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Langford N, Fargeot L, Blanchet S. Spatial covariation between genetic and epigenetic diversity in wild plant and animal populations: a meta-analysis. J Exp Biol 2024; 227:jeb246009. [PMID: 38449323 DOI: 10.1242/jeb.246009] [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] [Indexed: 03/08/2024]
Abstract
Epigenetic variation may be crucial in understanding the structure of wild populations, thereby aiding in their management and conservation. However, the relationship between epigenetic and genetic variation remains poorly understood, especially in wild populations. To address this, we conducted a meta-analysis of studies that examined the genetic and epigenetic structures of wild plant and animal populations. We aimed to determine whether epigenetic variation is spatially independent of genetic variation in the wild and to highlight the conditions under which epigenetic variation might be informative. We show a significant positive correlation between genetic and epigenetic pairwise differentiation, indicating that in wild populations, epigenetic diversity is closely linked to genetic differentiation. The correlation was weaker for population pairs that were weakly differentiated genetically, suggesting that in such cases, epigenetic marks might be independent of genetic marks. Additionally, we found that global levels of genetic and epigenetic differentiation were similar across plant and animal populations, except when populations were weakly differentiated genetically. In such cases, epigenetic differentiation was either higher or lower than genetic differentiation. Our results suggest that epigenetic information is particularly relevant in populations that have recently diverged genetically or are connected by gene flow. Future studies should consider the genetic structure of populations when inferring the role of epigenetic diversity in local adaptation in wild populations. Furthermore, there is a need to identify the factors that sustain the links between genetic and epigenetic diversity to improve our understanding of the interplay between these two forms of variation in wild populations.
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Affiliation(s)
- Nadia Langford
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UAR 2029, F-09200 Moulis, France
| | - Laura Fargeot
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UAR 2029, F-09200 Moulis, France
| | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UAR 2029, F-09200 Moulis, France
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2
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Plant DNA Methylation Responds to Nutrient Stress. Genes (Basel) 2022; 13:genes13060992. [PMID: 35741754 PMCID: PMC9222553 DOI: 10.3390/genes13060992] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 12/16/2022] Open
Abstract
Nutrient stress as abiotic stress has become one of the important factors restricting crop yield and quality. DNA methylation is an essential epigenetic modification that can effectively regulate genome stability. Exploring DNA methylation responses to nutrient stress could lay the foundation for improving plant tolerance to nutrient stress. This article summarizes the plant DNA methylation patterns, the effects of nutrient stress, such as nitrogen, phosphorus, iron, zinc and sulfur stress, on plant DNA methylation and research techniques for plant DNA methylation, etc. Our discussion provides insight for further research on epigenetics response to nutrient stress in the future.
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3
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Entrambasaguas L, Ruocco M, Verhoeven KJF, Procaccini G, Marín-Guirao L. Gene body DNA methylation in seagrasses: inter- and intraspecific differences and interaction with transcriptome plasticity under heat stress. Sci Rep 2021; 11:14343. [PMID: 34253765 PMCID: PMC8275578 DOI: 10.1038/s41598-021-93606-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
The role of DNA methylation and its interaction with gene expression and transcriptome plasticity is poorly understood, and current insight comes mainly from studies in very few model plant species. Here, we study gene body DNA methylation (gbM) and gene expression patterns in ecotypes from contrasting thermal environments of two marine plants with contrasting life history strategies in order to explore the potential role epigenetic mechanisms could play in gene plasticity and responsiveness to heat stress. In silico transcriptome analysis of CpGO/E ratios suggested that the bulk of Posidonia oceanica and Cymodocea nodosa genes possess high levels of intragenic methylation. We also observed a correlation between gbM and gene expression flexibility: genes with low DNA methylation tend to show flexible gene expression and plasticity under changing conditions. Furthermore, the empirical determination of global DNA methylation (5-mC) showed patterns of intra and inter-specific divergence that suggests a link between methylation level and the plants' latitude of origin and life history. Although we cannot discern whether gbM regulates gene expression or vice versa, or if other molecular mechanisms play a role in facilitating transcriptome responsiveness, our findings point to the existence of a relationship between gene responsiveness and gbM patterns in marine plants.
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Affiliation(s)
- Laura Entrambasaguas
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Miriam Ruocco
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Koen J F Verhoeven
- Terrestrial Ecology Department, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Gabriele Procaccini
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
| | - Lazaro Marín-Guirao
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
- Seagrass Ecology Group, Oceanographic Center of Murcia, Spanish Institute of Oceanography, C/Varadero, 30740, San Pedro del Pinatar, Spain
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4
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Liu R, Xia R, Xie Q, Wu Y. Endoplasmic reticulum-related E3 ubiquitin ligases: Key regulators of plant growth and stress responses. PLANT COMMUNICATIONS 2021; 2:100186. [PMID: 34027397 PMCID: PMC8132179 DOI: 10.1016/j.xplc.2021.100186] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/23/2021] [Accepted: 04/15/2021] [Indexed: 05/28/2023]
Abstract
Accumulating evidence has revealed that the ubiquitin proteasome system plays fundamental roles in the regulation of diverse cellular activities in eukaryotes. The ubiquitin protein ligases (E3s) are central to the proteasome system because of their ability to determine its substrate specificity. Several studies have demonstrated the essential role of a group of ER (endoplasmic reticulum)-localized E3s in the positive or negative regulation of cell homeostasis. Most ER-related E3s are conserved between plants and mammals, and a few plant-specific components have been reported. In this review, we summarize the functions of ER-related E3s in plant growth, ER-associated protein degradation and ER-phagy, abiotic and biotic stress responses, and hormone signaling. Furthermore, we highlight several questions that remain to be addressed and suggest directions for further research on ER-related E3 ubiquitin ligases.
