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Del Toro-De León G, van Boven J, Santos-González J, Jiao WB, Peng H, Schneeberger K, Köhler C. Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis. Nucleic Acids Res 2024:gkae572. [PMID: 38967011 DOI: 10.1093/nar/gkae572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024] Open
Abstract
Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals-tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia element ONSEN on genomic imprinting in Arabidopsis thaliana. Through the combination of chemical TE mobilization and doubled haploid induction, we generated a line with 40 new ONSEN copies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs-both previously identified as promoters of ONSEN insertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdown of MEG imprinting. This study provides insights into the consequences of chemically induced TE remobilization in the endosperm, revealing that chemically-induced epigenome changes can have long-term consequences on imprinted gene expression.
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Affiliation(s)
- Gerardo Del Toro-De León
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Joram van Boven
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala 75007, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala 75007, Sweden
| | - Wen-Biao Jiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Haoran Peng
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Faculty for Biology, LMU Munich, Planegg-Martinsried 82152, Germany
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Düsseldorf 40225, Germany
| | - Claudia Köhler
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala 75007, Sweden
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2
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Zhang W, Zhang L, Feng Y, Lin D, Yang Z, Zhang Z, Ma Y. Genome-wide profiling of DNA methylome and transcriptome reveals epigenetic regulation of Urechis unicinctus response to sulfide stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172238. [PMID: 38582121 DOI: 10.1016/j.scitotenv.2024.172238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
Sulfide is a well-known environmental pollutant that can have detrimental effects on most organisms. However, few metazoans living in sulfide-rich environments have developed mechanisms to tolerate and adapt to sulfide stress. Epigenetic mechanisms, including DNA methylation, have been shown to play a vital role in environmental stress adaptation. Nevertheless, the precise function of DNA methylation in biological sulfide adaptation remains unclear. Urechis unicinctus, a benthic organism inhabiting sulfide-rich intertidal environments, is an ideal model organism for studying adaptation to sulfide environments. In this study, we conducted a comprehensive analysis of the DNA methylome and transcriptome of U. unicinctus after exposure to 50 μM sulfide. The results revealed dynamic changes in the DNA methylation (5-methylcytosine) landscape in response to sulfide stress, with U. unicinctus exhibiting elevated DNA methylation levels following stress exposure. Integrating differentially expressed genes (DEGs) and differentially methylated regions (DMRs), we identified a crucial role of gene body methylation in predicting gene expression. Furthermore, using a DNA methyltransferase inhibitor, we validated the involvement of DNA methylation in the sulfide stress response and the gene regulatory network influenced by DNA methylation. The results indicated that by modulating DNA methylation levels during sulfide stress, the expression of glutathione S-transferase, glutamyl aminopeptidase, and cytochrome c oxidase could be up-regulated, thereby facilitating the metabolism and detoxification of exogenous sulfides. Moreover, DNA methylation was found to regulate and enhance the oxidative phosphorylation pathway, including NADH dehydrogenase, isocitrate dehydrogenase, and ATP synthase. Additionally, DNA methylation influenced the regulation of Cytochrome P450 and macrophage migration inhibitory factor, both of which are closely associated with oxidative stress and stress resistance. Our findings not only emphasize the role of DNA methylation in sulfide adaptation but also provide novel insights into the potential mechanisms through which marine organisms adapt to environmental changes.
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Affiliation(s)
- Wenqing Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Long Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Yuxin Feng
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Dawei Lin
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Zhi Yang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Zhifeng Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China; Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
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3
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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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4
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Bogan SN, Yi SV. Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations. Genome Biol Evol 2024; 16:evae022. [PMID: 38324384 PMCID: PMC10899001 DOI: 10.1093/gbe/evae022] [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: 07/13/2023] [Revised: 01/09/2024] [Accepted: 01/23/2024] [Indexed: 02/09/2024] Open
Abstract
There is great interest in exploring epigenetic modifications as drivers of adaptive organismal responses to environmental change. Extending this hypothesis to populations, epigenetically driven plasticity could influence phenotypic changes across environments. The canonical model posits that epigenetic modifications alter gene regulation and subsequently impact phenotypes. We first discuss origins of epigenetic variation in nature, which may arise from genetic variation, spontaneous epimutations, epigenetic drift, or variation in epigenetic capacitors. We then review and synthesize literature addressing three facets of the aforementioned model: (i) causal effects of epigenetic modifications on phenotypic plasticity at the organismal level, (ii) divergence of epigenetic patterns in natural populations distributed across environmental gradients, and (iii) the relationship between environmentally induced epigenetic changes and gene expression at the molecular level. We focus on DNA methylation, the most extensively studied epigenetic modification. We find support for environmentally associated epigenetic structure in populations and selection on stable epigenetic variants, and that inhibition of epigenetic enzymes frequently bears causal effects on plasticity. However, there are pervasive confounding issues in the literature. Effects of chromatin-modifying enzymes on phenotype may be independent of epigenetic marks, alternatively resulting from functions and protein interactions extrinsic of epigenetics. Associations between environmentally induced changes in DNA methylation and expression are strong in plants and mammals but notably absent in invertebrates and nonmammalian vertebrates. Given these challenges, we describe emerging approaches to better investigate how epigenetic modifications affect gene regulation, phenotypic plasticity, and divergence among populations.
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Affiliation(s)
- Samuel N Bogan
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Soojin V Yi
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
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5
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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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6
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Su J, Song S, Dou Y, Jia X, Song S, Ding X. Methylation specific enzyme-linked oligonucleotide assays (MS-ELONA) for ultrasensitive DNA methylation analysis. Biosens Bioelectron 2023; 238:115587. [PMID: 37586263 DOI: 10.1016/j.bios.2023.115587] [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: 06/15/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/18/2023]
Abstract
Methylation of the promoter region of cancer related genes plays a crucial role in the occurrence and development of cancer, and the degree of methylation has great potential for the early cancer diagnosis. At present, the technology used to quantify DNA methylation is mainly based on the DNA sequencing which are time-consuming and high-cost in the relating application. We have developed an ultrasensitive method of methylation specific enzyme-linked oligonucleotide assays (MS-ELONA) to detect and quantify the level of DNA methylation. We could detect as little as 2 pg of methylated DNA in the 100000-fold excess of unmethylated genes, and discriminate prostate cancer from benign prostatic hyperplasia (BPH) and control with serum samples. We also demonstrate the reversibility of DNA methylation modification by treatment with demethylation drugs. With 16-channel electrochemical work station, our research reveals a simple and inexpensive method to quantify the methylation level of specially appointed genes, and have the potential to be applied in the clinical research.
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Affiliation(s)
- Jing Su
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China; State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Shasha Song
- Pathology Department, Yantai Fushan People's Hospital, Yantai, China
| | - Yanzhi Dou
- Shanghai Institute of Microsystem and Information Technology, Chinse Academy of Sciences, Shanghai 200050, China
| | - Xiaolong Jia
- Department of Urology, The First Affiliated Hospital of Ningbo University, Liuting Street, Ningbo 315010, China
| | - Shiping Song
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China; Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
| | - Xianting Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China; State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China.
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7
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Colicchio JM, Amstutz CL, Garcia N, Prabhu KN, Cairns TM, Akman M, Gottilla T, Gollery T, Stricklin SL, Bayer TS. A tool for rapid, automated characterization of population epigenomics in plants. Sci Rep 2023; 13:12915. [PMID: 37591855 PMCID: PMC10435466 DOI: 10.1038/s41598-023-38356-7] [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: 02/16/2023] [Accepted: 07/06/2023] [Indexed: 08/19/2023] Open
Abstract
Epigenetic variation in plant populations is an important factor in determining phenotype and adaptation to the environment. However, while advances have been made in the molecular and computational methods to analyze the methylation status of a given sample of DNA, tools to profile and compare the methylomes of multiple individual plants or groups of plants at high resolution and low cost are lacking. Here, we describe a computational approach and R package (sounDMR) that leverages the benefits of long read nanopore sequencing to enable robust identification of differential methylation from complex experimental designs, as well as assess the variability within treatment groups and identify individual plants of interest. We demonstrate the utility of this approach by profiling a population of Arabidopsis thaliana exposed to a demethylating agent and identify genomic regions of high epigenetic variability between individuals. Given the low cost of nanopore sequencing devices and the ease of sample preparation, these results show that high resolution epigenetic profiling of plant populations can be made more broadly accessible in plant breeding and biotechnology.
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Affiliation(s)
| | | | | | | | | | - Melis Akman
- Sound Agriculture Company, Emeryville, CA, USA
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8
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Yang LL, Zhang XY, Wang LY, Li YG, Li XT, Yang Y, Su Q, Chen N, Zhang YL, Li N, Deng CL, Li SF, Gao WJ. Lineage-specific amplification and epigenetic regulation of LTR-retrotransposons contribute to the structure, evolution, and function of Fabaceae species. BMC Genomics 2023; 24:423. [PMID: 37501164 PMCID: PMC10373317 DOI: 10.1186/s12864-023-09530-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/22/2023] [Indexed: 07/29/2023] Open
Abstract
BACKGROUND Long terminal repeat (LTR)-retrotransposons (LTR-RTs) are ubiquitous and make up the majority of nearly all sequenced plant genomes, whereas their pivotal roles in genome evolution, gene expression regulation as well as their epigenetic regulation are still not well understood, especially in a large number of closely related species. RESULTS Here, we analyzed the abundance and dynamic evolution of LTR-RTs in 54 species from an economically and agronomically important family, Fabaceae, and also selected two representative species for further analysis in expression of associated genes, transcriptional activity and DNA methylation patterns of LTR-RTs. Annotation results revealed highly varied proportions of LTR-RTs in these genomes (5.1%~68.4%) and their correlation with genome size was highly positive, and they were significantly contributed to the variance in genome size through species-specific unique amplifications. Almost all of the intact LTR-RTs were inserted into the genomes 4 Mya (million years ago), and more than 50% of them were inserted in the last 0.5 million years, suggesting that recent amplifications of LTR-RTs were an important force driving genome evolution. In addition, expression levels of genes with intronic, promoter, and downstream LTR-RT insertions of Glycine max and Vigna radiata, two agronomically important crops in Fabaceae, showed that the LTR-RTs located in promoter or downstream regions suppressed associated gene expression. However, the LTR-RTs within introns promoted gene expression or had no contribution to gene expression. Additionally, shorter and younger LTR-RTs maintained higher mobility and transpositional potential. Compared with the transcriptionally silent LTR-RTs, the active elements showed significantly lower DNA methylation levels in all three contexts. The distributions of transcriptionally active and silent LTR-RT methylation varied across different lineages due to the position of LTR-RTs located or potentially epigenetic regulation. CONCLUSION Lineage-specific amplification patterns were observed and higher methylation level may repress the activity of LTR-RTs, further influence evolution in Fabaceae species. This study offers valuable clues into the evolution, function, transcriptional activity and epigenetic regulation of LTR-RTs in Fabaceae genomes.
