modifications, plants of C. bungeana were treated at 4°C (chilling) and -4°C (freezing) over five periods of time (0–24 h). Methylation-sensitive amplified fragment-length polymorphism markers were used to investigate the variation in DNA methylation of C. bungeana in response to chilling and freezing. It was found that the alterations in DNA methylation of C. bungeana largely occurred over the period of chilling and freezing. Moreover, chilling and freezing appeared to gradually induce distinct DNA methylation variations, as the treatment went on (e.g., after 12 h). Forty-three cold-induced polymorphic fragments were randomly selected and further analyzed, and three of the cloned fragments were homologous to genes encoding alcohol dehydrogenase, UDP-glucosyltransferase and polygalacturonase-inhibiting protein. These candidate genes verified the existence of different expressive patterns between chilling and freezing. Our results showed that C. bungeana responded to cold stresses rapidly through the alterations of DNA methylation, and that chilling and freezing induced different DNA methylation changes. Therefore, we conclude that epigenetic modifications can potentially serve as a rapid and flexible mechanism for C. bungeana to adapt to the intricate cold stresses in the alpine areas.
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Affiliation(s)
- Yuan Song
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- * E-mail: (LA); (YS)
| | - Lijun Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yanhao Feng
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, Germany
| | - Yunzhu Wei
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xiule Yue
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wenliang He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hua Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- * E-mail: (LA); (YS)
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Li RQ, Huang JZ, Zhao HJ, Fu HW, Li YF, Liu GZ, Shu QY. A down-regulated epi-allele of the genomes uncoupled 4 gene generates a xantha marker trait in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2491-501. [PMID: 25208645 DOI: 10.1007/s00122-014-2393-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 08/28/2014] [Indexed: 05/08/2023]
Abstract
A γ-ray-induced xantha trait is epigenetically controlled by the genomes uncoupled 4 gene with enhanced promoter segment methylation and down-regulated expression in rice. For easy testing and to increase varietal purity, a xantha mutation (xnt), which turns plants yellow and makes them visually distinguishable from normal green rice, has been generated and bred into male sterile lines for hybrid rice production. The xnt locus was previously fine mapped to a ~100-kb interval on chromosome 11, but its identity was unknown. In this study, xnt was further narrowed down to a 57-kb fragment carrying eight opening reading frames (ORFs). All eight ORFs had identical genomic sequences and all but ORF2 (g enomes uncoupled 4, OsGUN4) had similar transcript abundance in the xantha mutant Huangyu B (HYB) and its parental variety Longtefu B (LTB). The expression of OsGUN4, however, was significantly reduced in HYB compared with LTB in terms of both transcript abundance (0.2% that of LTB) and expressed protein level (barely detectable in HYB but greater than the heat shock protein reference in LTB). Therefore, OsGUN4 was identified as the candidate gene underlying the xantha trait. The function of OsGUN4 in the xantha phenotype was confirmed by identification and characterization of new allelic OsGUN4 mutations. Comparative bisulfite genomic sequencing of OsGUN4 revealed increased methylation in a promoter region in the mutant, and the correlation between increased methylation and the xantha phenotype was further verified by demethylation treatment. In summary, we have identified an epi-allele of OsGUN4 as the causal gene of the xantha marker trait and revealed that enhanced methylation in its promoter down-regulated its expression in rice.