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Affiliation(s)
- Ruijun Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ran Xia
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaorong Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
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5
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Korotko U, Chwiałkowska K, Sańko-Sawczenko I, Kwasniewski M. DNA Demethylation in Response to Heat Stress in Arabidopsis thaliana. Int J Mol Sci 2021; 22:ijms22041555. [PMID: 33557095 PMCID: PMC7913789 DOI: 10.3390/ijms22041555] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
Environmental stress is one of the most important factors affecting plant growth and development. Recent studies have shown that epigenetic mechanisms, such as DNA methylation, play a key role in adapting plants to stress conditions. Here, we analyzed the dynamics of changes in the level of DNA methylation in Arabidopsis thaliana (L.) Heynh. (Brassicaceae) under the influence of heat stress. For this purpose, whole-genome sequencing of sodium bisulfite-treated DNA was performed. The analysis was performed at seven time points, taking into account the control conditions, heat stress, and recovery to control conditions after the stress treatment was discontinued. In our study we observed decrease in the level of DNA methylation under the influence of heat stress, especially after returning to control conditions. Analysis of the gene ontology enrichment and regulatory pathways showed that genes characterized by differential DNA methylation are mainly associated with stress response, including heat stress. These are the genes encoding heat shock proteins and genes associated with translation regulation. A decrease in the level of DNA methylation in such specific sites suggests that under the influence of heat stress we observe active demethylation phenomenon rather than passive demethylation, which is not locus specific.
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Affiliation(s)
- Urszula Korotko
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-089 Bialystok, Poland; (U.K.); (K.C.)
- Department of Genetics, University of Silesia in Katowice, 40-007 Katowice, Poland
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-089 Bialystok, Poland; (U.K.); (K.C.)
| | - Izabela Sańko-Sawczenko
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warszawa, Poland;
| | - Miroslaw Kwasniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-089 Bialystok, Poland; (U.K.); (K.C.)
- Correspondence:
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6
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Inoue T, Kokubo T, Daino K, Yanagihara H, Watanabe F, Tsuruoka C, Amasaki Y, Morioka T, Homma‐Takeda S, Kobayashi T, Hino O, Shimada Y, Kakinuma S. Interstitial chromosomal deletion of the tuberous sclerosis complex 2 locus is a signature for radiation-associated renal tumors in Eker rats. Cancer Sci 2020; 111:840-848. [PMID: 31925975 PMCID: PMC7060461 DOI: 10.1111/cas.14307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 12/23/2019] [Accepted: 12/31/2019] [Indexed: 01/01/2023] Open
Abstract
Ionizing radiation can damage DNA and, therefore, is a risk factor for cancer. Eker rats, which carry a heterozygous germline mutation in the tumor-suppressor gene tuberous sclerosis complex 2 (Tsc2), are susceptible to radiation-induced renal carcinogenesis. However, the molecular mechanisms involved in Tsc2 inactivation are unclear. We subjected Fischer 344 × Eker (Long Evans Tsc2+/- ) F1 hybrid rats to gamma-irradiation (2 Gy) at gestational day 19 (GD19) or postnatal day 5 (PND5) and investigated the patterns of genomic alterations in the Tsc2 allele of renal tumors that developed at 1 year after irradiation (N = 24 tumors for GD19, N = 10 for PND5), in comparison with spontaneously developed tumors (N = 8 tumors). Gamma-irradiation significantly increased the multiplicity of renal tumors. The frequency of LOH at the chromosome 10q12 region, including the Tsc2 locus, was 38%, 29% and 60% in renal carcinomas developed from the nonirradiated, GD19 and PND5 groups, respectively. Array comparative genomic hybridization analysis revealed that the LOH patterns on chromosome 10 in renal carcinomas were classified into chromosomal missegregation, mitotic recombination and chromosomal deletion types. LOH of the interstitial chromosomal deletion type was observed only in radiation-associated carcinomas. Sequence analysis for the wild-type Tsc2 allele in the LOH-negative carcinomas identified deletions (nonirradiated: 26%; GD19: 21%) and base-substitution mutations (GD19: 4%). Reduced expression of Tsc2 was also observed in the majority of the LOH-negative carcinomas. Our results suggest that interstitial chromosomal deletion is a characteristic mutagenic event caused by ionizing radiation, and it may contribute to the assessment of radiation-induced cancer risk.