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Affiliation(s)
- Long-Long Yang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Xin-Yu Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Li-Ying Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Yan-Ge Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Xiao-Ting Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Yi Yang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Qing Su
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Ning Chen
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Yu-Lan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China.
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China.
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9
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Agius DR, Kapazoglou A, Avramidou E, Baranek M, Carneros E, Caro E, Castiglione S, Cicatelli A, Radanovic A, Ebejer JP, Gackowski D, Guarino F, Gulyás A, Hidvégi N, Hoenicka H, Inácio V, Johannes F, Karalija E, Lieberman-Lazarovich M, Martinelli F, Maury S, Mladenov V, Morais-Cecílio L, Pecinka A, Tani E, Testillano PS, Todorov D, Valledor L, Vassileva V. Exploring the crop epigenome: a comparison of DNA methylation profiling techniques. FRONTIERS IN PLANT SCIENCE 2023; 14:1181039. [PMID: 37389288 PMCID: PMC10306282 DOI: 10.3389/fpls.2023.1181039] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/27/2023] [Indexed: 07/01/2023]
Abstract
Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.
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Affiliation(s)
- Dolores Rita Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
- Biology Department, Ġ.F.Abela Junior College, Msida, Malta
| | - Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Evangelia Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Miroslav Baranek
- Mendeleum-Insitute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czechia
| | - Elena Carneros
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Stefano Castiglione
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Angela Cicatelli
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Aleksandra Radanovic
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
| | - Jean-Paul Ebejer
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Francesco Guarino
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Andrea Gulyás
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Norbert Hidvégi
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Hans Hoenicka
- Genomic Research Department, Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | - Vera Inácio
- BioISI – BioSystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Frank Johannes
- Plant Epigenomics, Technical University of Munich (TUM), Freising, Germany
| | - Erna Karalija
- Faculty of Science, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Michal Lieberman-Lazarovich
- Department of Vegetables and Field Crops, Agricultural Research Organization, Volcani Center, Institute of Plant Sciences, Rishon LeZion, Israel
| | | | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures EA1207 USC1328, INRAE, Université d’Orléans, Orléans, France
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Pilar S. Testillano
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Dimitar Todorov
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias, University of Oviedo, Oviedo, Spain
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
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10
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Brestovitsky A, Iwasaki M, Cho J, Adulyanukosol N, Paszkowski J, Catoni M. Specific suppression of long terminal repeat retrotransposon mobilization in plants. PLANT PHYSIOLOGY 2023; 191:2245-2255. [PMID: 36583226 PMCID: PMC10069891 DOI: 10.1093/plphys/kiac605] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 05/19/2023]
Abstract
The tissue culture passage necessary for the generation of transgenic plants induces genome instability. This instability predominantly involves the uncontrolled mobilization of LTR retrotransposons (LTR-TEs), which are the most abundant class of mobile genetic elements in plant genomes. Here, we demonstrate that in conditions inductive for high LTR-TE mobilization, like abiotic stress in Arabidopsis (Arabidopsis thaliana) and callus culture in rice (Oryza sativa), application of the reverse transcriptase (RT) inhibitor known as Tenofovir substantially affects LTR-TE RT activity without interfering with plant development. We observed that Tenofovir reduces extrachromosomal DNA accumulation and prevents new genomic integrations of the active LTR-TE ONSEN in heat-stressed Arabidopsis seedlings, and transposons of O. sativa 17 and 19 (Tos17 and Tos19) in rice calli. In addition, Tenofovir allows the recovery of plants free from new LTR-TE insertions. We propose the use of Tenofovir as a tool for studies of LTR-TE transposition and for limiting genetic instabilities of plants derived from tissue culture.
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Affiliation(s)
- Anna Brestovitsky
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - Mayumi Iwasaki
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
- Department of Plant Biology, University of Geneva, Geneva CH-1211, Switzerland
| | - Jungnam Cho
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | | | - Jerzy Paszkowski
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
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11
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Yang H, Shi X, Chen C, Hou J, Ji T, Cheng J, Birchler JA. Genomic imbalance modulates transposable element expression in maize. PLANT COMMUNICATIONS 2023; 4:100467. [PMID: 36307986 PMCID: PMC10030319 DOI: 10.1016/j.xplc.2022.100467] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/19/2022] [Accepted: 10/23/2022] [Indexed: 05/04/2023]
Abstract
Genomic imbalance refers to the more severe phenotypic consequences of changing part of a chromosome compared with the whole genome set. Previous genome imbalance studies in maize have identified prevalent inverse modulation of genes on the unvaried chromosomes (trans) with both the addition or subtraction of chromosome arms. Transposable elements (TEs) comprise a substantial fraction of the genome, and their reaction to genomic imbalance is therefore of interest. Here, we analyzed TE expression using RNA-seq data of aneuploidy and ploidy series and found that most aneuploidies showed an inverse modulation of TEs, but reductions in monosomy and increases in disomy and trisomy were also common. By contrast, the ploidy series showed little TE modulation. The modulation of TEs and genes in the same experimental group were compared, and TEs showed greater modulation than genes, especially in disomy. Class I and II TEs were differentially modulated in most aneuploidies, and some superfamilies in each TE class also showed differential modulation. Finally, the significantly upregulated TEs in three disomies (TB-7Lb, TB9Lc, and TB-10L19) did not increase the proportion of adjacent gene expression when compared with non-differentially expressed TEs, indicating that modulations of TEs do not compound the effect on genes. These results suggest that the prevalent inverse TE modulation in aneuploidy results from stoichiometric upset of the regulatory machinery used by TEs, similar to the response of core genes to genomic imbalance.
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Affiliation(s)
- Hua Yang
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Xiaowen Shi
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Chen Chen
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA
| | - Jie Hou
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA
| | - Tieming Ji
- Department of Statistics, University of Missouri, Columbia, MO 65211, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.
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12
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Fortini EA, Batista DS, Felipe SHS, Silva TD, Correia LNF, Farias LM, Faria DV, Pinto VB, Santa-Catarina C, Silveira V, De-la-Peña C, Castillo-Castro E, Otoni WC. Physiological, epigenetic, and proteomic responses in Pfaffia glomerata growth in vitro under salt stress and 5-azacytidine. PROTOPLASMA 2023; 260:467-482. [PMID: 35788779 DOI: 10.1007/s00709-022-01789-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Plants adjust their complex molecular, biochemical, and metabolic processes to overcome salt stress. Here, we investigated the proteomic and epigenetic alterations involved in the morphophysiological responses of Pfaffia glomerata, a medicinal plant, to salt stress and the demethylating agent 5-azacytidine (5-azaC). Moreover, we investigated how these changes affected the biosynthesis of 20-hydroxyecdysone (20-E), a pharmacologically important specialized metabolite. Plants were cultivated in vitro for 40 days in Murashige and Skoog medium supplemented with NaCl (50 mM), 5-azaC (25 μM), and NaCl + 5-azaC. Compared with the control (medium only), the treatments reduced growth, photosynthetic rates, and photosynthetic pigment content, with increase in sucrose, total amino acids, and proline contents, but a reduction in starch and protein. Comparative proteomic analysis revealed 282 common differentially accumulated proteins involved in 87 metabolic pathways, most of them related to amino acid and carbohydrate metabolism, and specialized metabolism. 5-azaC and NaCl + 5-azaC lowered global DNA methylation levels and 20-E content, suggesting that 20-E biosynthesis may be regulated by epigenetic mechanisms. Moreover, downregulation of a key protein in jasmonate biosynthesis indicates the fundamental role of this hormone in the 20-E biosynthesis. Taken together, our results highlight possible regulatory proteins and epigenetic changes related to salt stress tolerance and 20-E biosynthesis in P. glomerata, paving the way for future studies of the mechanisms involved in this regulation.
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Affiliation(s)
- Evandro Alexandre Fortini
- Laboratório de Cultura de Tecidos Vegetais (LCTII), Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - Diego Silva Batista
- Departamento de Agricultura, Universidade Federal da Paraíba, Campus III, Bananeiras, PB, 58220-000, Brazil
| | - Sérgio Heitor Sousa Felipe
- PPG em Agroecologia, Universidade Estadual do Maranhão, Av. Lourenço Vieira da Silva, s/nº, Cidade Universitária Paulo VI, São Luís, MA, Brazil
| | - Tatiane Dulcineia Silva
- Laboratório de Cultura de Tecidos Vegetais (LCTII), Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - Ludmila Nayara Freitas Correia
- Laboratório de Cultura de Tecidos Vegetais (LCTII), Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - Letícia Monteiro Farias
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Daniele Vidal Faria
- Laboratório de Cultura de Tecidos Vegetais (LCTII), Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - Vitor Batista Pinto
- Laboratório de Biotecnologia (LBT), Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Claudete Santa-Catarina
- Laboratório de Biologia Celular e Tecidual (LBCT), CBB-UENF, Campos dos Goytacazes, RJ, Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia (LBT), Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A. C. (CICY), 97205, Mérida, Yucatán, Mexico
| | - Eduardo Castillo-Castro
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A. C. (CICY), 97205, Mérida, Yucatán, Mexico
| | - Wagner Campos Otoni
- Laboratório de Cultura de Tecidos Vegetais (LCTII), Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil.