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Affiliation(s)
- Rui-Qing Li
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, 310029, Hangzhou, China
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Veerappan V, Chen N, Reichert AI, Allen RD. HSI2/VAL1 PHD-like domain promotes H3K27 trimethylation to repress the expression of seed maturation genes and complex transgenes in Arabidopsis seedlings. BMC PLANT BIOLOGY 2014; 14:293. [PMID: 25367506 PMCID: PMC4232687 DOI: 10.1186/s12870-014-0293-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/17/2014] [Indexed: 05/22/2023]
Abstract
BACKGROUND The novel mutant allele hsi2-4 was isolated in a genetic screen to identify Arabidopsis mutants with constitutively elevated expression of a glutathione S-transferase F8::luciferase (GSTF8::LUC) reporter gene in Arabidopsis. The hsi2-4 mutant harbors a point mutation that affects the plant homeodomain (PHD)-like domain in HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE GENE2 (HSI2)/VIVIPAROUS1/ABI3-LIKE1 (VAL1). In hsi2-4 seedlings, expression of this LUC transgene and certain endogenous seed-maturation genes is constitutively enhanced. The parental reporter line (WT LUC ) that was used for mutagenesis harbors two independent transgene loci, Kan R and Kan S . Both loci express luciferase whereas only the Kan R locus confers resistance to kanamycin. RESULTS Here we show that both transgene loci harbor multiple tandem insertions at single sites. Luciferase expression from these sites is regulated by the HSI2 PHD-like domain, which is required for the deposition of repressive histone methylation marks (H3K27me3) at both Kan R and Kan S loci. Expression of LUC and Neomycin Phosphotransferase II transgenes is associated with dynamic changes in H3K27me3 levels, and the activation marks H3K4me3 and H3K36me3 but does not appear to involve repressive H3K9me2 marks, DNA methylation or histone deacetylation. However, hsi2-2 and hsi2-4 mutants are partially resistant to growth inhibition associated with exposure to the DNA methylation inhibitor 5-aza-2'-deoxycytidine. HSI2 is also required for the repression of a subset of regulatory and structural seed maturation genes in vegetative tissues and H3K27me3 marks associated with most of these genes are also HSI2-dependent. CONCLUSIONS These data implicate HSI2 PHD-like domain in the regulation of gene expression involving histone modifications and DNA methylation-mediated epigenetic mechanisms.
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Affiliation(s)
- Vijaykumar Veerappan
- />Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401 USA
- />Current address: Department of Biological Sciences, University of North Texas, Denton, TX 76203-5017 USA
| | - Naichong Chen
- />Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401 USA
| | - Angelika I Reichert
- />Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401 USA
| | - Randy D Allen
- />Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401 USA
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Li BC, Zhang C, Chai QX, Han YY, Wang XY, Liu MX, Feng H, Xu ZQ. Plasmalemma localisation of DOUBLE HYBRID PROLINE-RICH PROTEIN 1 and its function in systemic acquired resistance of Arabidopsis thaliana. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:768-779. [PMID: 32481031 DOI: 10.1071/fp13314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 01/23/2014] [Indexed: 05/03/2023]
Abstract
The protein encoded by AtDHyPRP1 (DOUBLE HYBRID PROLINE-RICH PROTEIN 1) contains two tandem PRD-8CMs (proline-rich domain-eight cysteine motif) and represents a new type of HyPRPs (hybrid proline-rich proteins). Confocal microscopy to transgenic Arabidopsis plants revealed that AtDHyPRP1-GFP was localised to plasmalemma, especially plasmodesmata. AtDHyPRP1 mainly expressed in leaf tissues and could be induced by salicylic acid, methyl jasmonate, virulent Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) and avirulent P. syringae pv. tomato DC3000 harbouring avrRPM1 (Pst avrRPM1), suggesting it is involved in defence response of Arabidopsis thaliana (L. Heynh.). After treatments with bacterial suspension of virulent Pst DC3000 or conidial suspension of Botrytis cinerea, AtDHyPRP1 overexpressing lines exhibited enhanced resistance, whereas AtDHyPRP1 RNA interference lines became more susceptible to the pathogens with obvious chlorosis or necrosis phenotypes. In systemic acquired resistance (SAR) analyses, distal leaves were challenged with virulent Pst DC3000 after inoculation of the primary leaves with avirulent Pst avrRPM1 (AV) or MgSO4 (MV). Compared with MV, the infection symptoms in systemic leaves of wild-type plants and AtDHyPRP1 overexpressing lines were significantly alleviated in AV treatment, whereas the systemic leaves of AtDHyPRP1 RNAi lines were vulnerable to Pst DC3000, indicating AtDHyPRP1 was functionally associated with SAR.