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Affiliation(s)
- Tatsuya Inoue
- Department of Radiation Effects ResearchNational Institute of Radiological SciencesNational Institutes for Quantum and Radiological Science and TechnologyChibaJapan
- Department of RadiologyJuntendo University Urayasu HospitalChibaJapan
| | - Toshiaki Kokubo
- Laboratory Animal and Genome Sciences SectionNational Institute of Radiological SciencesNational Institutes for Quantum and Radiological Science and TechnologyChibaJapan
| | - Kazuhiro Daino
- Department of Radiation Effects ResearchNational Institute of Radiological SciencesNational Institutes for Quantum and Radiological Science and TechnologyChibaJapan
| | - Hiromi Yanagihara
- Department of Radiation Effects ResearchNational Institute of Radiological SciencesNational Institutes for Quantum and Radiological Science and TechnologyChibaJapan
| | - Fumiko Watanabe
- Department of Radiation Effects ResearchNational Institute of Radiological SciencesNational Institutes for Quantum and Radiological Science and TechnologyChibaJapan
| | - Chizuru Tsuruoka
- Department of Radiation Effects ResearchNational Institute of Radiological SciencesNational Institutes for Quantum and Radiological Science and TechnologyChibaJapan
| | - Yoshiko Amasaki
- Department of Radiation Effects ResearchNational Institute of Radiological SciencesNational Institutes for Quantum and Radiological Science and TechnologyChibaJapan
| | - Takamitsu Morioka
- Department of Radiation Effects ResearchNational Institute of Radiological SciencesNational Institutes for Quantum and Radiological Science and TechnologyChibaJapan
| | - Shino Homma‐Takeda
- Department of Basic Medical Sciences for Radiation DamagesNational Institute of Radiological SciencesNational Institutes for Quantum and Radiological Science and TechnologyChibaJapan
| | - Toshiyuki Kobayashi
- Department of Pathology and OncologyFaculty of MedicineJuntendo UniversityTokyoJapan
| | - Okio Hino
- Department of Pathology and OncologyFaculty of MedicineJuntendo UniversityTokyoJapan
| | - Yoshiya Shimada
- National Institutes for Quantum and Radiological Science and TechnologyChibaJapan
- Present address:
Institute for Environmental SciencesAomoriJapan
| | - Shizuko Kakinuma
- Department of Radiation Effects ResearchNational Institute of Radiological SciencesNational Institutes for Quantum and Radiological Science and TechnologyChibaJapan
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7
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Beetch M, Harandi-Zadeh S, Shen K, Lubecka K, Kitts DD, O'Hagan HM, Stefanska B. Dietary antioxidants remodel DNA methylation patterns in chronic disease. Br J Pharmacol 2019; 177:1382-1408. [PMID: 31626338 DOI: 10.1111/bph.14888] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/19/2019] [Accepted: 09/23/2019] [Indexed: 12/14/2022] Open
Abstract
Chronic diseases account for over 60% of all deaths worldwide according to the World Health Organization reports. Majority of cases are triggered by environmental exposures that lead to aberrant changes in the epigenome, specifically, the DNA methylation patterns. These changes result in altered expression of gene networks and activity of signalling pathways. Dietary antioxidants, including catechins, flavonoids, anthocyanins, stilbenes and carotenoids, demonstrate benefits in the prevention and/or support of therapy in chronic diseases. This review provides a comprehensive discussion of potential epigenetic mechanisms of antioxidant compounds in reversing altered patterns of DNA methylation in chronic disease. Antioxidants remodel the DNA methylation patterns through multiple mechanisms, including regulation of epigenetic enzymes and chromatin remodelling complexes. These effects can further contribute to antioxidant properties of the compounds. On the other hand, decrease in oxidative stress itself can impact DNA methylation delivering additional link between antioxidant mechanisms and epigenetic effects of the compounds. LINKED ARTICLES: This article is part of a themed section on The Pharmacology of Nutraceuticals. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v177.6/issuetoc.
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Affiliation(s)
- Megan Beetch
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Sadaf Harandi-Zadeh
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Kate Shen
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Katarzyna Lubecka
- Department of Biomedical Chemistry, Medical University of Lodz, Lodz, Poland
| | - David D Kitts
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Heather M O'Hagan
- Cell, Molecular and Cancer Biology, Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana, USA
| | - Barbara Stefanska
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
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8
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Pimpinelli S, Piacentini L. Environmental change and the evolution of genomes: Transposable elements as translators of phenotypic plasticity into genotypic variability. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13497] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sergio Pimpinelli
- Istituto Pasteur Italia Fondazione Cenci‐Bolognetti and Department of Biology and Biotechnology ‘C. Darwin’ Sapienza University of Rome Rome Italy
| | - Lucia Piacentini
- Istituto Pasteur Italia Fondazione Cenci‐Bolognetti and Department of Biology and Biotechnology ‘C. Darwin’ Sapienza University of Rome Rome Italy
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9
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Viana Ferreira AM, Marajó L, Matoso DA, Ribeiro LB, Feldberg E. Chromosomal Mapping of Rex Retrotransposons in Tambaqui (Colossoma macropomum Cuvier, 1818) Exposed to Three Climate Change Scenarios. Cytogenet Genome Res 2019; 159:39-47. [PMID: 31593951 DOI: 10.1159/000502926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2019] [Indexed: 11/19/2022] Open
Abstract
Greenhouse gas emissions are known to influence the planet's temperature, mainly due to human activities. To allow hypothesis testing, as well as to seek viable alternatives for mitigation, the Intergovernmental Panel on Climate Change (IPCC) suggested 3 main scenarios for changes projected for the year 2100. In this paper, we subjected Colossoma macropomum Cuvier, 1818 (tambaqui) individuals in a microcosm to IPCC scenarios B1 (mild), A1B (intermediate), and A2 (extreme) to test possible impacts on their genome. We found chromosome heterochromatinization in specimens exposed to the A2 scenario, where terminal blocks and interstitial bands were detected on several chromosome pairs. The behavior of Rex1 and Rex3 sequences differed between the test scenarios. Hybridization of Rex1 resulted in diffuse signals which showed a gradual increase in the tested scenarios. For Rex3, an increase was observed in the A2 scenario with blocks on several chromosomes, some of which coincided with heterochromatin. Heterochromatinization is an epigenetic process, which may have occurred as a mechanism for regulating Rex3 activity. The signal pattern of Rex6 did not change, suggesting that other mechanisms are acting to regulate its activity.
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10
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Liu Y, El-Kassaby YA. Novel Insights into Plant Genome Evolution and Adaptation as Revealed through Transposable Elements and Non-Coding RNAs in Conifers. Genes (Basel) 2019; 10:genes10030228. [PMID: 30889931 PMCID: PMC6470726 DOI: 10.3390/genes10030228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 01/03/2023] Open
Abstract
Plant genomes are punctuated by repeated bouts of proliferation of transposable elements (TEs), and these mobile bursts are followed by silencing and decay of most of the newly inserted elements. As such, plant genomes reflect TE-related genome expansion and shrinkage. In general, these genome activities involve two mechanisms: small RNA-mediated epigenetic repression and long-term mutational decay and deletion, that is, genome-purging. Furthermore, the spatial relationships between TE insertions and genes are an important force in shaping gene regulatory networks, their downstream metabolic and physiological outputs, and thus their phenotypes. Such cascading regulations finally set up a fitness differential among individuals. This brief review demonstrates factual evidence that unifies most updated conceptual frameworks covering genome size, architecture, epigenetic reprogramming, and gene expression. It aims to give an overview of the impact that TEs may have on genome and adaptive evolution and to provide novel insights into addressing possible causes and consequences of intimidating genome sizes (20⁻30 Gb) in a taxonomic group, conifers.
