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Vo BT, Mas P, Johannes F. Time's up: Epigenetic clocks in plants. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102602. [PMID: 39024859 DOI: 10.1016/j.pbi.2024.102602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/30/2024] [Accepted: 06/26/2024] [Indexed: 07/20/2024]
Abstract
For over a decade, the animal field has led the way in using DNA methylation measurements to construct epigenetic clocks of aging. These clocks can predict organismal age with a level of accuracy that surpasses any other molecular proxy known to date. Evidence is finally emerging that epigenetic clocks also exist in plants. However, these clocks appear to differ from those in animals in some key aspects, including in their ability to measure time beyond the life span of an individual. Clock-like epigenetic changes can be found in plant circadian rhythms (scale: 24 h), during plant aging (scale: weeks/centuries), and across plant lineage evolution (scale: decades/millennia). Here, we provide a first classification of these different types of epigenetic clocks, highlight their main features, and discuss their biological basis.
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Affiliation(s)
- Binh Thanh Vo
- Plant Epigenomics, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Paloma Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain; Consejo Superior de Investigaciones Científicas (CSIC), 08028 Barcelona, Spain
| | - Frank Johannes
- Plant Epigenomics, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.
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2
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Fan Y, Sun C, Yan K, Li P, Hein I, Gilroy EM, Kear P, Bi Z, Yao P, Liu Z, Liu Y, Bai J. Recent Advances in Studies of Genomic DNA Methylation and Its Involvement in Regulating Drought Stress Response in Crops. PLANTS (BASEL, SWITZERLAND) 2024; 13:1400. [PMID: 38794470 PMCID: PMC11125032 DOI: 10.3390/plants13101400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
As global arid conditions worsen and groundwater resources diminish, drought stress has emerged as a critical impediment to plant growth and development globally, notably causing declines in crop yields and even the extinction of certain cultivated species. Numerous studies on drought resistance have demonstrated that DNA methylation dynamically interacts with plant responses to drought stress by modulating gene expression and developmental processes. However, the precise mechanisms underlying these interactions remain elusive. This article consolidates the latest research on the role of DNA methylation in plant responses to drought stress across various species, focusing on methods of methylation detection, mechanisms of methylation pattern alteration (including DNA de novo methylation, DNA maintenance methylation, and DNA demethylation), and overall responses to drought conditions. While many studies have observed significant shifts in genome-wide or gene promoter methylation levels in drought-stressed plants, the identification of specific genes and pathways involved remains limited. This review aims to furnish a reference for detailed research into plant responses to drought stress through epigenetic approaches, striving to identify drought resistance genes regulated by DNA methylation, specific signaling pathways, and their molecular mechanisms of action.
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Affiliation(s)
- Youfang Fan
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Kan Yan
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China;
| | - Pengcheng Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Ingo Hein
- The James Hutton Institute, Dundee DD2 5DA, UK; (I.H.); (E.M.G.)
| | | | - Philip Kear
- International Potato Center (CIP), CIP China Center for Asia Pacific (CCCAP), Beijing 102199, China;
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Panfeng Yao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
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Lian Q, Huettel B, Walkemeier B, Mayjonade B, Lopez-Roques C, Gil L, Roux F, Schneeberger K, Mercier R. A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range. Nat Genet 2024; 56:982-991. [PMID: 38605175 PMCID: PMC11096106 DOI: 10.1038/s41588-024-01715-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 03/11/2024] [Indexed: 04/13/2024]
Abstract
Although originally primarily a system for functional biology, Arabidopsis thaliana has, owing to its broad geographical distribution and adaptation to diverse environments, developed into a powerful model in population genomics. Here we present chromosome-level genome assemblies of 69 accessions from a global species range. We found that genomic colinearity is very conserved, even among geographically and genetically distant accessions. Along chromosome arms, megabase-scale rearrangements are rare and typically present only in a single accession. This indicates that the karyotype is quasi-fixed and that rearrangements in chromosome arms are counter-selected. Centromeric regions display higher structural dynamics, and divergences in core centromeres account for most of the genome size variations. Pan-genome analyses uncovered 32,986 distinct gene families, 60% being present in all accessions and 40% appearing to be dispensable, including 18% private to a single accession, indicating unexplored genic diversity. These 69 new Arabidopsis thaliana genome assemblies will empower future genetic research.
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Affiliation(s)
- Qichao Lian
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bruno Huettel
- Max Planck-Genome-centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Birgit Walkemeier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Baptiste Mayjonade
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | | | - Lisa Gil
- INRAE, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Fabrice Roux
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany.
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Düsseldorf, Germany.
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Düsseldorf, Germany.
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4
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Vanden Broeck A, Meese T, Verschelde P, Cox K, Heinze B, Deforce D, De Meester E, Van Nieuwerburgh F. Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar. BMC Biol 2024; 22:30. [PMID: 38317114 PMCID: PMC10845628 DOI: 10.1186/s12915-024-01816-1] [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: 03/30/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Despite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome. RESULTS We present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we investigated methylome variability during a growing season and across vegetatively reproduced generations. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts. In contrast, seasonal dynamics occurred in methylation patterns in CHH context. In the second experiment, we investigated whether methylome patterns of plants grown in a non-parental environment correlate with the parental climate. We did not observe a biological relevant pattern that significantly correlates with the parental climate. Finally, we investigated whether the parental environment has persistent carry-over effects on the vegetative offspring's phenotype. We combined new bud set observations of three consecutive growing seasons with former published bud set data. Using a linear mixed effects analysis, we found a statistically significant but weak short-term, parental carry-over effect on the timing of bud set. However, this effect was negligible compared to the direct effects of the offspring environment. CONCLUSIONS Genome-wide cytosine methylation patterns in symmetrical CG-context are stable in Lombardy poplar and appear to be mainly the result of random processes. In this widespread poplar clone, methylation patterns in CG-context can be used as biomarkers to infer a common ancestor and thus to investigate the recent environmental history of a specific Lombardy poplar. The Lombardy poplar shows high phenotypic plasticity in a novel environment which enabled this clonal tree to adapt and survive all over the temperate regions of the world.
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Affiliation(s)
- An Vanden Broeck
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium.
| | - Tim Meese
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Pieter Verschelde
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium
| | - Karen Cox
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium
| | - Berthold Heinze
- Department of Forest Growth, Silviculture and Genetics, Austrian Federal Research Centre for Forests (BFW), Vienna, Austria
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Ellen De Meester
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
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5
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Sarkies P. Evolution beyond DNA: epigenetic drivers for evolutionary change? BMC Biol 2023; 21:272. [PMID: 38155359 PMCID: PMC10755928 DOI: 10.1186/s12915-023-01770-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023] Open
Affiliation(s)
- Peter Sarkies
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX13QU, UK.
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Williams CJ, Dai D, Tran KA, Monroe JG, Williams BP. Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants. Genome Biol 2023; 24:227. [PMID: 37828516 PMCID: PMC10571256 DOI: 10.1186/s13059-023-03059-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 09/14/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND In several eukaryotes, DNA methylation occurs within the coding regions of many genes, termed gene body methylation (GbM). Whereas the role of DNA methylation on the silencing of transposons and repetitive DNA is well understood, gene body methylation is not associated with transcriptional repression, and its biological importance remains unclear. RESULTS We report a newly discovered type of GbM in plants, which is under constitutive addition and removal by dynamic methylation modifiers in all cells, including the germline. Methylation at Dynamic GbM genes is removed by the DRDD demethylation pathway and added by an unknown source of de novo methylation, most likely the maintenance methyltransferase MET1. We show that the Dynamic GbM state is present at homologous genes across divergent lineages spanning over 100 million years, indicating evolutionary conservation. We demonstrate that Dynamic GbM is tightly associated with the presence of a promoter or regulatory chromatin state within the gene body, in contrast to other gene body methylated genes. We find Dynamic GbM is associated with enhanced gene expression plasticity across development and diverse physiological conditions, whereas stably methylated GbM genes exhibit reduced plasticity. Dynamic GbM genes exhibit reduced dynamic range in drdd mutants, indicating a causal link between DNA demethylation and enhanced gene expression plasticity. CONCLUSIONS We propose a new model for GbM in regulating gene expression plasticity, including a novel type of GbM in which increased gene expression plasticity is associated with the activity of DNA methylation writers and erasers and the enrichment of a regulatory chromatin state.
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Affiliation(s)
- Clara J Williams
- Department of Plant & Microbial Biology, University of California, Berkeley, USA
| | - Dawei Dai
- Department of Plant & Microbial Biology, University of California, Berkeley, USA
| | - Kevin A Tran
- Department of Plant & Microbial Biology, University of California, Berkeley, USA
| | - J Grey Monroe
- Department of Plant Sciences, University of California, Davis, USA
| | - Ben P Williams
- Department of Plant & Microbial Biology, University of California, Berkeley, USA.
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7
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Martins LM, Law JA. Moving targets: Mechanisms regulating siRNA production and DNA methylation during plant development. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102435. [PMID: 37598540 PMCID: PMC10581331 DOI: 10.1016/j.pbi.2023.102435] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023]
Abstract
DNA methylation is a conserved modification that must be precisely regulated during development to facilitate its roles in silencing transposable elements and regulating gene expression. In plants, DNA methylation changes during reproduction are widely documented and, in many cases, the underlying mechanisms are well understood. In somatic tissues, the diversity of methylation patterns are only recently emerging but they are often associated with the RNA-directed DNA methylation (RdDM) pathway. Here, we discuss advances in our understanding of how the locus-specific targeting and tissue-specific expression of RdDM proteins regulate methylation patterns, how the targeting of methylation at loci with imperfect homology expands the purview of RdDM, and how natural variation within RdDM factors impacts DNA methylation patterns.