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Affiliation(s)
- Ben-Chang Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi, College of Life Sciences, Northwest University, Xi'an 710069, PR China
| | - Chen Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi, College of Life Sciences, Northwest University, Xi'an 710069, PR China
| | - Qiu-Xia Chai
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi, College of Life Sciences, Northwest University, Xi'an 710069, PR China
| | - Yao-Yao Han
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi, College of Life Sciences, Northwest University, Xi'an 710069, PR China
| | - Xiao-Yan Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi, College of Life Sciences, Northwest University, Xi'an 710069, PR China
| | - Meng-Xin Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi, College of Life Sciences, Northwest University, Xi'an 710069, PR China
| | - Huan Feng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi, College of Life Sciences, Northwest University, Xi'an 710069, PR China
| | - Zi-Qin Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi, College of Life Sciences, Northwest University, Xi'an 710069, PR China
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41
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Pecinka A, Liu CH. Drugs for Plant Chromosome and Chromatin Research. Cytogenet Genome Res 2014; 143:51-9. [DOI: 10.1159/000360774] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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42
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Higashiyama R, Miyaki S, Yamashita S, Yoshitaka T, Lindman G, Ito Y, Sasho T, Takahashi K, Lotz M, Asahara H. Correlation between MMP-13 and HDAC7 expression in human knee osteoarthritis. Mod Rheumatol 2014. [DOI: 10.3109/s10165-009-0224-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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43
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Zhang H, Wang B, Duan CG, Zhu JK. Chemical probes in plant epigenetics studies. PLANT SIGNALING & BEHAVIOR 2013; 8:25364. [PMID: 23838953 PMCID: PMC4002629 DOI: 10.4161/psb.25364] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 06/11/2013] [Indexed: 06/01/2023]
Abstract
Transcription potential is determined by the accessibility of DNA sequences within the context of chromatin, which is coordinately controlled by various epigenetic modifications. Chemical inhibition of epigenetic regulators provides a quick and effective approach to investigate the roles of epigenetic modifications in controlling many biological processes, especially for species in which genetic information is limited. This mini-review provides a brief overview of epigenetic regulators in the model organism Arabidopsis thaliana and summarizes compounds that have been applied in plant epigenetics studies, with highlights in the applications of these chemical probes in mechanistic and functional investigations.
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Affiliation(s)
- Huiming Zhang
- Department of Horticulture and Landscape Architecture; Purdue University; West Lafayette, IN USA
| | - Bangshing Wang
- Department of Horticulture and Landscape Architecture; Purdue University; West Lafayette, IN USA
| | - Cheng-Guo Duan
- Department of Horticulture and Landscape Architecture; Purdue University; West Lafayette, IN USA
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture; Purdue University; West Lafayette, IN USA
- Shanghai Center for Plant Stress Biology; Shanghai Institutes of Biological Sciences; Chinese Academy of Sciences; Shanghai, PR China
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44
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Yaacob JS, Loh HS, Mat Taha R. Protein profiling and histone deacetylation activities in somaclonal variants of oil palm (Elaeis guineensis Jacq.). ScientificWorldJournal 2013; 2013:613635. [PMID: 23844406 PMCID: PMC3686130 DOI: 10.1155/2013/613635] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/09/2013] [Indexed: 12/21/2022] Open
Abstract
Mantled fruits as a result of somaclonal variation are often observed from the oil palm plantlets regenerated via tissue culture. The mantling of fruits with finger-like and thick outer coating phenotypes significantly reduces the seed size and oil content, posing a threat to oil palm planters, and may jeopardize the economic growth of countries that depend particularly on oil palm plantation. The molecular aspects of the occurrence of somaclonal variations are yet to be known, possibly due to gene repression such as DNA methylation, histone methylation and histone deacetylation. Histone deacetylases (HDACs), involved in eukaryotic gene regulation by catalyzing the acetyl groups are removal from lysine residues on histone, hence transcriptionally repress gene expression. This paper described the total protein polymorphism profiles of somaclonal variants of oil palm and the effects of histone deacetylation on this phenomenon. Parallel to the different phenotypes, the protein polymorphism profiles of the mantled samples (leaves, fruits, and florets) and the phenotypically normal samples were proven to be different. Higher HDAC activity was found in mantled leaf samples than in the phenotypically normal leaf samples, leading to a preliminary conclusion that histone deacetylation suppressed gene expression and contributed to the development of somaclonal variants.