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Affiliation(s)
- Yang Liu
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada.
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada.
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11
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Hu L, Xiao P, Jiang Y, Dong M, Chen Z, Li H, Hu Z, Lei A, Wang J. Transgenerational Epigenetic Inheritance Under Environmental Stress by Genome-Wide DNA Methylation Profiling in Cyanobacterium. Front Microbiol 2018; 9:1479. [PMID: 30022974 PMCID: PMC6039552 DOI: 10.3389/fmicb.2018.01479] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/13/2018] [Indexed: 11/19/2022] Open
Abstract
Epigenetic modifications such as DNA methylation are well known as connected with many important biological processes. Rapid accumulating evidence shows environmental stress can generate particular defense epigenetic changes across generations in eukaryotes. This transgenerational epigenetic inheritance in animals and plants has gained interest over the last years. Cyanobacteria play very crucial role in the earth, and as the primary producer they can adapt to nearly all diverse environments. However, few knowledge about the genome wide epigenetic information such as methylome information in cyanobacteria, especially under any environment stress, was reported so far. In this study we profiled the genome-wide cytosine methylation from a model cyanobacterium Synechocystis sp. PCC 6803, and explored the possibility of transgenerational epigenetic process in this ancient single-celled prokaryote by comparing the DNA methylomes among normal nitrogen medium cultivation, nitrogen starvation for 72 h and nitrogen recovery for about 12 generations. Our results shows that DNA methylation patterns in nitrogen starvation and nitrogen recovery are much more similar with each other, significantly different from that of the normal nitrogen. This study reveals the difference in global DNA methylation pattern of cyanobacteria between normal and nutrient stress conditions and reports the evidence of transgenerational epigenetic process in cyanobacteria. The results of this study may contribute to a better understanding of epigenetic regulation in prokaryotic adaptation to and survive in the ever changing environment.
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Affiliation(s)
- Lang Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Nanshan District Key Lab for Biopolymers and Safety Evaluation, College of Materials Science and Engineering, Shenzhen University, Shenzhen, China
| | - Peng Xiao
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yongguang Jiang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Mingjie Dong
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zixi Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Hui Li
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zhangli Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Anping Lei
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jiangxin Wang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Nanshan District Key Lab for Biopolymers and Safety Evaluation, College of Materials Science and Engineering, Shenzhen University, Shenzhen, China
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12
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Groot MP, Wagemaker N, Ouborg NJ, Verhoeven KJF, Vergeer P. Epigenetic population differentiation in field- and common garden-grown Scabiosa columbaria plants. Ecol Evol 2018; 8:3505-3517. [PMID: 29607042 PMCID: PMC5869358 DOI: 10.1002/ece3.3931] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/27/2017] [Accepted: 12/06/2017] [Indexed: 12/12/2022] Open
Abstract
Populations often differ in phenotype and these differences can be caused by adaptation by natural selection, random neutral processes, and environmental responses. The most straightforward way to divide mechanisms that influence phenotypic variation is heritable variation and environmental‐induced variation (e.g., plasticity). While genetic variation is responsible for most heritable phenotypic variation, part of this is also caused by nongenetic inheritance. Epigenetic processes may be one of the underlying mechanisms of plasticity and nongenetic inheritance and can therefore possibly contribute to heritable differences through drift and selection. Epigenetic variation may be influenced directly by the environment, and part of this variation can be transmitted to next generations. Field screenings combined with common garden experiments will add valuable insights into epigenetic differentiation, epigenetic memory and can help to reveal part of the relative importance of epigenetics in explaining trait variation. We explored both genetic and epigenetic diversity, structure and differentiation in the field and a common garden for five British and five French Scabiosa columbaria populations. Genetic and epigenetic variation was subsequently correlated with trait variation. Populations showed significant epigenetic differentiation between populations and countries in the field, but also when grown in a common garden. By comparing the epigenetic variation between field and common garden‐grown plants, we showed that a considerable part of the epigenetic memory differed from the field‐grown plants and was presumably environmentally induced. The memory component can consist of heritable variation in methylation that is not sensitive to environments and possibly genetically based, or environmentally induced variation that is heritable, or a combination of both. Additionally, random epimutations might be responsible for some differences as well. By comparing epigenetic variation in both the field and common environment, our study provides useful insight into the environmental and genetic components of epigenetic variation.