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Affiliation(s)
- Laura M Martins
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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8
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Yao N, Zhang Z, Yu L, Hazarika R, Yu C, Jang H, Smith LM, Ton J, Liu L, Stachowicz JJ, Reusch TBH, Schmitz RJ, Johannes F. An evolutionary epigenetic clock in plants. Science 2023; 381:1440-1445. [PMID: 37769069 DOI: 10.1126/science.adh9443] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/08/2023] [Indexed: 09/30/2023]
Abstract
Molecular clocks are the basis for dating the divergence between lineages over macroevolutionary timescales (~105 to 108 years). However, classical DNA-based clocks tick too slowly to inform us about the recent past. Here, we demonstrate that stochastic DNA methylation changes at a subset of cytosines in plant genomes display a clocklike behavior. This "epimutation clock" is orders of magnitude faster than DNA-based clocks and enables phylogenetic explorations on a scale of years to centuries. We show experimentally that epimutation clocks recapitulate known topologies and branching times of intraspecies phylogenetic trees in the self-fertilizing plant Arabidopsis thaliana and the clonal seagrass Zostera marina, which represent two major modes of plant reproduction. This discovery will open new possibilities for high-resolution temporal studies of plant biodiversity.
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Affiliation(s)
- N Yao
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Z Zhang
- Plant Epigenomics, Technical University of Munich, Freising, Germany
| | - L Yu
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - R Hazarika
- Plant Epigenomics, Technical University of Munich, Freising, Germany
| | - C Yu
- Plant Epigenomics, Technical University of Munich, Freising, Germany
| | - H Jang
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - L M Smith
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - J Ton
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - L Liu
- Department of Statistics, University of Georgia, Athens, GA, USA
| | - J J Stachowicz
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - T B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - R J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - F Johannes
- Plant Epigenomics, Technical University of Munich, Freising, Germany
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Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications of long-term epigenetic inheritance. Curr Opin Genet Dev 2023; 81:102087. [PMID: 37441873 DOI: 10.1016/j.gde.2023.102087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023]
Abstract
Many modes and mechanisms of epigenetic inheritance have been elucidated in eukaryotes. Most of them are relatively short-term, generally not exceeding one or a few organismal generations. However, emerging evidence indicates that one mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much longer timescales, which are mostly or completely inaccessible in the laboratory. Here we discuss the evidence for, and mechanisms and implications of, such long-term epigenetic inheritance. We argue that compelling evidence supports the long-term epigenetic inheritance of gene body methylation, at least in the model angiosperm Arabidopsis thaliana, and that variation in such methylation can therefore serve as an epigenetic basis for phenotypic variation in natural populations.
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Affiliation(s)
| | - Amy Briffa
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Daniel Zilberman
- Institute of Science and Technology, 3400 Klosterneuburg, Austria.
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10
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Pisupati R, Nizhynska V, Mollá Morales A, Nordborg M. On the causes of gene-body methylation variation in Arabidopsis thaliana. PLoS Genet 2023; 19:e1010728. [PMID: 37141384 DOI: 10.1371/journal.pgen.1010728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/16/2023] [Accepted: 03/31/2023] [Indexed: 05/06/2023] Open
Abstract
Gene-body methylation (gbM) refers to sparse CG methylation of coding regions, which is especially prominent in evolutionarily conserved house-keeping genes. It is found in both plants and animals, but is directly and stably (epigenetically) inherited over multiple generations in the former. Studies in Arabidopsis thaliana have demonstrated that plants originating from different parts of the world exhibit genome-wide differences in gbM, which could reflect direct selection on gbM, but which could also reflect an epigenetic memory of ancestral genetic and/or environmental factors. Here we look for evidence of such factors in F2 plants resulting from a cross between a southern Swedish line with low gbM and a northern Swedish line with high gbM, grown at two different temperatures. Using bisulfite-sequencing data with nucleotide-level resolution on hundreds of individuals, we confirm that CG sites are either methylated (nearly 100% methylation across sampled cells) or unmethylated (approximately 0% methylation across sampled cells), and show that the higher level of gbM in the northern line is due to more sites being methylated. Furthermore, methylation variants almost always show Mendelian segregation, consistent with their being directly and stably inherited through meiosis. To explore how the differences between the parental lines could have arisen, we focused on somatic deviations from the inherited state, distinguishing between gains (relative to the inherited 0% methylation) and losses (relative to the inherited 100% methylation) at each site in the F2 generation. We demonstrate that deviations predominantly affect sites that differ between the parental lines, consistent with these sites being more mutable. Gains and losses behave very differently in terms of the genomic distribution, and are influenced by the local chromatin state. We find clear evidence for different trans-acting genetic polymorphism affecting gains and losses, with those affecting gains showing strong environmental interactions (G×E). Direct effects of the environment were minimal. In conclusion, we show that genetic and environmental factors can change gbM at a cellular level, and hypothesize that these factors can also lead to transgenerational differences between individuals via the inclusion of such changes in the zygote. If true, this could explain genographic pattern of gbM with selection, and would cast doubt on estimates of epimutation rates from inbred lines in constant environments.
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Affiliation(s)
- Rahul Pisupati
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Vienna Graduate School of Population Genetics, Institut für Populationsgenetik, Vetmeduni, Vienna, Austria
| | - Viktoria Nizhynska
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Almudena Mollá Morales
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
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11
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Niccolò T, Anderson AW, Emidio A. Apomixis: oh, what a tangled web we have! PLANTA 2023; 257:92. [PMID: 37000270 PMCID: PMC10066125 DOI: 10.1007/s00425-023-04124-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Apomixis is a complex evolutionary trait with many possible origins. Here we discuss various clues and causes, ultimately proposing a model harmonizing the three working hypotheses on the topic. Asexual reproduction through seeds, i.e., apomixis, is the holy grail of plant biology. Its implementation in modern breeding could be a game-changer for agriculture. It has the potential to generate clonal crops and maintain valuable complex genotypes and their associated heterotic traits without inbreeding depression. The genetic basis and origins of apomixis are still unclear. There are three central hypothesis for the development of apomixis that could be: i) a deviation from the sexual developmental program caused by an asynchronous development, ii) environmentally triggered through epigenetic regulations (a polyphenism of sex), iii) relying on one or more genes/alleles. Because of the ever-increasing complexity of the topic, the path toward a detailed understanding of the mechanisms underlying apomixis remains unclear. Here, we discuss the most recent advances in the evolution perspective of this multifaceted trait. We incorporated our understanding of the effect of endogenous effectors, such as small RNAs, epigenetic regulation, hormonal pathways, protein turnover, and cell wall modification in response to an upside stress. This can be either endogenous (hybridization or polyploidization) or exogenous environmental stress, mainly due to oxidative stress and the corresponding ROS (Reacting Oxygen Species) effectors. Finally, we graphically represented this tangled web.
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Affiliation(s)
- Terzaroli Niccolò
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy.
| | - Aaron W Anderson
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
- Fulbright Scholar From Department of Plant Sciences, University of California, Davis, USA
| | - Albertini Emidio
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
- Consorzio Interuniversitario per le Biotecnologie (CIB), Trieste, Italy
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12
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Yao N, Zhang Z, Yu L, Hazarika R, Yu C, Jang H, Smith LM, Ton J, Liu L, Stachowicz J, Reusch T, Schmitz RJ, Johannes F. An evolutionary epigenetic clock in plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532766. [PMID: 36993545 PMCID: PMC10055040 DOI: 10.1101/2023.03.15.532766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Molecular clocks are the basis for dating the divergence between lineages over macro-evolutionary timescales (~10 5 -10 8 years). However, classical DNA-based clocks tick too slowly to inform us about the recent past. Here, we demonstrate that stochastic DNA methylation changes at a subset of cytosines in plant genomes possess a clock-like behavior. This 'epimutation-clock' is orders of magnitude faster than DNA-based clocks and enables phylogenetic explorations on a scale of years to centuries. We show experimentally that epimutation-clocks recapitulate known topologies and branching times of intra-species phylogenetic trees in the selfing plant A. thaliana and the clonal seagrass Z. marina , which represent two major modes of plant reproduction. This discovery will open new possibilities for high-resolution temporal studies of plant biodiversity.