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13
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Shanker OR, Kumar S, Dixit AB, Banerjee J, Tripathi M, Sarat Chandra P. Epigenetics of neurological diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:165-184. [DOI: 10.1016/bs.pmbts.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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14
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Minow MAA, Coneva V, Lesy V, Misyura M, Colasanti J. Plant gene silencing signals move from the phloem to influence gene expression in shoot apical meristems. BMC PLANT BIOLOGY 2022; 22:606. [PMID: 36550422 PMCID: PMC9783409 DOI: 10.1186/s12870-022-03998-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Small RNAs (sRNA) are potent regulators of gene expression that can diffuse short distances between cells and move long distances through plant vasculature. However, the degree to which sRNA silencing signals can move from the phloem to the shoot apical meristem (SAM) remains unclear. RESULTS Two independent transgenic approaches were used to examine whether phloem sRNA silencing can reach different domains of the SAM and silence SAM-expressed genes. First, the phloem companion-cell specific SUCROSE-PROTON SYMPORTER2 (SUC2) promoter was used to drive expression of an inverted repeat to target the FD gene, an exclusively SAM-localized floral regulator. Second, the SUC2 promoter was used to express an artificial microRNA (aMiR) designed to target a synthetic CLAVATA3 (CLV3) transgene in SAM stem cells. Both phloem silencing signals phenocopied the loss of function of their targets and altered target gene expression suggesting that a phloem-to-SAM silencing communication axis exists, connecting distal regions of the plant to SAM stem cells. CONCLUSIONS Demonstration of phloem-to-SAM silencing reveals a regulatory link between somatic sRNA expressed in distal regions of the plant and the growing shoot. Since the SAM stem cells ultimately produce the gametes, we discuss the intriguing possibility that phloem-to-SAM sRNA trafficking could allow transient somatic sRNA expression to manifest stable, transgenerational epigenetic changes.
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Affiliation(s)
- Mark A. A. Minow
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East Guelph, Ontario, Canada
| | - Viktoriya Coneva
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East Guelph, Ontario, Canada
| | - Victoria Lesy
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East Guelph, Ontario, Canada
| | - Max Misyura
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East Guelph, Ontario, Canada
| | - Joseph Colasanti
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East Guelph, Ontario, Canada
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15
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Morgan BL, Donohue K. Parental methylation mediates how progeny respond to environments of parents and of progeny themselves. ANNALS OF BOTANY 2022; 130:883-899. [PMID: 36201313 PMCID: PMC9758305 DOI: 10.1093/aob/mcac125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND AIMS Environments experienced by both parents and offspring influence progeny traits, but the epigenetic mechanisms that regulate the balance of parental vs. progeny control of progeny phenotypes are not known. We tested whether DNA methylation in parents and/or progeny mediates responses to environmental cues experienced in both generations. METHODS Using Arabidopsis thaliana, we manipulated parental and progeny DNA methylation both chemically, via 5-azacytidine, and genetically, via mutants of methyltransferase genes, then measured progeny germination responses to simulated canopy shade in parental and progeny generations. KEY RESULTS We first found that germination of offspring responded to parental but not seed demethylation. We further found that parental demethylation reversed the parental effect of canopy in seeds with low (Cvi-1) to intermediate (Col) dormancy, but it obliterated the parental effect in seeds with high dormancy (Cvi-0). Demethylation did so by either suppressing germination of seeds matured under white-light (Cvi-1) or under canopy (Cvi-0), or by increasing the germination of seeds matured under canopy (Col). Disruption of parental methylation also prevented seeds from responding to their own light environment in one genotype (Cvi-0, most dormant), but it enabled seeds to respond to their own environment in another genotype (Cvi-1, least dormant). Using mutant genotypes, we found that both CG and non-CG DNA methylation were involved in parental effects on seed germination. CONCLUSIONS Parental methylation state influences seed germination more strongly than does the progeny's own methylation state, and it influences how seeds respond to environments of parents and progeny in a genotype-specific manner.
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Affiliation(s)
- Britany L Morgan
- University Program in Ecology Duke University, Durham, NC 27705, USA
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Kathleen Donohue
- University Program in Ecology Duke University, Durham, NC 27705, USA
- Biology Department, Duke University, Durham, NC 27705, USA
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16
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Weiss T, Crisp PA, Rai KM, Song M, Springer NM, Zhang F. Epigenetic features drastically impact CRISPR-Cas9 efficacy in plants. PLANT PHYSIOLOGY 2022; 190:1153-1164. [PMID: 35689624 PMCID: PMC9516779 DOI: 10.1093/plphys/kiac285] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/25/2022] [Indexed: 05/19/2023]
Abstract
CRISPR-Cas9-mediated genome editing has been widely adopted for basic and applied biological research in eukaryotic systems. While many studies consider DNA sequences of CRISPR target sites as the primary determinant for CRISPR mutagenesis efficiency and mutation profiles, increasing evidence reveals the substantial role of chromatin context. Nonetheless, most prior studies are limited by the lack of sufficient epigenetic resources and/or by only transiently expressing CRISPR-Cas9 in a short time window. In this study, we leveraged the wealth of high-resolution epigenomic resources in Arabidopsis (Arabidopsis thaliana) to address the impact of chromatin features on CRISPR-Cas9 mutagenesis using stable transgenic plants. Our results indicated that DNA methylation and chromatin features could lead to substantial variations in mutagenesis efficiency by up to 250-fold. Low mutagenesis efficiencies were mostly associated with repressive heterochromatic features. This repressive effect appeared to persist through cell divisions but could be alleviated through substantial reduction of DNA methylation at CRISPR target sites. Moreover, specific chromatin features, such as H3K4me1, H3.3, and H3.1, appear to be associated with significant variation in CRISPR-Cas9 mutation profiles mediated by the non-homologous end joining repair pathway. Our findings provide strong evidence that specific chromatin features could have substantial and lasting impacts on both CRISPR-Cas9 mutagenesis efficiency and DNA double-strand break repair outcomes.
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Affiliation(s)
- Trevor Weiss
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, Minnesota 55108, USA
- Microbial and Plant Genomics Institute, University of Minnesota, Minneapolis, Minnesota 55108, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55108, USA
| | - Peter A Crisp
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, Minnesota 55108, USA
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Krishan M Rai
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Meredith Song
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55108, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, Minnesota 55108, USA
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17
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Wang M, He L, Chen B, Wang Y, Wang L, Zhou W, Zhang T, Cao L, Zhang P, Xie L, Zhang Q. Transgenerationally Transmitted DNA Demethylation of a Spontaneous Epialleles Using CRISPR/dCas9-TET1cd Targeted Epigenetic Editing in Arabidopsis. Int J Mol Sci 2022; 23:ijms231810492. [PMID: 36142407 PMCID: PMC9504898 DOI: 10.3390/ijms231810492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/24/2022] Open
Abstract
CRISPR/dCas9 is an important DNA modification tool in which a disarmed Cas9 protein with no nuclease activity is fused with a specific DNA modifying enzyme. A previous study reported that overexpression of the TET1 catalytic domain (TET1cd) reduces genome-wide methylation in Arabidopsis. A spontaneous naturally occurring methylation region (NMR19-4) was identified in the promoter region of the PPH (Pheophytin Pheophorbide Hydrolase) gene, which encodes an enzyme that can degrade chlorophyll and accelerate leaf senescence. The methylation status of NMR19-4 is associated with PPH expression and leaf senescence in Arabidopsis natural accessions. In this study, we show that the CRISPR/dCas9-TET1cd system can be used to target the methylation of hypermethylated NMR19-4 region to reduce the level of methylation, thereby increasing the expression of PPH and accelerating leaf senescence. Furthermore, hybridization between transgenic demethylated plants and hypermethylated ecotypes showed that the demethylation status of edited NMR19-4, along with the enhanced PPH expression and accelerated leaf senescence, showed Mendelian inheritance in F1 and F2 progeny, indicating that spontaneous epialleles are stably transmitted trans-generationally after demethylation editing. Our results provide a rational approach for future editing of spontaneously mutated epialleles and provide insights into the epigenetic mechanisms that control plant leaf senescence.
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Affiliation(s)
- Min Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Li He
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Bowei Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanwei Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Lishan Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Wei Zhou
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Lesheng Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Peng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Linan Xie
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Correspondence:
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18
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Morgan BL, Donohue K. Parental
DNA
methylation influences plasticity of early offspring traits, but offspring
DNA
methylation influences trait plasticity throughout life. Ecol Evol 2022. [DOI: 10.1002/ece3.9224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Britany L. Morgan
- University Program in Ecology Duke University Durham North Carolina USA
- Center for Agricultural Synthetic Biology University of Tennessee Knoxville Tennessee USA
| | - Kathleen Donohue
- University Program in Ecology Duke University Durham North Carolina USA
- Biology Department Duke University Durham North Carolina USA
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19
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Yu WH, Zhang LM, Luo FL, Yu FH, Li MH. Roles of clonal parental effects in regulating interspecific competition between two floating plants. FRONTIERS IN PLANT SCIENCE 2022; 13:924001. [PMID: 35937331 PMCID: PMC9355590 DOI: 10.3389/fpls.2022.924001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Parental effects can influence offspring fitness, which may further impact interspecific competition. However, few studies have tested the role of clonal parental effects in regulating interspecific interactions and examined the underlying mechanisms. We conducted two consecutive experiments with two clonal plants (Pistia stratiotes and Eichhornia crassipes). In the first experiment, the mother ramet of P. stratiotes and E. crassipes were grown in two nutrient levels and treated with a DNA demethylation reagent (5-azacytidine) or not. In the second experiment, the offspring ramets from each of the four treatments in the first experiment were grown alone (no competition) or with a heterospecific neighbor (with interspecific competition). We found no parental nutrient effect on the competitive ability of E. crassipes, but a significant parental nutrient effect of both E. crassipes and P. stratiotes on the competitive ability of P. stratiotes. Furthermore, the parental nutrient effect of P. stratiotes on the competitive ability of P. stratiotes varied depending on the DNA methylation status of both P. stratiotes and E. crassipes. These clonal parental effects were related to resource provisioning and/or DNA methylation. We conclude that clonal parental nutrient effects can regulate interspecific competition between P. stratiotes and E. crassipes by altering the competitive ability of P. stratiotes. Both resource provisioning and epigenetic mechanisms can be involved in these clonal parental effects. By regulating interspecific competition, clonal parental effects may further influence species coexistence, community structure, and ecosystem functioning.