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Affiliation(s)
- Maartje P Groot
- Experimental Plant Ecology Institute for Water and Wetland Research Radboud University Nijmegen Nijmegen The Netherlands
| | - Niels Wagemaker
- Experimental Plant Ecology Institute for Water and Wetland Research Radboud University Nijmegen Nijmegen The Netherlands
| | - N Joop Ouborg
- Experimental Plant Ecology Institute for Water and Wetland Research Radboud University Nijmegen Nijmegen The Netherlands
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology Netherlands Institute of Ecology (NIOO-KNAW) Wageningen The Netherlands
| | - Philippine Vergeer
- Experimental Plant Ecology Institute for Water and Wetland Research Radboud University Nijmegen Nijmegen The Netherlands.,Plant Ecology and Nature Conservation Group Wageningen The Netherlands
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13
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Wen Y, He Y, Ji X, Li S, Chen L, Zhou Y, Wang M, Chen B. Isolation of an indigenous Chlorella vulgaris from swine wastewater and characterization of its nutrient removal ability in undiluted sewage. BIORESOURCE TECHNOLOGY 2017; 243:247-253. [PMID: 28672187 DOI: 10.1016/j.biortech.2017.06.094] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/12/2017] [Accepted: 06/17/2017] [Indexed: 05/13/2023]
Abstract
Bio-treatment of wastewater mediated by microalgae is considered as a promising solution. This work aimed to isolate an indigenous microalgal strain (named MBFJNU-1) from swine wastewater effluent and identify as Chlorella vulgaris. After 12days, the removal efficiencies of total nitrogen (TN) and total phosphorus (TP) in undiluted swine slurry were 90.51% and 91.54%, respectively. Stress tolerance in response to wastewater was verified by cultivating in artificial wastewater containing different levels of chemical oxygen demand (COD), TN and TP. MBFJNU-1 could grow well in undiluted swine slurry and artificial wastewater containing 30,000mg/L COD or 2000mg/L TN. Furthermore, global nuclear DNA methylation (5-mC) of MBFJNU-1 was employed to explore the possible mechanism in response to wastewater stress. The results showed that the level of 5-mC was inversely proportional to the growth of MBFJNU-1 in different diluted swine slurry, helping to understand 5-mC variation in response to stress environment.
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Affiliation(s)
- Yangmin Wen
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; Quanzhou Medical College, Quanzhou 362000, China
| | - Yongjin He
- College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Xiaowei Ji
- College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Shaofeng Li
- College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Ling Chen
- College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Youcai Zhou
- College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Mingzi Wang
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou 350117, China
| | - Bilian Chen
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou 350117, China.
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14
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Vanstone M, Kandasamy S, Giacomini M, DeJean D, McDonald SD. Pregnant women's perceptions of gestational weight gain: A systematic review and meta-synthesis of qualitative research. MATERNAL & CHILD NUTRITION 2017; 13:e12374. [PMID: 27873484 PMCID: PMC6866018 DOI: 10.1111/mcn.12374] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 07/25/2016] [Accepted: 08/10/2016] [Indexed: 01/01/2023]
Abstract
Excess gestational weight gain has numerous negative health outcomes for women and children, including high blood pressure, diabetes, and cesarean section (maternal) and high birth weight, trauma at birth, and asphyxia (infants). Excess weight gain in pregnancy is associated with a higher risk of long-term obesity in both mothers and children. Despite a concerted public health effort, the proportion of pregnant women gaining weight in excess of national guidelines continues to increase. To understand this phenomenon and offer suggestions for improving interventions, we conducted a systematic review of qualitative research on pregnant women's perceptions and experiences of weight gain in pregnancy. We used the methodology of qualitative meta-synthesis to analyze 42 empirical qualitative research studies conducted in high-income countries and published between 2005 and 2015. With this synthesis, we provide an account of the underlying factors and circumstances (barriers, facilitators, and motivators) that pregnant women identify as important for appropriate weight gain. We also offer a description of the strategies identified by pregnant women as acceptable and appropriate ways to promote healthy weight gain. Through our integrative analysis, we identify women's common perception on the struggle to enact health behaviors and physical, social, and environmental factors outside of their control. Effective and sensitive interventions to encourage healthy weight gain in pregnancy must consider the social environment in which decisions about weight take place.
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Affiliation(s)
- Meredith Vanstone
- Department of Family MedicineMcMaster UniversityHamiltonOntarioCanada
- Centre for Health Economics and Policy AnalysisMcMaster UniversityHamiltonOntarioCanada
| | - Sujane Kandasamy
- Department of Clinical Epidemiology and BiostatisticsMcMaster UniversityHamiltonOntarioCanada
| | - Mita Giacomini
- Centre for Health Economics and Policy AnalysisMcMaster UniversityHamiltonOntarioCanada
- Department of Clinical Epidemiology and BiostatisticsMcMaster UniversityHamiltonOntarioCanada
| | - Deirdre DeJean
- Centre for Health Economics and Policy AnalysisMcMaster UniversityHamiltonOntarioCanada
- Department of Clinical Epidemiology and BiostatisticsMcMaster UniversityHamiltonOntarioCanada
| | - Sarah D. McDonald
- Department of Clinical Epidemiology and BiostatisticsMcMaster UniversityHamiltonOntarioCanada
- Departments of Obstetrics and Gynecology, RadiologyMcMaster UniversityHamiltonOntarioCanada
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15
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Pandey G, Sharma N, Sahu PP, Prasad M. Chromatin-Based Epigenetic Regulation of Plant Abiotic Stress Response. Curr Genomics 2016; 17:490-498. [PMID: 28217005 PMCID: PMC5282600 DOI: 10.2174/1389202917666160520103914] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 12/10/2015] [Accepted: 12/13/2015] [Indexed: 12/15/2022] Open
Abstract
Plants are continuously exposed to various abiotic and biotic factors limiting their growth and reproduction. In response, they need various sophisticated ways to adapt to adverse environmental conditions without compromising their proper development, reproductive success and eventually survival. This requires an intricate network to regulate gene expression at transcriptional and post-transcriptional levels, including epigenetic switches. Changes in chromatin modifications such as DNA and histone methylation have been observed in plants upon exposure to several abiotic stresses. In the present review, we highlight the changes of DNA methylation in diverse plants in response to several abiotic stresses such as salinity, drought, cold and heat. We also discuss the progresses made in understanding how these DNA methylation changes might contribute to the abiotic stress tolerance.