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Affiliation(s)
- N Yao
- Department of Genetics, University of Georgia, Athens, USA
| | - Z Zhang
- Plant Epigenomics, Technical University of Munich, Freising, Germany
| | - L Yu
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - R Hazarika
- Plant Epigenomics, Technical University of Munich, Freising, Germany
| | - C Yu
- Plant Epigenomics, Technical University of Munich, Freising, Germany
| | - H Jang
- Department of Genetics, University of Georgia, Athens, USA
| | - L M Smith
- School of Biosciences, University of Sheffield, UK
| | - J Ton
- School of Biosciences, University of Sheffield, UK
| | - L Liu
- Department of Statistics, University of Georgia, Athens, USA
| | - J Stachowicz
- Department of Evolution and Ecology, University of California, Davis, USA
| | - Tbh Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - R J Schmitz
- Department of Genetics, University of Georgia, Athens, USA
| | - F Johannes
- Plant Epigenomics, Technical University of Munich, Freising, Germany
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Ibañez VN, van Antro M, Peña-Ponton C, Milanovic-Ivanovic S, Wagemaker CAM, Gawehns F, Verhoeven KJF. Environmental and genealogical effects on DNA methylation in a widespread apomictic dandelion lineage. J Evol Biol 2023; 36:663-674. [PMID: 36810811 DOI: 10.1111/jeb.14162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/08/2022] [Accepted: 01/05/2023] [Indexed: 02/24/2023]
Abstract
DNA methylation in plant genomes occurs in different sequences and genomic contexts that have very different properties. DNA methylation that occurs in CG (mCG) sequence context shows transgenerational stability and high epimutation rate, and can thus provide genealogical information at short time scales. However, due to meta-stability and because mCG variants may arise due to other factors than epimutation, such as environmental stress exposure, it is not clear how well mCG captures genealogical information at micro-evolutionary time scales. Here, we analysed DNA methylation variation between accessions from a geographically widespread, apomictic common dandelion (Taraxacum officinale) lineage when grown experimentally under different light conditions. Using a reduced-representation bisulphite sequencing approach, we show that the light treatment induced differentially methylated cytosines (DMCs) in all sequence contexts, with a bias towards transposable elements. Accession differences were associated mainly with DMCs in CG context. Hierarchical clustering of samples based on total mCG profiles revealed a perfect clustering of samples by accession identity, irrespective of light conditions. Using microsatellite information as a benchmark of genetic divergence within the clonal lineage, we show that genetic divergence between accessions correlates strongly with overall mCG profiles. However, our results suggest that environmental effects that do occur in CG context may produce a heritable signal that partly dilutes the genealogical signal. Our study shows that methylation information in plants can be used to reconstruct micro-evolutionary genealogy, providing a useful tool in systems that lack genetic variation such as clonal and vegetatively propagated plants.
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Affiliation(s)
- Verónica Noé Ibañez
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Université Paris Diderot, Gif sur Yvette, France.,Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Morgane van Antro
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Cristian Peña-Ponton
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Slavica Milanovic-Ivanovic
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | | | - Fleur Gawehns
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
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14
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Zhou J, Xiao L, Huang R, Song F, Li L, Li P, Fang Y, Lu W, Lv C, Quan M, Zhang D, Du Q. Local diversity of drought resistance and resilience in Populus tomentosa correlates with the variation of DNA methylation. PLANT, CELL & ENVIRONMENT 2023; 46:479-497. [PMID: 36385613 DOI: 10.1111/pce.14490] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/25/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Little information is known about DNA methylation variation in shaping environment-specific drought resistance and resilience for tree adaptation. In this study, we leveraged RNA sequencing and whole-genome bisulfite sequencing data to dissect the distinction of epigenetic regulation under drought stress and rewater condition of Populus tomentosa accessions from three geographical regions. We demonstrated low resistance and high resilience for accessions from South. Non-CG methylation levels in promoter regions of Southern accessions were lower than accessions from higher latitudes and negatively regulated gene expression. CHH context methylation was more sensitive to drought stress, and the geographical-specific differentially methylated regions were scarcely changed by environmental fluctuation. We identified 60 conserved hub genes within the co-expression networks that correlate with photosynthetic and stomatal morphological traits. Epigenome-wide association studies and genome-wide association studies of these 60 hub genes revealed the interdependency between genetic and epigenetic variation in GATA9 and LECRK-VIII.2, which was associated with stomatal morphology and chlorophyll content. The natural epigenetic variation in GATA9 was also faithfully transmitted to progenies in two family-based F1 populations. This study indicates a functional relationship of DNA methylation diversity with drought resistance and resilience which offers new insights into plants' local adaptation to a stressful environment.
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Affiliation(s)
- Jiaxuan Zhou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Liang Xiao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Rui Huang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Fangyuan Song
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Lianzheng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Peng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Yuanyuan Fang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Wenjie Lu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Chenfei Lv
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Mingyang Quan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Deqiang Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Qingzhang Du
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
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15
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Sun L, Xue C, Guo C, Jia C, Yuan H, Pan X, Tai P. Maintenance of grafting reducing cadmium accumulation in soybean (Glycinemax) is mediated by DNA methylation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157488. [PMID: 35870595 DOI: 10.1016/j.scitotenv.2022.157488] [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: 03/04/2022] [Revised: 06/17/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Cadmium (Cd) pollution in farmland soil increases the probability of wastage of land resources and compromised food safety. Grafting can change the absorption rates of elements in crops; however, there are few studies on grafting in bulk grain and cash crops. In this study, Glycine max was used as a scion and Luffa aegyptiaca as a rootstock for grafting experiments. The changes in total sulfur and Cd content in the leaves and grains of grafted species were determined for three consecutive generations, and the gene expression and DNA methylation status of the leaves were analyzed. The results show that grafting significantly reduced the total sulfur and Cd content in soybean leaves and grains; the Cd content in soybean leaves and grains decreased by >50 %. The plant's primary sulfur metabolism pathway was not significantly affected. Glucosinolates and DNA methylation may play important roles in reducing total sulfur and Cd accumulation. Notably, low sulfur and low Cd traits can be maintained over two generations. Our study establishes that grafting can reduce the total sulfur and Cd content in soybean, and these traits can be inherited. In summary, grafting technology can be used to prevent soybean from accumulating Cd in farmland soil. This provides a theoretical basis for grafting to cultivate crops with low Cd accumulation.
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Affiliation(s)
- Lizong Sun
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenyang Xue
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Guo
- School of Environmental and Safety Engineering, Liaoning Petrochemical University, Fushun 113001, China
| | - Chunyun Jia
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Honghong Yuan
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Xiangwen Pan
- Key Laboratory of Molecular Breeding and Design, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Peidong Tai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
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16
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Lempe J, Flachowsky H, Peil A. Exploring epigenetic variation for breeding climate resilient apple crops. PHYSIOLOGIA PLANTARUM 2022; 174:e13782. [PMID: 36151889 DOI: 10.1111/ppl.13782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/10/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Climate change with warmer winter and spring temperatures poses major challenges to apple fruit production. Long-term observations confirm the trend toward earlier flowering, which leads to an increased risk of frost damage. New breeding strategies are needed to generate cultivars that are able to stay largely unaffected by warmer temperatures. Recently, epigenetic variation has been proposed as a new resource for breeding purposes and seems suitable in principle for apple breeding. However, to serve as a new resource for apple breeding, it is necessary to clarify whether epigenetic variation can be induced by the environment, whether it can create phenotypic variation, and whether this variation is stable across generations. In this brief review, we summarize the impact of climate change on the timing of apple phenology, highlight how epigenetic variation can potentially support novel breeding strategies, and point out important features of epigenetic variation that are required for its application in breeding programs.
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Affiliation(s)
- Janne Lempe
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany
| | - Henryk Flachowsky
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany
| | - Andreas Peil
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany
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17
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Leung C, Grulois D, Chevin LM. Plasticity across levels: relating epigenomic, transcriptomic, and phenotypic responses to osmotic stress in a halotolerant microalga. Mol Ecol 2022; 31:4672-4687. [PMID: 35593517 PMCID: PMC9543585 DOI: 10.1111/mec.16542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 05/12/2022] [Indexed: 12/01/2022]
Abstract
Phenotypic plasticity, the ability of a given genotype to produce alternative phenotypes in response to its environment of development, is an important mechanism for coping with variable environments. While the mechanisms underlying phenotypic plasticity are diverse, their relative contributions need to be investigated quantitatively to better understand the evolvability of plasticity across biological levels. This requires relating plastic responses of the epigenome, transcriptome, and organismal phenotype, and investigating how they vary with the genotype. Here we carried out this approach for responses to osmotic stress in Dunaliella salina, a green microalga that is a model organism for salinity tolerance. We compared two strains that show markedly different demographic responses to osmotic stress, and showed that these phenotypic responses involve strain‐ and environment‐specific variation in gene expression levels, but a relative low—albeit significant—effect of strain × environment interaction. We also found an important genotype effect on the genome‐wide methylation pattern, but little contribution from environmental conditions to the latter. However, we did detect a significant marginal effect of epigenetic variation on gene expression, beyond the influence of genetic differences on epigenetic state, and we showed that hypomethylated regions are correlated with higher gene expression. Our results indicate that epigenetic mechanisms are either not involved in the rapid plastic response to environmental change in this species, or involve only few changes in trans that are sufficient to trigger concerted changes in the expression of many genes, and phenotypic responses by multiple traits.
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Affiliation(s)
- Christelle Leung
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Daphné Grulois
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
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18
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Hazarika RR, Serra M, Zhang Z, Zhang Y, Schmitz RJ, Johannes F. Molecular properties of epimutation hotspots. NATURE PLANTS 2022; 8:146-156. [PMID: 35087209 PMCID: PMC8866225 DOI: 10.1038/s41477-021-01086-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Mistakes in the maintenance of CG methylation are a source of heritable epimutations in plants. Multigenerational surveys indicate that the rate of these stochastic events varies substantially across the genome, with some regions harbouring localized 'epimutation hotspots'. Using Arabidopsis as a model, we show that epimutation hotspots are indexed by a specific set of chromatin states that map to subregions of gene body methylation genes. Although these regions comprise only ~12% of all CGs in the genome, they account for ~63% of all epimutation events per unit time. Molecular profiling revealed that these regions contain unique sequence features, harbour steady-state intermediate methylation levels and act as putative targets of antagonistic DNA methylation pathways. We further demonstrate that experimentally induced shifts in steady-state methylation in these hotspot regions are sufficient to significantly alter local epimutation intensities. Our work lays the foundation for dissecting the molecular mechanisms and evolutionary consequences of epimutation hotspots in plants.