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Affiliation(s)
- Jamilah Syafawati Yaacob
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia. jam
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45
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Lee HA, Lee DY, Cho HM, Kim SY, Iwasaki Y, Kim IK. Histone Deacetylase Inhibition Attenuates Transcriptional Activity of Mineralocorticoid Receptor Through Its Acetylation and Prevents Development of Hypertension. Circ Res 2013; 112:1004-12. [DOI: 10.1161/circresaha.113.301071] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Rationale:
Inhibition of histone deacetylases (HDACs) results in attenuated development of hypertension in deoxycorticosterone acetate–induced hypertensive rats and spontaneously hypertensive rats. However, the molecular mechanism remains elusive.
Objective:
We hypothesized that HDAC inhibition attenuates transcriptional activity of mineralocorticoid receptor (MR) through its acetylation and prevents development of hypertension in deoxycorticosterone acetate–induced hypertensive rats.
Methods and Results:
Expression of MR target genes was measured by quantitative real-time polymerase chain reaction. Recruitment of MR and RNA polymerase II on promoters of target genes was analyzed by chromatin immunoprecipitation assay. Live cell imaging was performed for visualization of nuclear translocation of MR. MR acetylation was determined by Western blot with anti-acetyl-lysine antibody after immunoprecipitation with anti-MR antibody. Transcriptional activity of MR was determined by luciferase assay. For establishment of a hyperaldosteronism animal, Sprague-Dawley rats underwent uninephrectomy and received subcutaneous injection of 40 mg/kg per week of deoxycorticosterone acetate and drinking water containing 1% NaCl. Treatment with a HDAC class I inhibitor resulted in reduced expression of MR target genes in accordance with reduced recruitment of MR and RNA polymerase II on promoters of target genes. HDAC inhibition promoted MR acetylation, leading to decreased transcriptional activity of MR. Knockdown or inhibition of HDAC3 resulted in reduced expression of MR target genes induced by mineralocorticoids.
Conclusions:
These results indicate that HDAC inhibition attenuates transcriptional activity of MR through its acetylation and prevents development of hypertension in deoxycorticosterone acetate–induced hypertensive rats.
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Affiliation(s)
- Hae-Ahm Lee
- From the Department of Pharmacology (H.-A.L., D.-Y.L., H.-M.C., I.K.), Cardiovascular Research Institute (H.-A.L., I.K.), Cell and Matrix Research Institute (H.-A.L., S.-Y.K., I.K.), and Department of Biochemistry and Cell Biology (S.-Y.K.), Kyungpook National University School of Medicine, Daegu, Republic of Korea; and Department of Endocrinology, Metabolism and Nephrology, Kochi Medical School, Kochi University, Nankoku, Japan (Y.I.)
| | - Dong-Youb Lee
- From the Department of Pharmacology (H.-A.L., D.-Y.L., H.-M.C., I.K.), Cardiovascular Research Institute (H.-A.L., I.K.), Cell and Matrix Research Institute (H.-A.L., S.-Y.K., I.K.), and Department of Biochemistry and Cell Biology (S.-Y.K.), Kyungpook National University School of Medicine, Daegu, Republic of Korea; and Department of Endocrinology, Metabolism and Nephrology, Kochi Medical School, Kochi University, Nankoku, Japan (Y.I.)
| | - Hyun-Min Cho
- From the Department of Pharmacology (H.-A.L., D.-Y.L., H.-M.C., I.K.), Cardiovascular Research Institute (H.-A.L., I.K.), Cell and Matrix Research Institute (H.-A.L., S.-Y.K., I.K.), and Department of Biochemistry and Cell Biology (S.-Y.K.), Kyungpook National University School of Medicine, Daegu, Republic of Korea; and Department of Endocrinology, Metabolism and Nephrology, Kochi Medical School, Kochi University, Nankoku, Japan (Y.I.)
| | - Sang-Yeob Kim
- From the Department of Pharmacology (H.-A.L., D.-Y.L., H.-M.C., I.K.), Cardiovascular Research Institute (H.-A.L., I.K.), Cell and Matrix Research Institute (H.-A.L., S.-Y.K., I.K.), and Department of Biochemistry and Cell Biology (S.-Y.K.), Kyungpook National University School of Medicine, Daegu, Republic of Korea; and Department of Endocrinology, Metabolism and Nephrology, Kochi Medical School, Kochi University, Nankoku, Japan (Y.I.)