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Affiliation(s)
- Garima Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Namisha Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Pranav Pankaj Sahu
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India,Address correspondence to this author at the National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India; Tel: 91-11-26735160; Fax: 91-11-26741658; 26741146;, E-mails: ,
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16
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Xia H, Huang W, Xiong J, Tao T, Zheng X, Wei H, Yue Y, Chen L, Luo L. Adaptive Epigenetic Differentiation between Upland and Lowland Rice Ecotypes Revealed by Methylation-Sensitive Amplified Polymorphism. PLoS One 2016; 11:e0157810. [PMID: 27380174 PMCID: PMC4933381 DOI: 10.1371/journal.pone.0157810] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/06/2016] [Indexed: 11/22/2022] Open
Abstract
The stress-induced epimutations could be inherited over generations and play important roles in plant adaption to stressful environments. Upland rice has been domesticated in water-limited environments for thousands of years and accumulated drought-induced epimutations of DNA methylation, making it epigenetically differentiated from lowland rice. To study the epigenetic differentiation between upland and lowland rice ecotypes on their drought-resistances, the epigenetic variation was investigated in 180 rice landraces under both normal and osmotic conditions via methylation-sensitive amplified polymorphism (MSAP) technique. Great alterations (52.9~54.3% of total individual-locus combinations) of DNA methylation are recorded when rice encountering the osmotic stress. Although the general level of epigenetic differentiation was very low, considerable level of ΦST (0.134~0.187) was detected on the highly divergent epiloci (HDE). The HDE detected in normal condition tended to stay at low levels in upland rice, particularly the ones de-methylated in responses to osmotic stress. Three out of four selected HDE genes differentially expressed between upland and lowland rice under normal or stressed conditions. Moreover, once a gene at HDE was up-/down-regulated in responses to the osmotic stress, its expression under the normal condition was higher/lower in upland rice. This result suggested expressions of genes at the HDE in upland rice might be more adaptive to the osmotic stress. The epigenetic divergence and its influence on the gene expression should contribute to the higher drought-resistance in upland rice as it is domesticated in the water-limited environment.
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Affiliation(s)
- Hui Xia
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Weixia Huang
- Shanghai Agrobiological Gene Center, Shanghai, China
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
| | - Jie Xiong
- Shanghai Agrobiological Gene Center, Shanghai, China
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
| | - Tao Tao
- Shanghai Agrobiological Gene Center, Shanghai, China
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaoguo Zheng
- Shanghai Agrobiological Gene Center, Shanghai, China
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
| | - Haibin Wei
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Yunxia Yue
- Shanghai Agrobiological Gene Center, Shanghai, China
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
| | - Liang Chen
- Shanghai Agrobiological Gene Center, Shanghai, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, China
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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17
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Rey O, Danchin E, Mirouze M, Loot C, Blanchet S. Adaptation to Global Change: A Transposable Element-Epigenetics Perspective. Trends Ecol Evol 2016; 31:514-526. [PMID: 27080578 DOI: 10.1016/j.tree.2016.03.013] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 12/21/2022]
Abstract
Understanding how organisms cope with global change is a major scientific challenge. The molecular pathways underlying rapid adaptive phenotypic responses to global change remain poorly understood. Here, we highlight the relevance of two environment-sensitive molecular elements: transposable elements (TEs) and epigenetic components (ECs). We first outline the sensitivity of these elements to global change stressors and review how they interact with each other. We then propose an integrative molecular engine coupling TEs and ECs and allowing organisms to fine-tune phenotypes in a real-time fashion, adjust the production of phenotypic and genetic variation, and produce heritable phenotypes with different levels of transmission fidelity. We finally discuss the implications of this molecular engine in the context of global change.
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Affiliation(s)
- Olivier Rey
- CNRS, UPS, Station d'Écologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France; Department of Biosciences, College of Science, Swansea University, Swansea SA2 8PP, UK.
| | - Etienne Danchin
- CNRS, UPS, ENFA, Évolution & Diversité Biologique (EDB) UMR 5174, 118 Route de Narbonne, 31062 Toulouse, Cedex 9, France; Université Paul Sabatier, Évolution & Diversité Biologique (EDB), 31062 Toulouse, Cedex 9, France
| | - Marie Mirouze
- Institut de Recherche pour le Développement, UMR232 DIADE Diversité Adaptation et Développement des Plantes, Laboratoire Génome et Développement des Plantes, 58 avenue Paul Alduy, 66860 Perpignan, France
| | - Céline Loot
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France; CNRS UMR3525, Paris, France
| | - Simon Blanchet
- CNRS, UPS, Station d'Écologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France; CNRS, UPS, ENFA, Évolution & Diversité Biologique (EDB) UMR 5174, 118 Route de Narbonne, 31062 Toulouse, Cedex 9, France.
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18
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Herrera CM, Medrano M, Bazaga P. Comparative spatial genetics and epigenetics of plant populations: heuristic value and a proof of concept. Mol Ecol 2016; 25:1653-64. [PMID: 26850938 DOI: 10.1111/mec.13576] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 01/29/2016] [Accepted: 02/01/2016] [Indexed: 11/26/2022]
Abstract
Despite the recent upsurge of interest on natural epigenetic variation of nonmodel organisms, factors conditioning the spatial structure of epigenetic diversity in wild plant populations remain virtually unexplored. We propose that information on processes shaping natural epigenetic variation can be gained using the spatial structure of genetic diversity as null model. Departures of epigenetic isolation-by-distance (IBD) patterns from genetic IBD patterns for the same sample, particularly differences in slope of similarity-distance regressions, will reflect the action of factors that operate specifically on epigenetic variation, including imperfect transgenerational inheritance and responsiveness to environmental factors of epigenetic marks. As a proof of concept, we provide a comparative analysis of spatial genetic and epigenetic structure of 200 mapped individuals of the perennial herb Helleborus foetidus. Plants were fingerprinted using nuclear microsatellites, amplified fragment length polymorphisms (AFLP) and methylation-sensitive AFLP markers. Expectations from individual-level IBD patterns were tested by means of kinship-distance regressions. Both genetic and epigenetic similarity between H. foetidus individuals conformed to theoretical expectations under individual-level IBD models. Irrespective of marker type, there were significant negative linear relationships between the kinship coefficient for plant pairs and their spatial separation. Regression slopes were significantly steeper for epigenetic markers. Epigenetic similarity between individuals was much greater than genetic similarity at shortest distances, such epigenetic 'kinship excess' tending to decrease as plant separation increased. Results suggest that moderate-to-high heritability and responsiveness to local environments are major drivers of epigenetic spatial structure in H. foetidus, and illustrate the heuristic value of comparing genetic and epigenetic spatial structure for formulating and testing hypotheses on forces shaping epigenetic diversity in wild plant populations.