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Affiliation(s)
- Rashmi R Hazarika
- Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany
- TUM Institute for Advanced Study, Garching, Germany
| | - Michele Serra
- Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany
| | - Zhilin Zhang
- Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany
| | - Yinwen Zhang
- Department of Genetics, The University of Georgia, Athens, GA, USA
| | - Robert J Schmitz
- TUM Institute for Advanced Study, Garching, Germany.
- Department of Genetics, The University of Georgia, Athens, GA, USA.
| | - Frank Johannes
- Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany.
- TUM Institute for Advanced Study, Garching, Germany.
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19
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Hüther P, Hagmann J, Nunn A, Kakoulidou I, Pisupati R, Langenberger D, Weigel D, Johannes F, Schultheiss SJ, Becker C. MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data. QUANTITATIVE PLANT BIOLOGY 2022; 3:e19. [PMID: 37077980 PMCID: PMC10095865 DOI: 10.1017/qpb.2022.14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 05/03/2023]
Abstract
Whole-genome bisulfite sequencing (WGBS) is the standard method for profiling DNA methylation at single-nucleotide resolution. Different tools have been developed to extract differentially methylated regions (DMRs), often built upon assumptions from mammalian data. Here, we present MethylScore, a pipeline to analyse WGBS data and to account for the substantially more complex and variable nature of plant DNA methylation. MethylScore uses an unsupervised machine learning approach to segment the genome by classification into states of high and low methylation. It processes data from genomic alignments to DMR output and is designed to be usable by novice and expert users alike. We show how MethylScore can identify DMRs from hundreds of samples and how its data-driven approach can stratify associated samples without prior information. We identify DMRs in the A. thaliana 1,001 Genomes dataset to unveil known and unknown genotype-epigenotype associations .
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Affiliation(s)
- Patrick Hüther
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
| | | | - Adam Nunn
- ecSeq Bioinformatics GmbH, 04103 Leipzig, Germany
- Department of Computer Science, Leipzig University, 04107 Leipzig, Germany
| | - Ioanna Kakoulidou
- Department of Plant Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Rahul Pisupati
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
| | | | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Frank Johannes
- Department of Plant Sciences, Technical University of Munich, 85354 Freising, Germany
- Institute for Advanced Study, Technical University of Munich, 85748 Garching, Germany
| | | | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
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20
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Gupta C, Salgotra RK. Epigenetics and its role in effecting agronomical traits. FRONTIERS IN PLANT SCIENCE 2022; 13:925688. [PMID: 36046583 PMCID: PMC9421166 DOI: 10.3389/fpls.2022.925688] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/11/2022] [Indexed: 05/16/2023]
Abstract
Climate-resilient crops with improved adaptation to the changing climate are urgently needed to feed the growing population. Hence, developing high-yielding crop varieties with better agronomic traits is one of the most critical issues in agricultural research. These are vital to enhancing yield as well as resistance to harsh conditions, both of which help farmers over time. The majority of agronomic traits are quantitative and are subject to intricate genetic control, thereby obstructing crop improvement. Plant epibreeding is the utilisation of epigenetic variation for crop development, and has a wide range of applications in the field of crop improvement. Epigenetics refers to changes in gene expression that are heritable and induced by methylation of DNA, post-translational modifications of histones or RNA interference rather than an alteration in the underlying sequence of DNA. The epigenetic modifications influence gene expression by changing the state of chromatin, which underpins plant growth and dictates phenotypic responsiveness for extrinsic and intrinsic inputs. Epigenetic modifications, in addition to DNA sequence variation, improve breeding by giving useful markers. Also, it takes epigenome diversity into account to predict plant performance and increase crop production. In this review, emphasis has been given for summarising the role of epigenetic changes in epibreeding for crop improvement.
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21
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Bruneaux M, Kronholm I, Ashrafi R, Ketola T. Roles of adenine methylation and genetic mutations in adaptation to different temperatures in Serratia marcescens. Epigenetics 2021; 17:861-881. [PMID: 34519613 DOI: 10.1080/15592294.2021.1966215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Epigenetic modifications can contribute to adaptation, but the relative contributions of genetic and epigenetic variation are unknown. Previous studies on the role of epigenetic changes in adaptation in eukaryotes have nearly exclusively focused on cytosine methylation (m5C), while prokaryotes exhibit a richer system of methyltransferases targetting adenines (m6A) or cytosines (m4C, m5C). DNA methylation in prokaryotes has many roles, but its potential role in adaptation still needs further investigation. We collected phenotypic, genetic, and epigenetic data using single molecule real-time sequencing of clones of the bacterium Serratia marcescens that had undergone experimental evolution in contrasting temperatures to investigate the relationship between environment and genetic, epigenetic, and phenotypic changes. The genomic distribution of GATC motifs, which were the main target for m6A methylation, and of variable m6A epiloci pointed to a potential link between m6A methylation and regulation of gene expression in S. marcescens. Evolved strains, while genetically homogeneous, exhibited many polymorphic m6A epiloci. There was no strong support for a genetic control of methylation changes in our experiment, and no clear evidence of parallel environmentally induced or environmentally selected methylation changes at specific epiloci was found. Both genetic and epigenetic variants were associated with some phenotypic traits. Overall, our results suggest that both genetic and adenine methylation changes have the potential to contribute to phenotypic adaptation in S. marcescens, but that any environmentally induced epigenetic change occurring in our experiment would probably have been quite labile.
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Affiliation(s)
- Matthieu Bruneaux
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Ilkka Kronholm
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Roghaieh Ashrafi
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Tarmo Ketola
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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22
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Yao N, Schmitz RJ, Johannes F. Epimutations Define a Fast-Ticking Molecular Clock in Plants. Trends Genet 2021; 37:699-710. [PMID: 34016450 PMCID: PMC8282728 DOI: 10.1016/j.tig.2021.04.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/16/2022]
Abstract
Stochastic gains and losses of DNA methylation at CG dinucleotides are a frequent occurrence in plants. These spontaneous 'epimutations' occur at a rate that is 100 000 times higher than the genetic mutation rate, are effectively neutral at the genome-wide scale, and are stably inherited across mitotic and meiotic cell divisions. Mathematical models have been extraordinarily successful at describing how epimutations accumulate in plant genomes over time, making this process one of the most predictable epigenetic phenomena to date. Here, we propose that their high rate and effective neutrality make epimutations a powerful new molecular clock for timing evolutionary events of the recent past and for age dating of long-lived perennials such as trees.
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Affiliation(s)
- Nan Yao
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, USA; Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Frank Johannes
- Institute for Advanced Study, Technical University of Munich, Garching, Germany; Population Epigenetics and Epigenomics, Technical University of Munich, Freising, Germany.
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23
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GSNOR Contributes to Demethylation and Expression of Transposable Elements and Stress-Responsive Genes. Antioxidants (Basel) 2021; 10:antiox10071128. [PMID: 34356361 PMCID: PMC8301139 DOI: 10.3390/antiox10071128] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 12/19/2022] Open
Abstract
In the past, reactive nitrogen species (RNS) were supposed to be stress-induced by-products of disturbed metabolism that cause oxidative damage to biomolecules. However, emerging evidence demonstrates a substantial role of RNS as endogenous signals in eukaryotes. In plants, S-nitrosoglutathione (GSNO) is the dominant RNS and serves as the •NO donor for S-nitrosation of diverse effector proteins. Remarkably, the endogenous GSNO level is tightly controlled by S-nitrosoglutathione reductase (GSNOR) that irreversibly inactivates the glutathione-bound NO to ammonium. Exogenous feeding of diverse RNS, including GSNO, affected chromatin accessibility and transcription of stress-related genes, but the triggering function of RNS on these regulatory processes remained elusive. Here, we show that GSNO reductase-deficient plants (gsnor1-3) accumulate S-adenosylmethionine (SAM), the principal methyl donor for methylation of DNA and histones. This SAM accumulation triggered a substantial increase in the methylation index (MI = [SAM]/[S-adenosylhomocysteine]), indicating the transmethylation activity and histone methylation status in higher eukaryotes. Indeed, a mass spectrometry-based global histone profiling approach demonstrated a significant global increase in H3K9me2, which was independently verified by immunological detection using a selective antibody. Since H3K9me2-modified regions tightly correlate with methylated DNA regions, we also determined the DNA methylation status of gsnor1-3 plants by whole-genome bisulfite sequencing. DNA methylation in the CG, CHG, and CHH contexts in gsnor1-3 was significantly enhanced compared to the wild type. We propose that GSNOR1 activity affects chromatin accessibility by controlling the transmethylation activity (MI) required for maintaining DNA methylation and the level of the repressive chromatin mark H3K9me2.
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Noshay JM, Springer NM. Stories that can't be told by SNPs; DNA methylation variation in plant populations. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:101989. [PMID: 33445144 DOI: 10.1016/j.pbi.2020.101989] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/18/2020] [Accepted: 12/11/2020] [Indexed: 05/23/2023]
Abstract
Epigenetic variation has been observed in many plant populations. This variation can influence qualitative and quantitative traits. A key question is whether there is novel information in the epigenome that is not captured by SNP-based genetic markers. The answer likely varies depending on the sources and stability of epigenetic variation as well as the type of population being studied. We consider the epigenetic variation in several plant systems and how this relates to potential for hidden information that could increase our understanding of phenotypic variation.