| | - Yasumasa Iwasaki
- From the Department of Pharmacology (H.-A.L., D.-Y.L., H.-M.C., I.K.), Cardiovascular Research Institute (H.-A.L., I.K.), Cell and Matrix Research Institute (H.-A.L., S.-Y.K., I.K.), and Department of Biochemistry and Cell Biology (S.-Y.K.), Kyungpook National University School of Medicine, Daegu, Republic of Korea; and Department of Endocrinology, Metabolism and Nephrology, Kochi Medical School, Kochi University, Nankoku, Japan (Y.I.)
| | - In Kyeom Kim
- From the Department of Pharmacology (H.-A.L., D.-Y.L., H.-M.C., I.K.), Cardiovascular Research Institute (H.-A.L., I.K.), Cell and Matrix Research Institute (H.-A.L., S.-Y.K., I.K.), and Department of Biochemistry and Cell Biology (S.-Y.K.), Kyungpook National University School of Medicine, Daegu, Republic of Korea; and Department of Endocrinology, Metabolism and Nephrology, Kochi Medical School, Kochi University, Nankoku, Japan (Y.I.)
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Coppotelli G, Mughal N, Callegari S, Sompallae R, Caja L, Luijsterburg MS, Dantuma NP, Moustakas A, Masucci MG. The Epstein-Barr virus nuclear antigen-1 reprograms transcription by mimicry of high mobility group A proteins. Nucleic Acids Res 2013; 41:2950-62. [PMID: 23358825 PMCID: PMC3597695 DOI: 10.1093/nar/gkt032] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Viral proteins reprogram their host cells by hijacking regulatory components of protein networks. Here we describe a novel property of the Epstein-Barr virus (EBV) nuclear antigen-1 (EBNA1) that may underlie the capacity of the virus to promote a global remodeling of chromatin architecture and cellular transcription. We found that the expression of EBNA1 in transfected human and mouse cells is associated with decreased prevalence of heterochromatin foci, enhanced accessibility of cellular DNA to micrococcal nuclease digestion and decreased average length of nucleosome repeats, suggesting de-protection of the nucleosome linker regions. This is a direct effect of EBNA1 because targeting the viral protein to heterochromatin promotes large-scale chromatin decondensation with slow kinetics and independent of the recruitment of adenosine triphosphate-dependent chromatin remodelers. The remodeling function is mediated by a bipartite Gly-Arg rich domain of EBNA1 that resembles the AT-hook of High Mobility Group A (HMGA) architectural transcription factors. Similar to HMGAs, EBNA1 is highly mobile in interphase nuclei and promotes the mobility of linker histone H1, which counteracts chromatin condensation and alters the transcription of numerous cellular genes. Thus, by regulating chromatin compaction, EBNA1 may reset cellular transcription during infection and prime the infected cells for malignant transformation.
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Affiliation(s)
- Giuseppe Coppotelli
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
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Transcriptional corepressor TOPLESS complexes with pseudoresponse regulator proteins and histone deacetylases to regulate circadian transcription. Proc Natl Acad Sci U S A 2012; 110:761-6. [PMID: 23267111 DOI: 10.1073/pnas.1215010110] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Circadian clocks are ubiquitous molecular time-keeping mechanisms that coordinate physiology and metabolism and provide an adaptive advantage to higher plants. The central oscillator of the plant clock is composed of interlocked feedback loops that involve multiple repressive factors acting throughout the circadian cycle. Pseudo response regulators (PRRs) comprise a five-member family that is essential to the function of the central oscillator. PRR5, PRR7, and PRR9 can bind the promoters of the core clock genes circadian clock associated 1 (CCA1) and late elongated hypocotyl (LHY) to restrict their expression to near dawn, but the mechanism has been unclear. Here we report that members of the plant Groucho/Tup1 corepressor family, topless/topless-related (TPL/TPR), interact with these three PRR proteins at the CCA1 and LHY promoters to repress transcription and alter circadian period. This activity is diminished in the presence of the inhibitor trichostatin A, indicating the requirement of histone deacetylase for full TPL activity. Additionally, a complex of PRR9, TPL, and histone deacetylase 6, can form in vivo, implicating this tripartite association as a central repressor of circadian gene expression. Our findings show that the TPL/TPR corepressor family are components of the central circadian oscillator mechanism and reinforces the role of this family as central to multiple signaling pathways in higher plants.