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Affiliation(s)
- Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio s/n, Isla de La Cartuja, 41092, Sevilla, Spain
| | - Mónica Medrano
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio s/n, Isla de La Cartuja, 41092, Sevilla, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio s/n, Isla de La Cartuja, 41092, Sevilla, Spain
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19
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Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J, Lister R. Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. eLife 2015; 4. [PMID: 26196146 DOI: 10.7554/elife.09343.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/20/2015] [Indexed: 05/20/2023] Open
Abstract
Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes in mC occurred after changes in nearby gene transcription, were mostly DCL3a-independent, and could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in Arabidopsis revealed a very limited effect of phosphate starvation on mC, suggesting a species-specific mechanism. Overall, this suggests that TEs in proximity to environmentally induced genes are silenced via hypermethylation, and establishes the temporal hierarchy of transcriptional and epigenomic changes in response to stress.
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Affiliation(s)
- David Secco
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
| | - Chuang Wang
- State Key laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China
| | - Huixia Shou
- State Key laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China
| | - Matthew D Schultz
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Serge Chiarenza
- UMR 6191 CEA, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement des Plantes, Université d'Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Laurent Nussaume
- UMR 6191 CEA, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement des Plantes, Université d'Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - James Whelan
- Joint Research Laboratory in Genomics and Nutriomics, Zhejiang University, Hangzhou, China
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
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20
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Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J, Lister R. Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. eLife 2015; 4:e09343. [PMID: 26196146 PMCID: PMC4534844 DOI: 10.7554/elife.09343] [Citation(s) in RCA: 235] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/20/2015] [Indexed: 01/19/2023] Open
Abstract
Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes in mC occurred after changes in nearby gene transcription, were mostly DCL3a-independent, and could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in Arabidopsis revealed a very limited effect of phosphate starvation on mC, suggesting a species-specific mechanism. Overall, this suggests that TEs in proximity to environmentally induced genes are silenced via hypermethylation, and establishes the temporal hierarchy of transcriptional and epigenomic changes in response to stress.
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Affiliation(s)
- David Secco
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
| | - Chuang Wang
- State Key laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China
- Joint Research Laboratory in Genomics and Nutriomics, Zhejiang University, Hangzhou, China
| | - Huixia Shou
- State Key laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China
- Joint Research Laboratory in Genomics and Nutriomics, Zhejiang University, Hangzhou, China
| | - Matthew D Schultz
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
| | - Serge Chiarenza
- UMR 6191 CEA, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement des Plantes, Université d'Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Laurent Nussaume
- UMR 6191 CEA, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement des Plantes, Université d'Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
| | - James Whelan
- Joint Research Laboratory in Genomics and Nutriomics, Zhejiang University, Hangzhou, China
- Department of Animal, Plant and Soil Science, School of Life Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Australia
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
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21
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Grandbastien MA. LTR retrotransposons, handy hitchhikers of plant regulation and stress response. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:403-16. [DOI: 10.1016/j.bbagrm.2014.07.017] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 11/30/2022]
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Schulz B, Eckstein RL, Durka W. Epigenetic variation reflects dynamic habitat conditions in a rare floodplain herb. Mol Ecol 2014; 23:3523-37. [DOI: 10.1111/mec.12835] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Benjamin Schulz
- Institute of Landscape Ecology and Resource Management; Interdisciplinary Research Centre (IFZ); Justus Liebig University Giessen; Heinrich-Buff-Ring 26-32 D-35393 Giessen Germany
| | - Rolf Lutz Eckstein
- Institute of Landscape Ecology and Resource Management; Interdisciplinary Research Centre (IFZ); Justus Liebig University Giessen; Heinrich-Buff-Ring 26-32 D-35393 Giessen Germany
| | - Walter Durka
- Department of Community Ecology (BZF); Helmholtz Centre for Environmental Research-UFZ; Theodor-Lieser-Straße 4 D-06120 Halle (Saale) Germany
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23
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Liang D, Zhang Z, Wu H, Huang C, Shuai P, Ye CY, Tang S, Wang Y, Yang L, Wang J, Yin W, Xia X. Single-base-resolution methylomes of Populus trichocarpa reveal the association between DNA methylation and drought stress. BMC Genet 2014; 15 Suppl 1:S9. [PMID: 25080211 PMCID: PMC4118614 DOI: 10.1186/1471-2156-15-s1-s9] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Background DNA methylation is an important biological form of epigenetic modification, playing key roles in plant development and environmental responses. Results In this study, we examined single-base resolution methylomes of Populus under control and drought stress conditions using high-throughput bisulfite sequencing for the first time. Our data showed methylation levels of methylated cytosines, upstream 2kp, downstream 2kb, and repeatitive sequences significantly increased after drought treatment in Populus. Interestingly, methylation in 100 bp upstream of the transcriptional start site (TSS) repressed gene expression, while methylations in 100-2000bp upstream of TSS and within the gene body were positively associated with gene expression. Integrated with the transcriptomic data, we found that all cis-splicing genes were non-methylated, suggesting that DNA methylation may not associate with cis-splicing. However, our results showed that 80% of trans-splicing genes were methylated. Moreover, we found 1156 transcription factors (TFs) with reduced methylation and expression levels and 690 TFs with increased methylation and expression levels after drought treatment. These TFs may play important roles in Populus drought stress responses through the changes of DNA methylation. Conclusions These findings may provide valuable new insight into our understanding of the interaction between gene expression and methylation of drought responses in Populus.