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Affiliation(s)
- Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA.
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25
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Provart NJ, Brady SM, Parry G, Schmitz RJ, Queitsch C, Bonetta D, Waese J, Schneeberger K, Loraine AE. Anno genominis XX: 20 years of Arabidopsis genomics. THE PLANT CELL 2021; 33:832-845. [PMID: 33793861 PMCID: PMC8226293 DOI: 10.1093/plcell/koaa038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/09/2020] [Indexed: 05/04/2023]
Abstract
Twenty years ago, the Arabidopsis thaliana genome sequence was published. This was an important moment as it was the first sequenced plant genome and explicitly brought plant science into the genomics era. At the time, this was not only an outstanding technological achievement, but it was characterized by a superb global collaboration. The Arabidopsis genome was the seed for plant genomic research. Here, we review the development of numerous resources based on the genome that have enabled discoveries across plant species, which has enhanced our understanding of how plants function and interact with their environments.
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Affiliation(s)
- Nicholas J Provart
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California, 95616, USA
| | - Geraint Parry
- GARNet, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Georgia, 30602, USA
| | - Christine Queitsch
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, 98195, USA
| | - Dario Bonetta
- Faculty of Science, Ontario Tech University, Oshawa, Ontario, L1G 0C5, Canada
| | - Jamie Waese
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
- Faculty of Biology, LMU Munich, 82152 Munich, Germany
| | - Ann E Loraine
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
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26
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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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27
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Shahryary Y, Symeonidi A, Hazarika RR, Denkena J, Mubeen T, Hofmeister B, van Gurp T, Colomé-Tatché M, Verhoeven KJ, Tuskan G, Schmitz RJ, Johannes F. AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants. Genome Biol 2020; 21:260. [PMID: 33023650 PMCID: PMC7539454 DOI: 10.1186/s13059-020-02161-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 09/02/2020] [Indexed: 01/28/2023] Open
Abstract
Stochastic changes in DNA methylation (i.e., spontaneous epimutations) contribute to methylome diversity in plants. Here, we describe AlphaBeta, a computational method for estimating the precise rate of such stochastic events using pedigree-based DNA methylation data as input. We demonstrate how AlphaBeta can be employed to study transgenerationally heritable epimutations in clonal or sexually derived mutation accumulation lines, as well as somatic epimutations in long-lived perennials. Application of our method to published and new data reveals that spontaneous epimutations accumulate neutrally at the genome-wide scale, originate mainly during somatic development and that they can be used as a molecular clock for age-dating trees.
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Affiliation(s)
- Yadollah Shahryary
- Technical University of Munich, Department of Plant Sciences, Liesel-Beckmann-Str. 2, Freising, 85354 Germany
- Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 2a, Garching, 85748 Germany
| | - Aikaterini Symeonidi
- Technical University of Munich, Department of Plant Sciences, Liesel-Beckmann-Str. 2, Freising, 85354 Germany
| | - Rashmi R. Hazarika
- Technical University of Munich, Department of Plant Sciences, Liesel-Beckmann-Str. 2, Freising, 85354 Germany
- Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 2a, Garching, 85748 Germany
| | - Johanna Denkena
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg, 85764 Germany
| | - Talha Mubeen
- Technical University of Munich, Department of Plant Sciences, Liesel-Beckmann-Str. 2, Freising, 85354 Germany
- Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 2a, Garching, 85748 Germany
| | | | - Thomas van Gurp
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, Wageningen, The Netherlands
| | - Maria Colomé-Tatché
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg, 85764 Germany
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, Groningen, 9713 AV Netherlands
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Erlenmeyer-Forum 2, Freising, 85354 Germany
| | - Koen J.F. Verhoeven
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, Wageningen, The Netherlands
| | - Gerald Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, USA
| | - Robert J. Schmitz
- Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 2a, Garching, 85748 Germany
- Department of Genetics, The University of Georgia, 120 East Green Street, Athens, 30602 USA
| | - Frank Johannes
- Technical University of Munich, Department of Plant Sciences, Liesel-Beckmann-Str. 2, Freising, 85354 Germany
- Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 2a, Garching, 85748 Germany
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28
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Hofmeister BT, Denkena J, Colomé-Tatché M, Shahryary Y, Hazarika R, Grimwood J, Mamidi S, Jenkins J, Grabowski PP, Sreedasyam A, Shu S, Barry K, Lail K, Adam C, Lipzen A, Sorek R, Kudrna D, Talag J, Wing R, Hall DW, Jacobsen D, Tuskan GA, Schmutz J, Johannes F, Schmitz RJ. A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa. Genome Biol 2020; 21:259. [PMID: 33023654 PMCID: PMC7539514 DOI: 10.1186/s13059-020-02162-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 09/02/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Plants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development contributes to local adaption in an ecoevolutionary context, particularly in long-lived perennials. RESULTS Here, we generate a new high-quality reference genome from the oldest branch of a wild Populus trichocarpa tree with two dominant stems which have been evolving independently for 330 years. By sampling multiple, age-estimated branches of this tree, we use a multi-omics approach to quantify age-related somatic changes at the genetic, epigenetic, and transcriptional level. We show that the per-year somatic mutation and epimutation rates are lower than in annuals and that transcriptional variation is mainly independent of age divergence and cytosine methylation. Furthermore, a detailed analysis of the somatic epimutation spectrum indicates that transgenerationally heritable epimutations originate mainly from DNA methylation maintenance errors during mitotic rather than during meiotic cell divisions. CONCLUSION Taken together, our study provides unprecedented insights into the origin of nucleotide and functional variation in a long-lived perennial plant.
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Affiliation(s)
| | - Johanna Denkena
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - Maria Colomé-Tatché
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Yadollah Shahryary
- Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany
| | - Rashmi Hazarika
- Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany
- Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Sujan Mamidi
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Jerry Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | | | | | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Kathleen Lail
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Catherine Adam
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Rod Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - David W Hall
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Daniel Jacobsen
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gerald A Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Frank Johannes
- Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany.
- Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany.
| | - Robert J Schmitz
- Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany.
- Department of Genetics, University of Georgia, Athens, GA, USA.
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29
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Beltran T, Shahrezaei V, Katju V, Sarkies P. Epimutations driven by small RNAs arise frequently but most have limited duration in Caenorhabditis elegans. Nat Ecol Evol 2020; 4:1539-1548. [PMID: 32868918 DOI: 10.1038/s41559-020-01293-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/21/2020] [Indexed: 01/25/2023]
Abstract
Epigenetic regulation involves changes in gene expression independent of DNA sequence variation that are inherited through cell division. In addition to a fundamental role in cell differentiation, some epigenetic changes can also be transmitted transgenerationally through meiosis. Epigenetic alterations (epimutations) could thus contribute to heritable variation within populations and be subject to evolutionary processes such as natural selection and drift. However, the rate at which epimutations arise and their typical persistence are unknown, making it difficult to evaluate their potential for evolutionary adaptation. Here, we perform a genome-wide study of epimutations in a metazoan organism. We use experimental evolution to characterize the rate, spectrum and stability of epimutations driven by small silencing RNAs in the model nematode Caenorhabditis elegans. We show that epimutations arise spontaneously at a rate approximately 25 times greater than DNA sequence changes and typically have short half-lives of two to three generations. Nevertheless, some epimutations last at least ten generations. Epimutations mediated by small RNAs may thus contribute to evolutionary processes over a short timescale but are unlikely to bring about long-term divergence in the absence of selection.
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Affiliation(s)
- Toni Beltran
- MRC London Institute of Medical Sciences, London, UK.,Institute of Clinical Sciences, Imperial College London, London, UK
| | - Vahid Shahrezaei
- Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Peter Sarkies
- MRC London Institute of Medical Sciences, London, UK. .,Institute of Clinical Sciences, Imperial College London, London, UK.
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30
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Williams BP, Gehring M. Principles of Epigenetic Homeostasis Shared Between Flowering Plants and Mammals. Trends Genet 2020; 36:751-763. [PMID: 32711945 DOI: 10.1016/j.tig.2020.06.019] [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] [Received: 04/21/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022]
Abstract
In diverse eukaryotes, epigenetic information such as DNA methylation is stably propagated over many cell divisions and generations, and can remain the same over thousands or millions of years. However, this stability is the product of dynamic processes that add and remove DNA methylation by specialized enzymatic pathways. The activities of these dynamic pathways must therefore be finely orchestrated in order to ensure that the DNA methylation landscape is maintained with high fidelity - a concept we term epigenetic homeostasis. In this review, we summarize recent insights into epigenetic homeostasis mechanisms in flowering plants and mammals, highlighting analogous mechanisms that have independently evolved to achieve the same goal of stabilizing the epigenetic landscape.