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48
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Shu H, Wildhaber T, Siretskiy A, Gruissem W, Hennig L. Distinct modes of DNA accessibility in plant chromatin. Nat Commun 2012; 3:1281. [DOI: 10.1038/ncomms2259] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 11/05/2012] [Indexed: 01/06/2023] Open
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Tsuboi H, Sutoh K, Wada M. Epigenetic memory of DNAi associated with cytosine methylation and histone modification in fern. PLANT SIGNALING & BEHAVIOR 2012; 7:1477-1483. [PMID: 22990449 PMCID: PMC3548873 DOI: 10.4161/psb.21974] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Gene silencing technology, such as RNA interference (RNAi), is commonly used to reduce gene expression in plant cells, and exogenous double-stranded RNA (dsRNA) can induce gene silencing in higher plants. Previously, we showed that the delivery of double-stranded DNA (dsDNA) fragments, such as PCR products of an endogenous gene sequence, into fern (Adiantum capillus-veneris) gametophytic cells induces a sequence-specific gene silencing that we termed DNAi. In this study, we used a neochrome 1 gene (NEO1) that mediates both red light-induced chloroplast movement and phototropism as a model of DNAi and confirmed that the NEO1 function was suppressed by the repression of the NEO1 gene. Interestingly, the gene silencing effect by DNAi was found in the progeny. Cytosine methylation was detected in the NEO1-silenced lines. The DNA modifications was present in the transcriptional region of NEO1, but no differences between wild type and the silenced lines were found in the downstream region of NEO1. Our data suggest that the DNAi gene silencing effect that was inherited throughout the next generation is regulated by epigenetic modification. Furthermore, the histone deacetylase inhibitor, trichostatin A (TSA), recovered the expression and function of NEO1 in the silenced lines, suggesting that histone deacetylation is essential for the direct suppression of target genes by DNAi.
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Affiliation(s)
- Hidenori Tsuboi
- Department of Biology; Faculty of Science; Kyushu University; Fukuoka, Japan
| | - Keita Sutoh
- Department of Biology; Faculty of Science; Kyushu University; Fukuoka, Japan
| | - Masamitsu Wada
- Department of Biology; Faculty of Science; Kyushu University; Fukuoka, Japan
- Department of Biological Sciences; Graduate School of Science and Engineering; Tokyo Metropolitan University; Tokyo, Japan
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50
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Sako K, Maki Y, Kanai T, Kato E, Maekawa S, Yasuda S, Sato T, Watahiki MK, Yamaguchi J. Arabidopsis RPT2a, 19S proteasome subunit, regulates gene silencing via DNA methylation. PLoS One 2012; 7:e37086. [PMID: 22615900 PMCID: PMC3353898 DOI: 10.1371/journal.pone.0037086] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 04/18/2012] [Indexed: 01/03/2023] Open
Abstract
The ubiquitin/proteasome pathway plays a crucial role in many biological processes. Here we report a novel role for the Arabidopsis 19S proteasome subunit RPT2a in regulating gene activity at the transcriptional level via DNA methylation. Knockout mutation of the RPT2a gene did not alter global protein levels; however, the transcriptional activities of reporter transgenes were severely reduced compared to those in the wild type. This transcriptional gene silencing (TGS) was observed for transgenes under control of either the constitutive CaMV 35S promoter or the cold-inducible RD29A promoter. Bisulfite sequencing analysis revealed that both the transgene and endogenous RD29A promoter regions were hypermethylated at CG and non-CG contexts in the rpt2a mutant. Moreover, the TGS of transgenes driven by the CaMV 35S promoters was released by treatment with the DNA methylation inhibitor 5-aza-2'-deoxycytidine, but not by application of the inhibitor of histone deacetylase Trichostatin A. Genetic crosses with the DNA methyltransferase met1 single or drm1drm2cmt3 triple mutants also resulted in a release of CaMV 35S transgene TGS in the rpt2a mutant background. Increased methylation was also found at transposon sequences, suggesting that the 19S proteasome containing AtRPT2a negatively regulates TGS at transgenes and at specific endogenous genes through DNA methylation.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Junji Yamaguchi
- Faculty of Science and Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- * E-mail:
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