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Affiliation(s)
- Wen-Han Yu
- Institute of Wetland Ecology and Clone Ecology/Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Li-Min Zhang
- Institute of Wetland Ecology and Clone Ecology/Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Fang-Li Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Fei-Hai Yu
- Institute of Wetland Ecology and Clone Ecology/Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Mai-He Li
- Forest Dynamics, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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20
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Kong J, Garcia V, Zehraoui E, Stammitti L, Hilbert G, Renaud C, Maury S, Delaunay A, Cluzet S, Lecourieux F, Lecourieux D, Teyssier E, Gallusci P. Zebularine, a DNA Methylation Inhibitor, Activates Anthocyanin Accumulation in Grapevine Cells. Genes (Basel) 2022; 13:genes13071256. [PMID: 35886036 PMCID: PMC9316115 DOI: 10.3390/genes13071256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 02/01/2023] Open
Abstract
Through its role in the regulation of gene expression, DNA methylation can participate in the control of specialized metabolite production. We have investigated the link between DNA methylation and anthocyanin accumulation in grapevine using the hypomethylating drug, zebularine and Gamay Teinturier cell suspensions. In this model, zebularine increased anthocyanin accumulation in the light, and induced its production in the dark. To unravel the underlying mechanisms, cell transcriptome, metabolic content, and DNA methylation were analyzed. The up-regulation of stress-related genes, as well as a decrease in cell viability, revealed that zebularine affected cell integrity. Concomitantly, the global DNA methylation level was only slightly decreased in the light and not modified in the dark. However, locus-specific analyses demonstrated a decrease in DNA methylation at a few selected loci, including a CACTA DNA transposon and a small region upstream from the UFGT gene, coding for the UDP glucose:flavonoid-3-O-glucosyltransferase, known to be critical for anthocyanin biosynthesis. Moreover, this decrease was correlated with an increase in UFGT expression and in anthocyanin content. In conclusion, our data suggest that UFGT expression could be regulated through DNA methylation in Gamay Teinturier, although the functional link between changes in DNA methylation and UFGT transcription still needs to be demonstrated.
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Affiliation(s)
- Junhua Kong
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Virginie Garcia
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Enric Zehraoui
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Linda Stammitti
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Ghislaine Hilbert
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Christel Renaud
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Stéphane Maury
- INRAe, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, 45067 Orléans, France; (S.M.); (A.D.)
| | - Alain Delaunay
- INRAe, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, 45067 Orléans, France; (S.M.); (A.D.)
| | - Stéphanie Cluzet
- Unité de Recherche Oenologie, Faculté des Sciences Pharmaceutiques, University Bordeaux, EA4577, USC 1366 INRA, Equipe Molécules d’Intérêt Biologique (GESVAB), ISVV, CEDEX, 33882 Villenave d’Ornon, France;
| | - Fatma Lecourieux
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - David Lecourieux
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Emeline Teyssier
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
- Correspondence: ; Tel.: +33-5-5757-5928
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
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21
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Liu S, Bao Y, Deng H, Liu G, Han Y, Wu Y, Zhang T, Chen C. The Methylation Inhibitor 5-Aza-2'-Deoxycytidine Induces Genome-Wide Hypomethylation in Rice. RICE (NEW YORK, N.Y.) 2022; 15:35. [PMID: 35779161 PMCID: PMC9250569 DOI: 10.1186/s12284-022-00580-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
DNA methylation is a conserved epigenetic modification which is vital for regulating gene expression and maintaining genome stability in both mammals and plants. Homozygous mutation of rice methyltransferase 1 (met1) gene can cause host death in rice, making it difficult to obtain plant material needed for hypomethylation research. To circumvent this challenge, the methylation inhibitor, 5-Aza-2'-deoxycytidine (AzaD), is used as a cytosine nucleoside analogue to reduce genome wide hypomethylation and is widely used in hypomethylation research. However, how AzaD affects plant methylation profiles at the genome scale is largely unknown. Here, we treated rice seedlings with AzaD and compared the AzaD treatment with osmet1-2 mutants, illustrating that there are similar CG hypomethylation and distribution throughout the whole genome. Along with global methylation loss class I transposable elements (TEs) which are farther from genes compared with class II TEs, were more significantly activated, and the RNA-directed DNA Methylation (RdDM) pathway was activated in specific genomic regions to compensate for severe CG loss. Overall, our results suggest that AzaD is an effective DNA methylation inhibitor that can influence genome wide methylation and cause a series of epigenetic variations.
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Affiliation(s)
- Shuo Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yu Bao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Hui Deng
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yangshuo Han
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yuechao Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
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22
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Saha D, Shaw AK, Datta S, Mitra J, Kar G. DNA hypomethylation is the plausible driver of heat stress adaptation in Linum usitatissimum. PHYSIOLOGIA PLANTARUM 2022; 174:e13689. [PMID: 35462427 DOI: 10.1111/ppl.13689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/31/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Heat stress has a significant impact on the climatic adaptation of flax, a cool-season economic crop. Genome-wide DNA methylation patterns are crucial for understanding how flax cultivars respond to heat adversities. It is worth noting that the DNA methylome in flax has yet to be investigated at the nucleotide level. Although heat stress above 40°C caused oxidative damage in flax leaves, 5-azacytidine, a hypomethylating agent, reduced this effect by 15%-24%. Differences in the expression of the LuMET1 (DNA methyltransferase) gene suggested that DNA methylation/demethylation may play a major role in the flax heat stress response. Thus, whole-genome bisulfite sequencing-derived DNA methylation profiles in flax, with or without heat stress and 5-azaC, were developed and analyzed here. In response to heat stress, a high percentage of significant differentially methylated regions (DMRs), particularly hypomethylated DMRs, were identified in the CHH nucleotide sequence context (H = A/T/C). Some of these DMRs overlapped with transposable element insertions. The majority of DMRs were discovered in intergenic regions, but several DMR loci were also found near genes relevant to heat stress response and epigenetic processes. These DMRs, in particular, are linked to CpG islands, implying a possible role in promoter methylation and gene silencing. The DMRs discovered in this study are crucial for understanding and identifying the key players in heat stress response in flax, which will help in developing climate-smart flax varieties.
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Affiliation(s)
- Dipnarayan Saha
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
| | - Arun Kumar Shaw
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
| | - Subhojit Datta
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
| | - Jiban Mitra
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
| | - Gouranga Kar
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
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23
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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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24
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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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25
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Wang MZ, Li HL, Tang M, Yu FH. DNA Methylation Correlates With Responses of Experimental Hydrocotyle vulgaris Populations to Different Flood Regimes. FRONTIERS IN PLANT SCIENCE 2022; 13:831175. [PMID: 35330870 PMCID: PMC8940293 DOI: 10.3389/fpls.2022.831175] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/11/2022] [Indexed: 06/10/2023]
Abstract
Epigenetic mechanisms such as DNA methylation are considered as an important pathway responsible for phenotypic responses and rapid acclimation of plants to different environments. To search for empirical evidence that DNA methylation is implicated in stress-responses of non-model species, we exposed genetically uniform, experimental populations of the wetland clonal plant Hydrocotyle vulgaris to two manipulated flood regimes, i.e., semi-submergence vs. submergence, measured phenotypic traits, and quantified different types of DNA methylation using MSAP (methylation-sensitive amplified polymorphism). We found different epi-phenotypes and significant epigenetic differentiation between semi-submerged and submerged populations. Compared to subepiloci (denoting DNA methylation conditions) for the CG-methylated state, unmethylation and CHG-hemimethylation subepiloci types contribute more prominently to the epigenetic structure of experimental populations. Moreover, we detected some epimarker outliers potentially facilitate population divergence between two flood regimes. Some phenotypic variation was associated with flood-induced DNA methylation variation through different types of subepiloci. Our study provides the indication that DNA methylation might be involved in plant responses to environmental variation without altering DNA sequences.
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Affiliation(s)
- Mo-Zhu Wang
- Institute of Wetland Ecology & Clone Ecology/Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Hong-Li Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Min Tang
- Institute of Wetland Ecology & Clone Ecology/Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Fei-Hai Yu
- Institute of Wetland Ecology & Clone Ecology/Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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26
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Huc J, Dziasek K, Pachamuthu K, Woh T, Köhler C, Borges F. Bypassing reproductive barriers in hybrid seeds using chemically induced epimutagenesis. THE PLANT CELL 2022; 34:989-1001. [PMID: 34792584 PMCID: PMC8894923 DOI: 10.1093/plcell/koab284] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/09/2021] [Indexed: 05/13/2023]
Abstract
The triploid block, which prevents interploidy hybridizations in flowering plants, is characterized by a failure in endosperm development, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed genes (PEGs), which are upregulated in tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed collapse is bypassed in Arabidopsis plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early growth. We identified strong suppressor lines showing stable transgenerational inheritance of hypomethylation in the CG context, as well as normalized expression of PEGs in triploid seeds. Importantly, differentially methylated loci segregate in the progeny of "epimutagenized" plants, which may allow epialleles involved in the triploid block response to be identified in future studies. Finally, we demonstrate that chemically induced epimutagenesis facilitates hybridization between different Capsella species, thus potentially emerging as a strategy for producing triploids and interspecific hybrids with high agronomic interest.