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Affiliation(s)
- Ben P Williams
- Whitehead Institute for Biomedical Research, 455 Main St, Cambridge, MA 02142, USA.
| | - Mary Gehring
- Whitehead Institute for Biomedical Research, 455 Main St, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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31
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Kartal Ö, Schmid MW, Grossniklaus U. Cell type-specific genome scans of DNA methylation divergence indicate an important role for transposable elements. Genome Biol 2020; 21:172. [PMID: 32660534 PMCID: PMC7359245 DOI: 10.1186/s13059-020-02068-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 06/10/2020] [Indexed: 01/01/2023] Open
Abstract
In population genomics, genetic diversity measures play an important role in genome scans for divergent sites. In population epigenomics, comparable tools are rare although the epigenome can vary at several levels of organization. We propose a model-free, information-theoretic approach, the Jensen-Shannon divergence (JSD), as a flexible diversity index for epigenomic diversity. Here, we demonstrate how JSD uncovers the relationship between genomic features and cell type-specific methylome diversity in Arabidopsis thaliana. However, JSD is applicable to any epigenetic mark and any collection of individuals, tissues, or cells, for example to assess the heterogeneity in healthy organs and tumors.
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Affiliation(s)
- Önder Kartal
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich, 8008 Switzerland
- Creoptix AG, Zugerstrasse 76, Wädenswil, 8820 Switzerland
| | - Marc W. Schmid
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich, 8008 Switzerland
- MWSchmid GmbH, Möhrlistrasse 25, Zurich, 8006 Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich, 8008 Switzerland
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32
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Van Dooren TJM, Silveira AB, Gilbault E, Jiménez-Gómez JM, Martin A, Bach L, Tisné S, Quadrana L, Loudet O, Colot V. Mild drought in the vegetative stage induces phenotypic, gene expression, and DNA methylation plasticity in Arabidopsis but no transgenerational effects. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3588-3602. [PMID: 32166321 DOI: 10.1101/370320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/09/2020] [Indexed: 05/27/2023]
Abstract
There is renewed interest in whether environmentally induced changes in phenotypes can be heritable. In plants, heritable trait variation can occur without DNA sequence mutations through epigenetic mechanisms involving DNA methylation. However, it remains unknown whether this alternative system of inheritance responds to environmental changes and if it can provide a rapid way for plants to generate adaptive heritable phenotypic variation. To assess potential transgenerational effects induced by the environment, we subjected four natural accessions of Arabidopsis thaliana together with the reference accession Col-0 to mild drought in a multi-generational experiment. As expected, plastic responses to drought were observed in each accession, as well as a number of intergenerational effects of the parental environments. However, after an intervening generation without stress, except for a very few trait-based parental effects, descendants of stressed and non-stressed plants were phenotypically indistinguishable irrespective of whether they were grown in control conditions or under water deficit. In addition, genome-wide analysis of DNA methylation and gene expression in Col-0 demonstrated that, while mild drought induced changes in the DNA methylome of exposed plants, these variants were not inherited. We conclude that mild drought stress does not induce transgenerational epigenetic effects.
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Affiliation(s)
- Tom J M Van Dooren
- CNRS - UMR 7618 Institute of Ecology and Environmental Sciences (iEES) Paris, Sorbonne University, Case 237, 4, place Jussieu, 75005 Paris, France
| | - Amanda Bortolini Silveira
- Institut de Biologie de l'Ecole Normale Supérieure, (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
| | - Elodie Gilbault
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - José M Jiménez-Gómez
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Antoine Martin
- Institut de Biologie de l'Ecole Normale Supérieure, (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
| | - Liên Bach
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Sébastien Tisné
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure, (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure, (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
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Van Dooren TJM, Silveira AB, Gilbault E, Jiménez-Gómez JM, Martin A, Bach L, Tisné S, Quadrana L, Loudet O, Colot V. Mild drought in the vegetative stage induces phenotypic, gene expression, and DNA methylation plasticity in Arabidopsis but no transgenerational effects. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3588-3602. [PMID: 32166321 PMCID: PMC7307858 DOI: 10.1093/jxb/eraa132] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/09/2020] [Indexed: 05/25/2023]
Abstract
There is renewed interest in whether environmentally induced changes in phenotypes can be heritable. In plants, heritable trait variation can occur without DNA sequence mutations through epigenetic mechanisms involving DNA methylation. However, it remains unknown whether this alternative system of inheritance responds to environmental changes and if it can provide a rapid way for plants to generate adaptive heritable phenotypic variation. To assess potential transgenerational effects induced by the environment, we subjected four natural accessions of Arabidopsis thaliana together with the reference accession Col-0 to mild drought in a multi-generational experiment. As expected, plastic responses to drought were observed in each accession, as well as a number of intergenerational effects of the parental environments. However, after an intervening generation without stress, except for a very few trait-based parental effects, descendants of stressed and non-stressed plants were phenotypically indistinguishable irrespective of whether they were grown in control conditions or under water deficit. In addition, genome-wide analysis of DNA methylation and gene expression in Col-0 demonstrated that, while mild drought induced changes in the DNA methylome of exposed plants, these variants were not inherited. We conclude that mild drought stress does not induce transgenerational epigenetic effects.
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Affiliation(s)
- Tom J M Van Dooren
- CNRS - UMR 7618 Institute of Ecology and Environmental Sciences (iEES) Paris, Sorbonne University, Case 237, 4, place Jussieu, 75005 Paris, France
| | - Amanda Bortolini Silveira
- Institut de Biologie de l’Ecole Normale Supérieure, (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
| | - Elodie Gilbault
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - José M Jiménez-Gómez
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Antoine Martin
- Institut de Biologie de l’Ecole Normale Supérieure, (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
| | - Liên Bach
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Sébastien Tisné
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Leandro Quadrana
- Institut de Biologie de l’Ecole Normale Supérieure, (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Vincent Colot
- Institut de Biologie de l’Ecole Normale Supérieure, (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
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Eichten SR, Srivastava A, Reddiex AJ, Ganguly DR, Heussler A, Streich JC, Wilson PB, Borevitz JO. Extending the Genotype in Brachypodium by Including DNA Methylation Reveals a Joint Contribution with Genetics on Adaptive Traits. G3 (BETHESDA, MD.) 2020; 10:1629-1637. [PMID: 32132166 PMCID: PMC7202021 DOI: 10.1534/g3.120.401189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenomic changes have been considered a potential missing link underlying phenotypic variation in quantitative traits but is potentially confounded with the underlying DNA sequence variation. Although the concept of epigenetic inheritance has been discussed in depth, there have been few studies attempting to directly dissect the amount of epigenomic variation within inbred natural populations while also accounting for genetic diversity. By using known genetic relationships between Brachypodium lines, multiple sets of nearly identical accession families were selected for phenotypic studies and DNA methylome profiling to investigate the dual role of (epi)genetics under simulated natural seasonal climate conditions. Despite reduced genetic diversity, appreciable phenotypic variation was still observable in the measured traits (height, leaf width and length, tiller count, flowering time, ear count) between as well as within the inbred accessions. However, with reduced genetic diversity there was diminished variation in DNA methylation within families. Mixed-effects linear modeling revealed large genetic differences between families and a minor contribution of DNA methylation variation on phenotypic variation in select traits. Taken together, this analysis suggests a limited but significant contribution of DNA methylation toward heritable phenotypic variation relative to genetic differences.
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Affiliation(s)
- Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Akanksha Srivastava
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Adam J Reddiex
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Alison Heussler
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Jared C Streich
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Pip B Wilson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
| | - Justin O Borevitz
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia
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Functional variants of DOG1 control seed chilling responses and variation in seasonal life-history strategies in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2020; 117:2526-2534. [PMID: 31964817 PMCID: PMC7007534 DOI: 10.1073/pnas.1912451117] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The seasonal timing of seed germination is critical for plant fitness in different climates. To germinate at the right time of year, seeds respond to seasonal environmental cues, such as cold temperatures. We characterized genetic variation in seed dormancy responses to cold across the geographic range of a widespread annual plant. Induction of secondary seed dormancy during winter conditions (which restricts germination to autumn) was positively correlated with flowering time, constructing winter and spring seasonal life-history strategies. Variation in seed chilling responses was strongly associated with functional variants of a known dormancy gene. These variants showed evidence of ancient diversification associated with Pleistocene glacial cycles, and were associated with climate gradients across the species’ geographical range. The seasonal timing of seed germination determines a plant’s realized environmental niche, and is important for adaptation to climate. The timing of seasonal germination depends on patterns of seed dormancy release or induction by cold and interacts with flowering-time variation to construct different seasonal life histories. To characterize the genetic basis and climatic associations of natural variation in seed chilling responses and associated life-history syndromes, we selected 559 fully sequenced accessions of the model annual species Arabidopsis thaliana from across a wide climate range and scored each for seed germination across a range of 13 cold stratification treatments, as well as the timing of flowering and senescence. Germination strategies varied continuously along 2 major axes: 1) Overall germination fraction and 2) induction vs. release of dormancy by cold. Natural variation in seed responses to chilling was correlated with flowering time and senescence to create a range of seasonal life-history syndromes. Genome-wide association identified several loci associated with natural variation in seed chilling responses, including a known functional polymorphism in the self-binding domain of the candidate gene DOG1. A phylogeny of DOG1 haplotypes revealed ancient divergence of these functional variants associated with periods of Pleistocene climate change, and Gradient Forest analysis showed that allele turnover of candidate SNPs was significantly associated with climate gradients. These results provide evidence that A. thaliana’s germination niche and correlated life-history syndromes are shaped by past climate cycles, as well as local adaptation to contemporary climate.