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Tang XM, Tao X, Wang Y, Ma DW, Li D, Yang H, Ma XR. Analysis of DNA methylation of perennial ryegrass under drought using the methylation-sensitive amplification polymorphism (MSAP) technique. Mol Genet Genomics 2014; 289:1075-84. [PMID: 24916310 DOI: 10.1007/s00438-014-0869-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/15/2014] [Indexed: 12/31/2022]
Abstract
Perennial ryegrass (Lolium perenne), an excellent grass for forage and turf, is widespread in temperate regions. Drought is an important factor that limits its growth, distribution, and yield. DNA methylation affects gene expression and plays an important role in adaptation to adverse environments. In this study, the DNA methylation changes in perennial ryegrass under drought stress were assessed using methylation-sensitive amplified polymorphism (MSAP). After 15 days of drought stress treatment, the plant height was less than half of the control, and the leaves were smaller and darker. Genome-wide, a total of 652 CCGG sites were detected by MSAP. The total methylation level was 57.67 and 47.39 % in the control and drought treatment, respectively, indicating a decrease of 10.28 % due to drought exposure. Fifteen differentially displayed DNA fragments in MSAP profiles were cloned for sequencing analysis. The results showed that most of the genes involved in stress responses. The relative expression levels revealed that three demethylated fragments were up-regulated. The expression of a predicted retrotransposon increased significantly, changing from hypermethylation to non-methylation. Although the extent of methylation in two other genes decreased, the sites of methylation remained, and the expression increased only slightly. All of these results suggested that drought stress decreased the total DNA methylation level in perennial ryegrass and demethylation up-regulated related gene expressions and that the extent of methylation was negatively correlated with expression. Overall, the induced epigenetic changes in genome probably are an important regulatory mechanism for acclimating perennial ryegrass to drought and possibly other environmental stresses.
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Affiliation(s)
- Xiao-Mei Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No 9, Section 4, Renmin South Road, Chengdu, 610041, China
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25
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Shapiro JA. Epigenetic control of mobile DNA as an interface between experience and genome change. Front Genet 2014; 5:87. [PMID: 24795749 PMCID: PMC4007016 DOI: 10.3389/fgene.2014.00087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/01/2014] [Indexed: 12/29/2022] Open
Abstract
Mobile DNA in the genome is subject to RNA-targeted epigenetic control. This control regulates the activity of transposons, retrotransposons and genomic proviruses. Many different life history experiences alter the activities of mobile DNA and the expression of genetic loci regulated by nearby insertions. The same experiences induce alterations in epigenetic formatting and lead to trans-generational modifications of genome expression and stability. These observations lead to the hypothesis that epigenetic formatting directed by non-coding RNA provides a molecular interface between life history events and genome alteration.
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Affiliation(s)
- James A. Shapiro
- Department of Biochemistry and Molecular Biology, University of ChicagoChicago, IL, USA
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26
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Epigenetics in an ecotoxicological context. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2014; 764-765:36-45. [DOI: 10.1016/j.mrgentox.2013.08.008] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 08/22/2013] [Indexed: 11/23/2022]
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27
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Abstract
The function of DNA methylation in species such as bivalves where the limited amount of DNA methylation is predominantly found in gene bodies remains unclear. An emerging possible explanation is that the role of gene body DNA methylation is dependent on gene function, a potential phenomenon that has arisen from selective pressure on lineage-specific life history traits. In genes contributing to phenotypes that benefit from increased plasticity, the absence of DNA methylation could contribute to stochastic transcriptional opportunities and increased transposable element activity. In genes where regulated control of activity is essential, DNA methylation may also play a role in targeted, predictable genome regulation. Here, we review the current knowledge concerning DNA methylation in bivalves and explore the putative role of DNA methylation in both an evolutionary and ecological context.
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Sahu PP, Pandey G, Sharma N, Puranik S, Muthamilarasan M, Prasad M. Epigenetic mechanisms of plant stress responses and adaptation. PLANT CELL REPORTS 2013; 32:1151-9. [PMID: 23719757 DOI: 10.1007/s00299-013-1462-x] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/20/2013] [Accepted: 05/20/2013] [Indexed: 05/20/2023]
Abstract
Epigenetics has become one of the hottest topics of research in plant functional genomics since it appears promising in deciphering and imparting stress-adaptive potential in crops and other plant species. Recently, numerous studies have provided new insights into the epigenetic control of stress adaptation. Epigenetic control of stress-induced phenotypic response of plants involves gene regulation. Growing evidence suggest that methylation of DNA in response to stress leads to the variation in phenotype. Transposon mobility, siRNA-mediated methylation and host methyltransferase activation have been implicated in this process. This review presents the current status of epigenetics of plant stress responses with a view to use this knowledge towards engineering plants for stress tolerance.
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Affiliation(s)
- Pranav Pankaj Sahu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
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Ocaña J, Walter B, Schellenbaum P. Stable MSAP Markers for the Distinction of Vitis vinifera cv Pinot Noir Clones. Mol Biotechnol 2013; 55:236-48. [DOI: 10.1007/s12033-013-9675-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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