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Affiliation(s)
- Jonathan Huc
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Katarzyna Dziasek
- Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Linnean Center of Plant Biology, Uppsala, Sweden
| | - Kannan Pachamuthu
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Tristan Woh
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Claudia Köhler
- Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Linnean Center of Plant Biology, Uppsala, Sweden
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Filipe Borges
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
- Author for correspondence:
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27
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Sammarco I, Münzbergová Z, Latzel V. DNA Methylation Can Mediate Local Adaptation and Response to Climate Change in the Clonal Plant Fragaria vesca: Evidence From a European-Scale Reciprocal Transplant Experiment. FRONTIERS IN PLANT SCIENCE 2022; 13:827166. [PMID: 35295625 PMCID: PMC8919072 DOI: 10.3389/fpls.2022.827166] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/07/2022] [Indexed: 06/01/2023]
Abstract
The ongoing climate crisis represents a growing threat for plants and other organisms. However, how and if plants will be able to adapt to future environmental conditions is still debated. One of the most powerful mechanisms allowing plants to tackle the changing climate is phenotypic plasticity, which can be regulated by epigenetic mechanisms. Environmentally induced epigenetic variation mediating phenotypic plasticity might be heritable across (a)sexual generations, thus potentially enabling rapid adaptation to climate change. Here, we assessed whether epigenetic mechanisms, DNA methylation in particular, enable for local adaptation and response to increased and/or decreased temperature of natural populations of a clonal plant, Fragaria vesca (wild strawberry). We collected ramets from three populations along a temperature gradient in each of three countries covering the southern (Italy), central (Czechia), and northern (Norway) edges of the native European range of F. vesca. After clonal propagation and alteration of DNA methylation status of half of the plants via 5-azacytidine, we reciprocally transplanted clones to their home locality and to the other two climatically distinct localities within the country of their origin. At the end of the growing season, we recorded survival and aboveground biomass as fitness estimates. We found evidence for local adaptation in intermediate and cold populations in Italy and maladaptation of plants of the warmest populations in all countries. Plants treated with 5-azacytidine showed either better or worse performance in their local conditions than untreated plants. Application of 5-azacytidine also affected plant response to changed climatic conditions when transplanted to the colder or warmer locality than was their origin, and the response was, however, country-specific. We conclude that the increasing temperature will probably be the limiting factor determining F. vesca survival and distribution. DNA methylation may contribute to local adaptation and response to climatic change in natural ecosystems; however, its role may depend on the specific environmental conditions. Since adaptation mediated by epigenetic variation may occur faster than via natural selection on genetic variants, epigenetic adaptation might to some degree help plants in keeping up with the ongoing environmental crisis.
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Affiliation(s)
- Iris Sammarco
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Zuzana Münzbergová
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Vít Latzel
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
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28
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Farrell C, Vaquero-Sedas MI, Cubiles MD, Thompson M, Vega-Vaquero A, Pellegrini M, Vega-Palas MA. A complex network of interactions governs DNA methylation at telomeric regions. Nucleic Acids Res 2022; 50:1449-1464. [PMID: 35061900 PMCID: PMC8860613 DOI: 10.1093/nar/gkac012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022] Open
Abstract
DNA methylation modulates telomere function. In Arabidopsis thaliana, telomeric regions have a bimodal chromatin organization with unmethylated telomeres and methylated subtelomeres. To gain insight into this organization we have generated TAIR10-Tel, a modified version of the Arabidopsis reference genome with additional sequences at most chromosome ends. TAIR10-Tel has allowed us to analyse DNA methylation at nucleotide resolution level in telomeric regions. We have analysed the wild-type strain and mutants that encode inactive versions of all currently known relevant methyltransferases involved in cytosine methylation. These analyses have revealed that subtelomeric DNA methylation extends 1 to 2 kbp from Interstitial Telomeric Sequences (ITSs) that abut or are very near to telomeres. However, DNA methylation drops at the telomeric side of the telomere-subtelomere boundaries and disappears at the inner part of telomeres. We present a comprehensive and integrative model for subtelomeric DNA methylation that should help to decipher the mechanisms that govern the epigenetic regulation of telomeres. This model involves a complex network of interactions between methyltransferases and subtelomeric DNA sequences.
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Affiliation(s)
- Colin Farrell
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA90095, USA
| | - María I Vaquero-Sedas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-US), Seville, E41092, Spain
| | - María D Cubiles
- Departamento de Estadística e Investigación Operativa, Facultad de Matemáticas, Universidad de Sevilla, Seville, E41012, Spain
| | - Michael Thompson
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA90095, USA
| | - Alejandro Vega-Vaquero
- Escuela Técnica Superior de Ingeniería Informática, Universidad de Sevilla, Seville, E41012, Spain
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA90095, USA.,Institute of Genomics and Proteomics, Los Angeles, CA90095, USA
| | - Miguel A Vega-Palas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-US), Seville, E41092, Spain
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Hodjat M, Jourshari PB, Amirinia F, Asadi N. 5-Azacitidine and Trichostatin A induce DNA damage and apoptotic responses in tongue squamous cell carcinoma: An in vitro study. Arch Oral Biol 2021; 133:105296. [PMID: 34735927 DOI: 10.1016/j.archoralbio.2021.105296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 10/17/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022]
Abstract
OBJECTIVE The present in vitro study aims to investigate the potential use of epigenetic inhibitors as treatment modalities in tongue squamous cell carcinoma. DESIGN The human tongue squamous cell carcinoma cell line (CAL-27) was cultured and exposed to varying concentrations of 5-Azacitidine (5-Aza) or Trichostatin A (TSA) in the culture medium. The cell apoptosis was evaluated using Annexin V/PI by flow cytometry. To evaluate DNA damage response, γH2AX foci analysis was performed using immunofluorescence. Single cell gel electrophoresis (SCGE) was applied to measure DNA strand breaks. Gene expression was assessed by quantitative real-time PCR. RESULTS The results showed that 5-Aza and TSA had apoptotic effects on the SCC cell line at concentrations of 50-200 µM and 0.5-5 µM, respectively. Immunofluorescence analysis showed increased expression of γH2AX, the marker of DNA damage response after treatment of 5-Aza and TSA that was associated with increased DNA strand breaks. The expressions of urokinase plasminogen activator, its receptor and matrix metalloproteinase-2, were significantly reduced in TSA- and 5-Aza-treated cells. CONCLUSIONS Our results showed that 5-Aza and TSA increase apoptotic and DNA damage response in squamous cell carcinoma cell line while reducing the expression of tumor invasion genes that further indicating the potential therapeutic value of two epigenetic modifiers in squamous cell carcinoma.
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Affiliation(s)
- Mahshid Hodjat
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences (TUMS), Tehran, Iran.
| | - Parisa Bina Jourshari
- Department of Genetics, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Fatemeh Amirinia
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Nasrin Asadi
- Department of Biochemistry, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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The Underlying Nature of Epigenetic Variation: Origin, Establishment, and Regulatory Function of Plant Epialleles. Int J Mol Sci 2021; 22:ijms22168618. [PMID: 34445323 PMCID: PMC8395315 DOI: 10.3390/ijms22168618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/03/2021] [Accepted: 08/08/2021] [Indexed: 11/17/2022] Open
Abstract
In plants, the gene expression and associated phenotypes can be modulated by dynamic changes in DNA methylation, occasionally being fixed in certain genomic loci and inherited stably as epialleles. Epiallelic variations in a population can occur as methylation changes at an individual cytosine position, methylation changes within a stretch of genomic regions, and chromatin changes in certain loci. Here, we focus on methylated regions, since it is unclear whether variations at individual methylated cytosines can serve any regulatory function, and the evidence for heritable chromatin changes independent of genetic changes is limited. While DNA methylation is known to affect and regulate wide arrays of plant phenotypes, most epialleles in the form of methylated regions have not been assigned any biological function. Here, we review how epialleles can be established in plants, serve a regulatory function, and are involved in adaptive processes. Recent studies suggest that most epialleles occur as byproducts of genetic variations, mainly from structural variants and Transposable Element (TE) activation. Nevertheless, epialleles that occur spontaneously independent of any genetic variations have also been described across different plant species. Here, we discuss how epialleles that are dependent and independent of genetic architecture are stabilized in the plant genome and how methylation can regulate a transcription relative to its genomic location.
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31
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Somasundaram S, Satheesh V, Singh M, Anandhan S. A simple flow cytometry-based assay to study global methylation levels in onion, a non-model species. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1859-1865. [PMID: 34539120 PMCID: PMC8405793 DOI: 10.1007/s12298-021-01047-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED DNA methylation is an important epigenetic mark and global methylation dynamics regulate plant developmental processes. Even though genome sequencing technologies have made DNA methylation studies easier, it is difficult in non-model species where genome information is not available. Therefore in this study, we developed a simple assay for analysing global methylation levels in plants by washless immunolabelling of unfixed nuclei using flow cytometry. Onion leaf tissue was used as a model system, and mean fluorescence intensity due to anti-5- methyl cytosine (5-mC) antibodies were used as a measure of global methylation levels. Among three nuclear isolation buffers evaluated, the highest nuclear yield with the low background was obtained with LB01. To maintain a balance between high DNA fluorescence value and low coefficient of variation of DNA peaks, 45 min of hydrolysis with 0.2 N hydrochloric acid was used for chromatin denaturation resulting in six-fold increase in 5-mC fluorescence compared to control. This method was used successfully to detect 5-Azacytidine induced DNA hypomethylation in onion leaf tissues. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01047-6.
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Affiliation(s)
- Saravanakumar Somasundaram
- ICAR-Directorate of Onion and Garlic Research, Pune, 410505 India
- Present Address: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Viswanathan Satheesh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Major Singh
- ICAR-Directorate of Onion and Garlic Research, Pune, 410505 India
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32
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Dalakouras A, Vlachostergios D. Epigenetic approaches to crop breeding: current status and perspectives. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5356-5371. [PMID: 34017985 DOI: 10.1093/jxb/erab227] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/18/2021] [Indexed: 05/10/2023]
Abstract
In order to tackle the cumulative adverse effects of global climate change, reduced farmland, and heightened needs of an ever-increasing world population, modern agriculture is in urgent search of solutions that can ensure world food security and sustainable development. Classical crop breeding is still a powerful method to obtain crops with valued agronomical traits, but its potential is gradually being compromised by the menacing decline of genetic variation. Resorting to the epigenome as a source of variation could serve as a promising alternative. Here, we discuss current status of epigenetics-mediated crop breeding (epibreeding), highlight its advances and limitations, outline currently available methodologies, and propose novel RNA-based strategies to modify the epigenome in a gene-specific and transgene-free manner.