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36
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Hu L, Li N, Zhang Z, Meng X, Dong Q, Xu C, Gong L, Liu B. CG hypomethylation leads to complex changes in DNA methylation and transpositional burst of diverse transposable elements in callus cultures of rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:188-203. [PMID: 31529551 DOI: 10.1111/tpj.14531] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/01/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
CG methylation (m CG) is essential for preserving genome stability in mammals, but this link remains obscure in plants. OsMET1-2, a major rice DNA methyltransferase, plays critical roles in maintaining m CG in rice. Null mutation of OsMET1-2 causes massive CG hypomethylation, rendering the mutant suitable to address the role of m CG in maintaining genome integrity in plants. Here, we analyzed m CG dynamics and genome stability in tissue cultures of OsMET1-2 homozygous (-/-) and heterozygous (+/-) mutants, and isogenic wild-type (WT). We found m CG levels in cultures of -/- were substantially lower than in those of WT and +/-, as expected. Unexpectedly, m CG levels in 1- and 3-year cultures of -/- were 77.6% and 48.7% higher, respectively, than in shoot, from which the cultures were initiated, suggesting substantial regain of m CG in -/- cultures, which contrasts to the general trend of m CG loss in all WT plant tissue cultures hitherto studied. Transpositional burst of diverse transposable elements (TEs) occurred only in -/- cultures, although no elevation of genome-wide mutation rate in the form of single nucleotide polymorphisms was detected. Altogether, our results establish an essential role of m CG in retaining TE immobility and hence genome stability in rice and likely in plants in general.
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Affiliation(s)
- Lanjuan Hu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- College of Plant Sciences, Faculty of Agriculture, Jilin University, Changchun, 130062, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xinchao Meng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Qianli Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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37
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Sarkies P. Molecular mechanisms of epigenetic inheritance: Possible evolutionary implications. Semin Cell Dev Biol 2020; 97:106-115. [PMID: 31228598 PMCID: PMC6945114 DOI: 10.1016/j.semcdb.2019.06.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/04/2019] [Accepted: 06/18/2019] [Indexed: 12/30/2022]
Abstract
Recently interest in multi-generational epigenetic phenomena have been fuelled by highly reproducible intergenerational and transgenerational inheritance paradigms in several model organisms. Such paradigms are essential in order to begin to use genetics to unpick the mechanistic bases of how epigenetic information may be transmitted between generations; indeed great strides have been made towards understanding these mechanisms. Far less well understood is the relationship between epigenetic inheritance, ecology and evolution. In this review I focus on potential connections between laboratory studies of transgenerational epigenetic inheritance phenomena and evolutionary processes that occur in natural populations. In the first section, I consider whether transgenerational epigenetic inheritance might provide an advantage to organisms over the short term in adapting to their environment. Second, I consider whether epigenetic changes can contribute to the evolution of species by contributing to stable phenotypic variation within a population. Finally I discuss whether epigenetic changes could influence evolution by either directly or indirectly promoting DNA sequence changes that could impact phenotypic divergence. Additionally, I will discuss how epigenetic changes could influence the evolution of human cancer and thus be directly relevant for the development of this disease.
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Affiliation(s)
- Peter Sarkies
- MRC London Institute of Medical Sciences, Du Cane Road, London, W120NN, United Kingdom; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W120NN, United Kingdom.
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38
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Wulfridge P, Langmead B, Feinberg AP, Hansen KD. Analyzing whole genome bisulfite sequencing data from highly divergent genotypes. Nucleic Acids Res 2019; 47:e117. [PMID: 31392989 PMCID: PMC6821270 DOI: 10.1093/nar/gkz674] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 07/03/2019] [Accepted: 07/25/2019] [Indexed: 11/13/2022] Open
Abstract
In the study of DNA methylation, genetic variation between species, strains or individuals can result in CpG sites that are exclusive to a subset of samples, and insertions and deletions can rearrange the spatial distribution of CpGs. How to account for this variation in an analysis of the interplay between sequence variation and DNA methylation is not well understood, especially when the number of CpG differences between samples is large. Here, we use whole-genome bisulfite sequencing data on two highly divergent mouse strains to study this problem. We show that alignment to personal genomes is necessary for valid methylation quantification. We introduce a method for including strain-specific CpGs in differential analysis, and show that this increases power. We apply our method to a human normal-cancer dataset, and show this improves accuracy and power, illustrating the broad applicability of our approach. Our method uses smoothing to impute methylation levels at strain-specific sites, thereby allowing strain-specific CpGs to contribute to the analysis, while accounting for differences in the spatial occurrences of CpGs. Our results have implications for joint analysis of genetic variation and DNA methylation using bisulfite-converted DNA, and unlocks the use of personal genomes for addressing this question.
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Affiliation(s)
- Phillip Wulfridge
- Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe St, Baltimore, MD 21205, USA
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe St, Baltimore, MD 21205, USA.,Department of Medicine, Johns Hopkins School of Medicine, 855 N. Wolfe St, Baltimore, MD 21205, USA.,Department of Biomedical Engineering, Whiting School of Engineering, 3400 N. Charles St, Baltimore, MD 21218, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, MD 21205, USA
| | - Kasper D Hansen
- Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe St, Baltimore, MD 21205, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
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39
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Greenbaum G, Rubin A, Templeton AR, Rosenberg NA. Network-based hierarchical population structure analysis for large genomic data sets. Genome Res 2019; 29:2020-2033. [PMID: 31694865 PMCID: PMC6886512 DOI: 10.1101/gr.250092.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 11/01/2019] [Indexed: 01/24/2023]
Abstract
Analysis of population structure in natural populations using genetic data is a common practice in ecological and evolutionary studies. With large genomic data sets of populations now appearing more frequently across the taxonomic spectrum, it is becoming increasingly possible to reveal many hierarchical levels of structure, including fine-scale genetic clusters. To analyze these data sets, methods need to be appropriately suited to the challenges of extracting multilevel structure from whole-genome data. Here, we present a network-based approach for constructing population structure representations from genetic data. The use of community-detection algorithms from network theory generates a natural hierarchical perspective on the representation that the method produces. The method is computationally efficient, and it requires relatively few assumptions regarding the biological processes that underlie the data. We show the approach by analyzing population structure in the model plant species Arabidopsis thaliana and in human populations. These examples illustrate how network-based approaches for population structure analysis are well-suited to extracting valuable ecological and evolutionary information in the era of large genomic data sets.
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Affiliation(s)
- Gili Greenbaum
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Amir Rubin
- Department of Computer Science, Ben-Gurion University of the Negev, Be'er-Sheva, 8410501, Israel
| | - Alan R Templeton
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA
- Department of Evolutionary and Environmental Ecology, University of Haifa, Haifa, 31905, Israel
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, California 94305, USA
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40
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Affiliation(s)
- Matin Miryeganeh
- Plant Epigenetics UnitOkinawa Institute of Science and Technology Graduate University Okinawa Japan
- Japan Society for the Promotion of Science Tokyo Japan
| | - Hidetoshi Saze
- Plant Epigenetics UnitOkinawa Institute of Science and Technology Graduate University Okinawa Japan
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41
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Simon L, Rabanal FA, Dubos T, Oliver C, Lauber D, Poulet A, Vogt A, Mandlbauer A, Le Goff S, Sommer A, Duborjal H, Tatout C, Probst AV. Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana. Nucleic Acids Res 2019. [PMID: 29518237 PMCID: PMC5887818 DOI: 10.1093/nar/gky163] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Organized in tandem repeat arrays in most eukaryotes and transcribed by RNA polymerase III, expression of 5S rRNA genes is under epigenetic control. To unveil mechanisms of transcriptional regulation, we obtained here in depth sequence information on 5S rRNA genes from the Arabidopsis thaliana genome and identified differential enrichment in epigenetic marks between the three 5S rDNA loci situated on chromosomes 3, 4 and 5. We reveal the chromosome 5 locus as the major source of an atypical, long 5S rRNA transcript characteristic of an open chromatin structure. 5S rRNA genes from this locus translocated in the Landsberg erecta ecotype as shown by linkage mapping and chromosome-specific FISH analysis. These variations in 5S rDNA locus organization cause changes in the spatial arrangement of chromosomes in the nucleus. Furthermore, 5S rRNA gene arrangements are highly dynamic with alterations in chromosomal positions through translocations in certain mutants of the RNA-directed DNA methylation pathway and important copy number variations among ecotypes. Finally, variations in 5S rRNA gene sequence, chromatin organization and transcripts indicate differential usage of 5S rDNA loci in distinct ecotypes. We suggest that both the usage of existing and new 5S rDNA loci resulting from translocations may impact neighboring chromatin organization.