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Affiliation(s)
- Athanasios Dalakouras
- Institute of Industrial and Forage Crops, HAO-DEMETER, 41335 Larissa, Greece
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, 57001 Thessaloniki, Greece
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Baránek M, Kováčová V, Gazdík F, Špetík M, Eichmeier A, Puławska J, Baránková K. Epigenetic Modulating Chemicals Significantly Affect the Virulence and Genetic Characteristics of the Bacterial Plant Pathogen Xanthomonas campestris pv. campestris. Genes (Basel) 2021; 12:genes12060804. [PMID: 34070403 PMCID: PMC8226645 DOI: 10.3390/genes12060804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Epigenetics is the study of heritable alterations in phenotypes that are not caused by changes in DNA sequence. In the present study, we characterized the genetic and phenotypic alterations of the bacterial plant pathogen Xanthomonas campestris pv. campestris (Xcc) under different treatments with several epigenetic modulating chemicals. The use of DNA demethylating chemicals unambiguously caused a durable decrease in Xcc bacterial virulence, even after its reisolation from infected plants. The first-time use of chemicals to modify the activity of sirtuins also showed some noticeable results in terms of increasing bacterial virulence, but this effect was not typically stable. Changes in treated strains were also confirmed by using methylation sensitive amplification (MSAP), but with respect to registered SNPs induction, it was necessary to consider their contribution to the observed polymorphism. The molecular basis of the altered virulence was deciphered by using dualRNA-seq analysis of treated Xcc strains infecting Brassica rapa plants. The results of the present study should promote more intensive research in the generally understudied field of bacterial epigenetics, where artificially induced modification by epigenetic modulating chemicals can significantly increase the diversity of bacterial properties and potentially contribute to the further development of the fields, such as bacterial ecology and adaptation.
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Affiliation(s)
- Miroslav Baránek
- Mendeleum—Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, 69144 Lednice, Czech Republic; (F.G.); (M.Š.); (A.E.); (K.B.)
- Correspondence: ; Tel.: +420-519367311
| | - Viera Kováčová
- Institute for Biological Physics, University of Cologne, 50923 Köln, Germany;
| | - Filip Gazdík
- Mendeleum—Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, 69144 Lednice, Czech Republic; (F.G.); (M.Š.); (A.E.); (K.B.)
| | - Milan Špetík
- Mendeleum—Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, 69144 Lednice, Czech Republic; (F.G.); (M.Š.); (A.E.); (K.B.)
| | - Aleš Eichmeier
- Mendeleum—Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, 69144 Lednice, Czech Republic; (F.G.); (M.Š.); (A.E.); (K.B.)
| | - Joanna Puławska
- Department of Phytopathology, Research Institute of Horticulture, 96-100 Skierniewice, Poland;
| | - Kateřina Baránková
- Mendeleum—Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, 69144 Lednice, Czech Republic; (F.G.); (M.Š.); (A.E.); (K.B.)
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Tian W, Wang R, Bo C, Yu Y, Zhang Y, Shin GI, Kim WY, Wang L. SDC mediates DNA methylation-controlled clock pace by interacting with ZTL in Arabidopsis. Nucleic Acids Res 2021; 49:3764-3780. [PMID: 33675668 PMCID: PMC8053106 DOI: 10.1093/nar/gkab128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 12/29/2022] Open
Abstract
Molecular bases of eukaryotic circadian clocks mainly rely on transcriptional-translational feedback loops (TTFLs), while epigenetic codes also play critical roles in fine-tuning circadian rhythms. However, unlike histone modification codes that play extensive and well-known roles in the regulation of circadian clocks, whether DNA methylation (5mC) can affect the circadian clock, and the associated underlying molecular mechanisms, remains largely unexplored in many organisms. Here we demonstrate that global genome DNA hypomethylation can significantly lengthen the circadian period of Arabidopsis. Transcriptomic and genetic evidence demonstrate that SUPPRESSOR OF drm1 drm2 cmt3 (SDC), encoding an F-box containing protein, is required for the DNA hypomethylation-tuned circadian clock. Moreover, SDC can physically interact with another F-box containing protein ZEITLUPE (ZTL) to diminish its accumulation. Genetic analysis further revealed that ZTL and its substrate TIMING OF CAB EXPRESSION 1 (TOC1) likely act downstream of DNA methyltransferases to control circadian rhythm. Together, our findings support the notion that DNA methylation is important to maintain proper circadian pace in Arabidopsis, and further established that SDC links DNA hypomethylation with a proteolytic cascade to assist in tuning the circadian clock.
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Affiliation(s)
- Wenwen Tian
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Ruyi Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Cunpei Bo
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yingjun Yu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuanyuan Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21Plus), Research Institute of Life Sciences (RILS) and Institute of Agricultural and Life Science(IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), Research Institute of Life Sciences (RILS) and Institute of Agricultural and Life Science(IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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35
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Genome-Wide Variation in DNA Methylation Predicts Variation in Leaf Traits in an Ecosystem-Foundational Oak Species. FORESTS 2021. [DOI: 10.3390/f12050569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Epigenetic modifications such as DNA methylation are a potential mechanism for trees to respond to changing environments. However, it remains controversial the extent to which DNA methylation impacts ecologically important traits that influence fitness. In this study, we used reduced-representation bisulfite sequencing to associate genomic and epigenomic variation with seven phenotypic traits related to growth, leaf function, and disease susceptibility in 160 valley oak (Quercus lobata) saplings planted across two common gardens in California. We found that DNA methylation was associated with a significant fraction of phenotypic variance in plant height, leaf lobedness, powdery mildew infection, and trichome density. Two of the seven traits were significantly associated with DNA methylation in the CG context, three traits were significantly associated with CHG methylation, and two traits were significantly associated with CHH methylation. Notably, controlling for genomic variation in SNPs generally reduced the amount of trait variation explained by DNA methylation. Our results suggest that DNA methylation may serve as a useful biomarker to predict phenotypic variation in trees, though it remains unclear the degree to which DNA methylation is a causal mechanism driving phenotypic variation in forest tree species.
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36
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Yari V, Roein Z, Sabouri A. Exogenous 5-azaCitidine accelerates flowering and external GA 3 increases ornamental value in Iranian Anemone accessions. Sci Rep 2021; 11:7478. [PMID: 33820923 PMCID: PMC8021551 DOI: 10.1038/s41598-021-86940-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023] Open
Abstract
The Anemone genus is a tuberous geophyte which undergoes a dormancy period during unfavorable environmental conditions for growth. Five species of the Anemone genus naturally grow in several regions of Iran. The diverse uses of Anemone in gardens for landscaping, cut flowers, and potted plants indicate its high ornamental potential. Its dormancy and flowering are influenced by various factors. The present paper was conducted to explore the flowering behavior of Anemone accessions in response to different pre-treatments. For this purpose, tubers of 18 Anemone accessions (A. coronaria and A. biflora) were collected from natural regions of six provinces in Iran. These tubers were subjected to different conditions of non-chilling (20 °C, 90 days), chilling (4 °C, 90 days), GA3 (150 mgL-1; 24 h), and 5-azaCitidine (5-azaC; 40 µM; 24 h) prior to the cultivation. Most of the accessions were able to enter the flowering stage without chilling. The shortest period for the sprouting of tubers (16.89 ± 7.83 days) belonged to 5-azaC pre-treatment. In addition, this treatment accelerated the flowering time (about 30 days earlier) and diameter of the stem, bud, and flower. Morphological characteristics, such as stem height, number of leaves, bud, and petal and the longevity of flowers on the plant were significantly affected by GA3 pre-treatment. Our results indicated a positive correlation between flower length, stem height, and stem diameter with flower longevity under different pre-treatment conditions. The present study demonstrated that accessions Anm3, Anm12, and Anm18 had ornamental values higher than the population mean across four conditions.
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Affiliation(s)
- Vahideh Yari
- grid.411528.b0000 0004 0611 9352Department of Horticultural Sciences, Faculty of Agriculture, Ilam University, Ilam, Iran
| | - Zeynab Roein
- grid.411528.b0000 0004 0611 9352Department of Horticultural Sciences, Faculty of Agriculture, Ilam University, Ilam, Iran
| | - Atefeh Sabouri
- grid.411872.90000 0001 2087 2250Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
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37
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Liu S, de Jonge J, Trejo‐Arellano MS, Santos‐González J, Köhler C, Hennig L. Role of H1 and DNA methylation in selective regulation of transposable elements during heat stress. THE NEW PHYTOLOGIST 2021; 229:2238-2250. [PMID: 33091182 PMCID: PMC7894476 DOI: 10.1111/nph.17018] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/09/2020] [Indexed: 05/03/2023]
Abstract
Heat-stressed Arabidopsis plants release heterochromatin-associated transposable element (TE) silencing, yet it is not accompanied by major reductions of epigenetic repressive modifications. In this study, we explored the functional role of histone H1 in repressing heterochromatic TEs in response to heat stress. We generated and analyzed RNA and bisulfite-sequencing data of wild-type and h1 mutant seedlings before and after heat stress. Loss of H1 caused activation of pericentromeric Gypsy elements upon heat treatment, despite these elements remaining highly methylated. By contrast, nonpericentromeric Copia elements became activated concomitantly with loss of DNA methylation. The same Copia elements became activated in heat-treated chromomethylase 2 (cmt2) mutants, indicating that H1 represses Copia elements through maintaining DNA methylation under heat. We discovered that H1 is required for TE repression in response to heat stress, but its functional role differs depending on TE location. Strikingly, H1-deficient plants treated with the DNA methyltransferase inhibitor zebularine were highly tolerant to heat stress, suggesting that both H1 and DNA methylation redundantly suppress the plant response to heat stress.
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Affiliation(s)
- Shujing Liu
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Jennifer de Jonge
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Minerva S. Trejo‐Arellano
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Juan Santos‐González
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Claudia Köhler
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Lars Hennig
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
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Konečná K, Sováková PP, Anteková K, Fajkus J, Fojtová M. Distinct Responses of Arabidopsis Telomeres and Transposable Elements to Zebularine Exposure. Int J Mol Sci 2021; 22:ijms22010468. [PMID: 33466545 PMCID: PMC7796508 DOI: 10.3390/ijms22010468] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 12/17/2022] Open
Abstract
Involvement of epigenetic mechanisms in the regulation of telomeres and transposable elements (TEs), genomic regions with the protective and potentially detrimental function, respectively, has been frequently studied. Here, we analyzed telomere lengths in Arabidopsis thaliana plants of Columbia, Landsberg erecta and Wassilevskija ecotypes exposed repeatedly to the hypomethylation drug zebularine during germination. Shorter telomeres were detected in plants growing from seedlings germinated in the presence of zebularine with a progression in telomeric phenotype across generations, relatively high inter-individual variability, and diverse responses among ecotypes. Interestingly, the extent of telomere shortening in zebularine Columbia and Wassilevskija plants corresponded to the transcriptional activation of TEs, suggesting a correlated response of these genomic elements to the zebularine treatment. Changes in lengths of telomeres and levels of TE transcripts in leaves were not always correlated with a hypomethylation of cytosines located in these regions, indicating a cytosine methylation-independent level of their regulation. These observations, including differences among ecotypes together with distinct dynamics of the reversal of the disruption of telomere homeostasis and TEs transcriptional activation, reflect a complex involvement of epigenetic processes in the regulation of crucial genomic regions. Our results further demonstrate the ability of plant cells to cope with these changes without a critical loss of the genome stability.
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Affiliation(s)
- Klára Konečná
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Pavla Polanská Sováková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Karin Anteková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute for Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic; (K.K.); (P.P.S.); (K.A.); (J.F.)
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
- Correspondence: ; Tel.: +420-54949-8063
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Zhi P, Chang C. Exploiting Epigenetic Variations for Crop Disease Resistance Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:692328. [PMID: 34149790 PMCID: PMC8212930 DOI: 10.3389/fpls.2021.692328] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/27/2021] [Indexed: 05/07/2023]
Abstract
Pathogen infections seriously threaten plant health and global crop production. Epigenetic processes such as DNA methylation, histone post-translational modifications, chromatin assembly and remodeling play important roles in transcriptional regulation of plant defense responses and could provide a new direction to drive breeding strategies for crop disease resistance improvement. Although past decades have seen unprecedented proceedings in understanding the epigenetic mechanism of plant defense response, most of these advances were derived from studies in model plants like Arabidopsis. In this review, we highlighted the recent epigenetic studies on crop-pathogen interactions and discussed the potentials, challenges, and strategies in exploiting epigenetic variations for crop disease resistance improvement.
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DNA methylation mutants in Physcomitrella patens elucidate individual roles of CG and non-CG methylation in genome regulation. Proc Natl Acad Sci U S A 2020; 117:33700-33710. [PMID: 33376225 DOI: 10.1073/pnas.2011361117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cytosine (DNA) methylation in plants regulates the expression of genes and transposons. While methylation in plant genomes occurs at CG, CHG, and CHH sequence contexts, the comparative roles of the individual methylation contexts remain elusive. Here, we present Physcomitrella patens as the second plant system, besides Arabidopsis thaliana, with viable mutants with an essentially complete loss of methylation in the CG and non-CG contexts. In contrast to A. thaliana, P. patens has more robust CHH methylation, similar CG and CHG methylation levels, and minimal cross-talk between CG and non-CG methylation, making it possible to study context-specific effects independently. Our data found CHH methylation to act in redundancy with symmetric methylation in silencing transposons and to regulate the expression of CG/CHG-depleted transposons. Specific elimination of CG methylation did not dysregulate transposons or genes. In contrast, exclusive removal of non-CG methylation massively up-regulated transposons and genes. In addition, comparing two exclusively but equally CG- or CHG-methylated genomes, we show that CHG methylation acts as a greater transcriptional regulator than CG methylation. These results disentangle the transcriptional roles of CG and non-CG, as well as symmetric and asymmetric methylation in a plant genome, and point to the crucial role of non-CG methylation in genome regulation.
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Mateo de Arias M, Gao L, Sherwood DA, Dwivedi KK, Price BJ, Jamison M, Kowallis BM, Carman JG. Whether Gametophytes are Reduced or Unreduced in Angiosperms Might Be Determined Metabolically. Genes (Basel) 2020; 11:genes11121449. [PMID: 33276690 PMCID: PMC7761559 DOI: 10.3390/genes11121449] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/23/2020] [Accepted: 11/27/2020] [Indexed: 02/07/2023] Open
Abstract
In angiosperms, meiotic failure coupled with the formation of genetically unreduced gametophytes in ovules (apomeiosis) constitute major components of gametophytic apomixis. These aberrant developmental events are generally thought to be caused by mutation. However, efforts to locate the responsible mutations have failed. Herein, we tested a fundamentally different hypothesis: apomeiosis is a polyphenism of meiosis, with meiosis and apomeiosis being maintained by different states of metabolic homeostasis. Microarray analyses of ovules and pistils were used to differentiate meiotic from apomeiotic processes in Boechera (Brassicaceae). Genes associated with translation, cell division, epigenetic silencing, flowering, and meiosis characterized sexual Boechera (meiotic). In contrast, genes associated with stress responses, abscisic acid signaling, reactive oxygen species production, and stress attenuation mechanisms characterized apomictic Boechera (apomeiotic). We next tested whether these metabolic differences regulate reproductive mode. Apomeiosis switched to meiosis when premeiotic ovules of apomicts were cultured on media that increased oxidative stress. These treatments included drought, starvation, and H2O2 applications. In contrast, meiosis switched to apomeiosis when premeiotic pistils of sexual plants were cultured on media that relieved oxidative stress. These treatments included antioxidants, glucose, abscisic acid, fluridone, and 5-azacytidine. High-frequency apomeiosis was initiated in all sexual species tested: Brassicaceae, Boechera stricta, Boechera exilis, and Arabidopsis thaliana; Fabaceae, Vigna unguiculata; Asteraceae, Antennaria dioica. Unreduced gametophytes formed from ameiotic female and male sporocytes, first division restitution dyads, and nucellar cells. These results are consistent with modes of reproduction and types of apomixis, in natural apomicts, being regulated metabolically.
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Affiliation(s)
- Mayelyn Mateo de Arias
- Plants, Soils, and Climate Department, Utah State University, Logan, UT 84322-4820, USA; (M.M.d.A.); (L.G.); (D.A.S.); (B.J.P.)
- Instituto Tecnológico de Santo Domingo, 10103 Santo Domingo, Dominican Republic
| | - Lei Gao
- Plants, Soils, and Climate Department, Utah State University, Logan, UT 84322-4820, USA; (M.M.d.A.); (L.G.); (D.A.S.); (B.J.P.)
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang 332000, China
| | - David A. Sherwood
- Plants, Soils, and Climate Department, Utah State University, Logan, UT 84322-4820, USA; (M.M.d.A.); (L.G.); (D.A.S.); (B.J.P.)
- Sherwood Pet Health, Logan, UT 84321, USA
| | - Krishna K. Dwivedi
- Caisson Laboratories, Inc., Smithfield, UT 84335, USA; (K.K.D.); (M.J.); (B.M.K.)
- Crop Improvement Division, Indian Grassland and Fodder Research Institute, 284003 Jhansi, India
| | - Bo J. Price
- Plants, Soils, and Climate Department, Utah State University, Logan, UT 84322-4820, USA; (M.M.d.A.); (L.G.); (D.A.S.); (B.J.P.)
- Molecular Biology Program, University of Utah, Salt Lake City, UT 84112-5750, USA
| | - Michelle Jamison
- Caisson Laboratories, Inc., Smithfield, UT 84335, USA; (K.K.D.); (M.J.); (B.M.K.)
- Wescor, Inc. An Elitech Company, Logan, UT 84321, USA
| | - Becky M. Kowallis
- Caisson Laboratories, Inc., Smithfield, UT 84335, USA; (K.K.D.); (M.J.); (B.M.K.)
- Cytiva, Inc., Logan, UT 84321, USA
| | - John G. Carman
- Plants, Soils, and Climate Department, Utah State University, Logan, UT 84322-4820, USA; (M.M.d.A.); (L.G.); (D.A.S.); (B.J.P.)
- Correspondence: ; Tel.: +1-435-512-4913
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Eckert S, Herden J, Stift M, Joshi J, van Kleunen M. Manipulation of cytosine methylation does not remove latitudinal clines in two invasive goldenrod species in Central Europe. Mol Ecol 2020; 30:222-236. [PMID: 33150604 DOI: 10.1111/mec.15722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/03/2020] [Accepted: 10/23/2020] [Indexed: 12/23/2022]
Abstract
Invasive species frequently differentiate phenotypically in novel environments within a few generations, often even with limited genetic variation. For the invasive plants Solidago canadensis and S. gigantea, we tested whether such differentiation might have occurred through heritable epigenetic changes in cytosine methylation. In a 2-year common-garden experiment, we grew plants from seeds collected along a latitudinal gradient in their non-native Central European range to test for trait differentiation and whether differentiation disappeared when seeds were treated with the demethylation agent zebularine. Microsatellite markers revealed no population structure along the latitudinal gradient in S. canadensis, but three genetic clusters in S. gigantea. Solidago canadensis showed latitudinal clines in flowering phenology and growth. In S. gigantea, the number of clonal offspring decreased with latitude. Although zebularine had a significant effect on early growth, probably through effects on cytosine methylation, latitudinal clines remained (or even got stronger) in plants raised from seeds treated with zebularine. Thus, our experiment provides no evidence that epigenetic mechanisms by selective cytosine methylation contribute to the observed phenotypic differentiation in invasive goldenrods in Central Europe.
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Affiliation(s)
- Silvia Eckert
- Biodiversity Research/Systematic Botany, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jasmin Herden
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Marc Stift
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Jasmin Joshi
- Biodiversity Research/Systematic Botany, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,Institute for Landscape and Open Space, Eastern Switzerland University of Applied Sciences, Rapperswil, Switzerland.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Mark van Kleunen
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany.,Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
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Boonjing P, Masuta Y, Nozawa K, Kato A, Ito H. The effect of zebularine on the heat-activated retrotransposon ONSEN in Arabidopsis thaliana and Vigna angularis. Genes Genet Syst 2020; 95:165-172. [PMID: 32741853 DOI: 10.1266/ggs.19-00046] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Ty1/copia-like retrotransposon ONSEN is conserved among Brassica species, as well as in beans, including adzuki bean (Vigna angularis (Willd.) Ohwi & Ohashi), which is one of the economically important crops in Japan. ONSEN has acquired a heat-responsive element that is recognized by plant heat stress defense factors, resulting in its transcription and the production of full-length extrachromosomal DNA under conditions with elevated temperatures. DNA methylation plays an important role in regulating the activation of this transposon in plants. Therefore, chemical inhibition of DNA methyltransferases has been utilized to study the effect of DNA methylation on transposon activation. To understand the effect of DNA methylation on ONSEN activation, Arabidopsis thaliana and adzuki bean seedlings were treated with zebularine, which is known to be an effective chemical demethylation agent. The results showed that ONSEN transcription levels were upregulated in zebularine-treated plants. Extrachromosomal DNA of ONSEN also accumulated in the treated plants.
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Affiliation(s)
| | | | - Kosuke Nozawa
- Graduate School of Life Science, Hokkaido University
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Epigenetics and epigenomics: underlying mechanisms, relevance, and implications in crop improvement. Funct Integr Genomics 2020; 20:739-761. [PMID: 33089419 DOI: 10.1007/s10142-020-00756-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 01/21/2023]
Abstract
Epigenetics is defined as changes in gene expression that are not associated with changes in DNA sequence but due to the result of methylation of DNA and post-translational modifications to the histones. These epigenetic modifications are known to regulate gene expression by bringing changes in the chromatin state, which underlies plant development and shapes phenotypic plasticity in responses to the environment and internal cues. This review articulates the role of histone modifications and DNA methylation in modulating biotic and abiotic stresses, as well as crop improvement. It also highlights the possibility of engineering epigenomes and epigenome-based predictive models for improving agronomic traits.
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Jueterbock A, Boström C, Coyer JA, Olsen JL, Kopp M, Dhanasiri AKS, Smolina I, Arnaud-Haond S, Van de Peer Y, Hoarau G. The Seagrass Methylome Is Associated With Variation in Photosynthetic Performance Among Clonal Shoots. FRONTIERS IN PLANT SCIENCE 2020; 11:571646. [PMID: 33013993 PMCID: PMC7498905 DOI: 10.3389/fpls.2020.571646] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/21/2020] [Indexed: 06/11/2023]
Abstract
Evolutionary theory predicts that clonal organisms are more susceptible to extinction than sexually reproducing organisms, due to low genetic variation and slow rates of evolution. In agreement, conservation management considers genetic variation as the ultimate measure of a population's ability to survive over time. However, clonal plants are among the oldest living organisms on our planet. Here, we test the hypothesis that clonal seagrass meadows display epigenetic variation that complements genetic variation as a source of phenotypic variation. In a clonal meadow of the seagrass Zostera marina, we characterized DNA methylation among 42 shoots. We also sequenced the whole genome of 10 shoots to correlate methylation patterns with photosynthetic performance under exposure to and recovery from 27°C, while controlling for somatic mutations. Here, we show for the first time that clonal seagrass shoots display DNA methylation variation that is independent from underlying genetic variation, and associated with variation in photosynthetic performance under experimental conditions. It remains unknown to what degree this association could be influenced by epigenetic responses to transplantation-related stress, given that the methylomes showed a strong shift under acclimation to laboratory conditions. The lack of untreated control samples in the heat stress experiment did not allow us to distinguish methylome shifts induced by acclimation from such induced by heat stress. Notwithstanding, the co-variation in DNA methylation and photosynthetic performance may be linked via gene expression because methylation patterns varied in functionally relevant genes involved in photosynthesis, and in the repair and prevention of heat-induced protein damage. While genotypic diversity has been shown to enhance stress resilience in seagrass meadows, we suggest that epigenetic variation plays a similar role in meadows dominated by a single genotype. Consequently, conservation management of clonal plants should consider epigenetic variation as indicator of resilience and stability.
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Affiliation(s)
- Alexander Jueterbock
- Algal and Microbial Biotechnology Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Marine Molecular Ecology Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - James A. Coyer
- Marine Molecular Ecology Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Shoals Marine Laboratory, University of New Hampshire, Durham, NH, United States
| | - Jeanine L. Olsen
- Ecological Genetics-Genomics Group, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Martina Kopp
- Marine Molecular Ecology Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Anusha K. S. Dhanasiri
- Marine Molecular Ecology Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Irina Smolina
- Marine Molecular Ecology Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Bioinformatics and Systems Biology, VIB Center for Plant Systems Biology, Ghent, Belgium
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Galice Hoarau
- Marine Molecular Ecology Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Lee SI, Park JW, Kwon SJ, Jo YD, Hong MJ, Kim JB, Choi HI. Epigenetic Variation Induced by Gamma Rays, DNA Methyltransferase Inhibitors, and Their Combination in Rice. PLANTS 2020; 9:plants9091088. [PMID: 32847097 PMCID: PMC7570246 DOI: 10.3390/plants9091088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/16/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023]
Abstract
DNA methylation plays important roles in the regulation of gene expression and maintenance of genome stability in many organisms, including plants. In this study, we treated rice with gamma rays (GRs) and DNA methyltransferase inhibitors (DNMTis) to induce variations in DNA methylation and evaluated epigenetic diversity using methylation-sensitive amplified polymorphism (MSAP) and transposon methylation display (TMD) marker systems. Comparative and integrated analyses of the data revealed that both GRs and DNMTis alone have epimutagenic effects and that combined treatment enhanced these effects. Calculation of methylation rates based on band scoring suggested that both GRs and DNMTis induce epigenetic diversity by demethylation in a dose-dependent manner, and combined treatment can induce variations more synergistically. The difference in the changes in full and hemi-methylation rates between MSAP and TMD is presumed to be caused by the different genomic contexts of the loci amplified in the two marker systems. Principal coordinate, phylogenic, and population structure analyses commonly yielded two clusters of individuals divided by DNMTi treatment. The clustering pattern was more apparent in TMD, indicating that DNMTis have a stronger effect on hypermethylated repetitive regions. These findings provide a foundation for understanding epigenetic variations induced by GRs and DNMTis and for epigenetic mutation breeding.
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Promoter and Terminator Optimization for DNA Methylation Targeting in Arabidopsis. EPIGENOMES 2020; 4:epigenomes4020009. [PMID: 34968243 PMCID: PMC8594676 DOI: 10.3390/epigenomes4020009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/17/2020] [Accepted: 06/09/2020] [Indexed: 12/05/2022] Open
Abstract
DNA methylation is an important epigenetic mark involved in gene regulation and silencing of transposable elements. The presence or absence of DNA methylation at specific sites can influence nearby gene expression and cause phenotypic changes that remain stable over generations. Recently, development of new technologies has enabled the targeted addition or removal of DNA methylation at specific sites of the genome. Of these new technologies, the targeting of the catalytic domain of Nicotiana tabacum DOMAINS REARRANGED METHYLTRANSFERASE 2 (ntDRM2cd) offers a promising tool for the addition of DNA methylation as it can directly methylate DNA. However, the methylation targeting efficiency of constructs using ntDRM2cd thus far has been relatively low. Previous studies have shown that the use of different promoters or terminators can greatly improve genome-editing efficiencies. In this study, we systematically survey a variety of promoter and terminator combinations to identify optimal combinations to use when targeting the addition of DNA methylation in Arabidopsis thaliana.
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Segregation of an MSH1 RNAi transgene produces heritable non-genetic memory in association with methylome reprogramming. Nat Commun 2020; 11:2214. [PMID: 32371941 PMCID: PMC7200659 DOI: 10.1038/s41467-020-16036-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 04/09/2020] [Indexed: 12/23/2022] Open
Abstract
MSH1 is a plant-specific protein. RNAi suppression of MSH1 results in phenotype variability for developmental and stress response pathways. Segregation of the RNAi transgene produces non-genetic msh1 ‘memory’ with multi-generational inheritance. First-generation memory versus non-memory comparison, and six-generation inheritance studies, identifies gene-associated, heritable methylation repatterning. Genome-wide methylome analysis integrated with RNAseq and network-based enrichment studies identifies altered circadian clock networks, and phytohormone and stress response pathways that intersect with circadian control. A total of 373 differentially methylated loci comprising these networks are sufficient to discriminate memory from nonmemory full sibs. Methylation inhibitor 5-azacytidine diminishes the differences between memory and wild type for growth, gene expression and methylation patterning. The msh1 reprogramming is dependent on functional HISTONE DEACETYLASE 6 and methyltransferase MET1, and transition to memory requires the RNA-directed DNA methylation pathway. This system of phenotypic plasticity may serve as a potent model for defining accelerated plant adaptation during environmental change. Segregation of an MSH1 RNAi transgene produces non-genetic memory that displays transgenerational inheritance in Arabidopsis. Here, the authors compare memory and non-memory full-sib progenies to show the involvement of DNA methylation reprogramming, involving the RdDM pathway, in transition to a heritable memory state.
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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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