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Affiliation(s)
- Lauriane Simon
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Fernando A Rabanal
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Tristan Dubos
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Cecilia Oliver
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Damien Lauber
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Axel Poulet
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Alexander Vogt
- Vienna Biocenter Core Facilities GmbH (VBCF), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Ariane Mandlbauer
- Vienna Biocenter Core Facilities GmbH (VBCF), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Samuel Le Goff
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Andreas Sommer
- Vienna Biocenter Core Facilities GmbH (VBCF), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Hervé Duborjal
- Plant Engineering Platform, BIOGEMMA, Route d'Ennezat Centre de Recherche de Chappes, 63720 Chappes, France
| | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
| | - Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont-Ferrand, France
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42
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Johnson JS, Cantrell RS, Cosner C, Hartig F, Hastings A, Rogers HS, Schupp EW, Shea K, Teller BJ, Yu X, Zurell D, Pufal G. Rapid changes in seed dispersal traits may modify plant responses to global change. AOB PLANTS 2019; 11:plz020. [PMID: 31198528 PMCID: PMC6548345 DOI: 10.1093/aobpla/plz020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 03/26/2019] [Indexed: 05/22/2023]
Abstract
When climatic or environmental conditions change, plant populations must either adapt to these new conditions, or track their niche via seed dispersal. Adaptation of plants to different abiotic environments has mostly been discussed with respect to physiological and demographic parameters that allow local persistence. However, rapid modifications in response to changing environmental conditions can also affect seed dispersal, both via plant traits and via their dispersal agents. Studying such changes empirically is challenging, due to the high variability in dispersal success, resulting from environmental heterogeneity, and substantial phenotypic variability of dispersal-related traits of seeds and their dispersers. The exact mechanisms that drive rapid changes are often not well understood, but the ecological implications of these processes are essential determinants of dispersal success, and deserve more attention from ecologists, especially in the context of adaptation to global change. We outline the evidence for rapid changes in seed dispersal traits by discussing variability due to plasticity or genetics broadly, and describe the specific traits and biological systems in which variability in dispersal is being studied, before discussing some of the potential underlying mechanisms. We then address future research needs and propose a simulation model that incorporates phenotypic plasticity in seed dispersal. We close with a call to action and encourage ecologists and biologist to embrace the challenge of better understanding rapid changes in seed dispersal and their consequences for the reaction of plant populations to global change.
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Affiliation(s)
- Jeremy S Johnson
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
- Dorena Genetic Resource Center, USDA Forest Service, Cottage Grove, OR, USA
| | | | - Chris Cosner
- Department of Mathematics, The University of Miami, Coral Gables, FL, USA
| | - Florian Hartig
- Theoretical Ecology, University of Regensburg, Regensburg, Germany
| | - Alan Hastings
- Department of Environmental Science and Policy, University of California, Davis, CA, USA
| | - Haldre S Rogers
- Department of Ecology, Evolution, and Behavior, Iowa State University, Ames, IA, USA
| | - Eugene W Schupp
- Department of Wildland Resources & Ecology Center, Utah State University, Logan, UT, USA
| | - Katriona Shea
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Brittany J Teller
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Xiao Yu
- Department of Mathematics, The University of Miami, Coral Gables, FL, USA
| | - Damaris Zurell
- Department of Geography, Humboldt-University Berlin, Berlin, Germany
- Department of Land Change and Science, Swiss Federal Institute WSL, Birmensdorf, Switzerland
| | - Gesine Pufal
- Nature Conservation and Landscape Ecology, University of Freiburg, Freiburg, Germany
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43
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Johannes F, Schmitz RJ. Spontaneous epimutations in plants. THE NEW PHYTOLOGIST 2019; 221:1253-1259. [PMID: 30216456 DOI: 10.1111/nph.15434] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/01/2018] [Indexed: 05/22/2023]
Abstract
Contents Summary 1253 I. Introduction 1253 II. What is the rate and molecular spectrum of spontaneous epimutations? 1254 III. Do spontaneous epimutations have phenotypic consequences? 1257 IV. Conclusion and discussion 1258 Acknowledgements 1258 References 1258 SUMMARY: Heritable gains or losses of cytosine methylation can arise stochastically in plant genomes independently of DNA sequence changes. These so-called 'spontaneous epimutations' appear to be a byproduct of imperfect DNA methylation maintenance and epigenome reinforcement events that occur in specialized cell types. There is continued interest in the plant epigenetics community in trying to understand the broader implications of these stochastic events, as some have been shown to induce heritable gene expression changes, shape patterns of methylation diversity within and among plant populations, and appear to be responsive to multi-generational environmental stressors. In this paper we synthesized our current knowledge of the molecular basis and functional consequences of spontaneous epimutations in plants, discuss technical and conceptual challenges, and highlight emerging research directions.
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Affiliation(s)
- Frank Johannes
- Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, 85354, Germany
- Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, 85748, Germany
| | - Robert J Schmitz
- Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, 85748, Germany
- Department of Genetics, The University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
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44
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Tedeschi F, Rizzo P, Huong BTM, Czihal A, Rutten T, Altschmied L, Scharfenberg S, Grosse I, Becker C, Weigel D, Bäumlein H, Kuhlmann M. EFFECTOR OF TRANSCRIPTION factors are novel plant-specific regulators associated with genomic DNA methylation in Arabidopsis. THE NEW PHYTOLOGIST 2019; 221:261-278. [PMID: 30252137 PMCID: PMC6585611 DOI: 10.1111/nph.15439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/01/2018] [Indexed: 05/02/2023]
Abstract
Plant-specific EFFECTORS OF TRANSCRIPTION (ET) are characterised by a variable number of highly conserved ET repeats, which are involved in zinc and DNA binding. In addition, ETs share a GIY-YIG domain, involved in DNA nicking activity. It was hypothesised that ETs might act as epigenetic regulators. Here, methylome, transcriptome and phenotypic analyses were performed to investigate the role of ET factors and their involvement in DNA methylation in Arabidopsis thaliana. Comparative DNA methylation and transcriptome analyses in flowers and seedlings of et mutants revealed ET-specific differentially expressed genes and mostly independently characteristic, ET-specific differentially methylated regions. Loss of ET function results in pleiotropic developmental defects. The accumulation of cyclobutane pyrimidine dimers after ultraviolet stress in et mutants suggests an ET function in DNA repair.
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Affiliation(s)
- Francesca Tedeschi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466Seeland OT GaterslebenGermany
| | - Paride Rizzo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466Seeland OT GaterslebenGermany
| | - Bui Thi Mai Huong
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466Seeland OT GaterslebenGermany
| | - Andreas Czihal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466Seeland OT GaterslebenGermany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466Seeland OT GaterslebenGermany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466Seeland OT GaterslebenGermany
| | | | - Ivo Grosse
- Department of BioinformaticsMartin‐Luther‐University06120HalleGermany
| | - Claude Becker
- Department of Molecular BiologyMax Planck Institute for Developmental Biology72076TübingenGermany
- Gregor Mendel Institute of Molecular Plant Biology1030ViennaAustria
| | - Detlef Weigel
- Department of Molecular BiologyMax Planck Institute for Developmental Biology72076TübingenGermany
| | - Helmut Bäumlein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466Seeland OT GaterslebenGermany
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466Seeland OT GaterslebenGermany
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45
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Ni P, Li S, Lin Y, Xiong W, Huang X, Zhan A. Methylation divergence of invasive Ciona ascidians: Significant population structure and local environmental influence. Ecol Evol 2018; 8:10272-10287. [PMID: 30397465 PMCID: PMC6206186 DOI: 10.1002/ece3.4504] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/02/2018] [Accepted: 08/03/2018] [Indexed: 12/16/2022] Open
Abstract
The geographical expansion of invasive species usually leads to temporary and/or permanent changes at multiple levels (genetics, epigenetics, gene expression, etc.) to acclimatize to abiotic and/or biotic stresses in novel environments. Epigenetic variation such as DNA methylation is often involved in response to diverse local environments, thus representing one crucial mechanism to promote invasion success. However, evidence is scant on the potential role of DNA methylation variation in rapid environmental response and invasion success during biological invasions. In particular, DNA methylation patterns and possible contributions of varied environmental factors to methylation differentiation have been largely unknown in many invaders, especially for invasive species in marine systems where extremely complex interactions exist between species and surrounding environments. Using the methylation-sensitive amplification polymorphism (MSAP) technique, here we investigated population methylation structure at the genome level in two highly invasive model ascidians, Ciona robusta and C. intestinalis, collected from habitats with varied environmental factors such as temperature and salinity. We found high intrapopulation methylation diversity and significant population methylation differentiation in both species. Multiple analyses, such as variation partitioning analysis, showed that both genetic variation and environmental factors contributed to the observed DNA methylation variation. Further analyses found that 24 and 20 subepiloci were associated with temperature and/or salinity in C. robusta and C. intestinalis, respectively. All these results clearly showed significant methylation divergence among populations of both invasive ascidians, and varied local environmental factors, as well as genetic variation, were responsible for the observed DNA methylation patterns. The consistent findings in both species here suggest that DNA methylation, coupled with genetic variation, may facilitate local environmental adaptation during biological invasions, and DNA methylation variation molded by local environments may contribute to invasion success.
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Affiliation(s)
- Ping Ni
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesBeijingChina
| | - Shiguo Li
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Yaping Lin
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Wei Xiong
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesBeijingChina
| | - Xuena Huang
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesBeijingChina
| | - Aibin Zhan
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesBeijingChina
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Perlaza-Jiménez L, Walther D. A genome-wide scan for correlated mutations detects macromolecular and chromatin interactions in Arabidopsis thaliana. Nucleic Acids Res 2018; 46:8114-8132. [PMID: 29986106 PMCID: PMC6144803 DOI: 10.1093/nar/gky576] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/14/2018] [Indexed: 01/05/2023] Open
Abstract
The concept of exploiting correlated mutations has been introduced and applied successfully to identify interactions within and between biological macromolecules. Its rationale lies in the preservation of physical interactions via compensatory mutations. With the massive increase of available sequence information, approaches based on correlated mutations have regained considerable attention. We analyzed a set of 10 707 430 single nucleotide polymorphisms detected in 1135 accessions of the plant Arabidopsis thaliana. To measure their covariance and to reveal the global genome-wide sequence correlation structure of the Arabidopsis genome, the adjusted mutual information has been estimated for each possible pair of polymorphic sites. We developed a series of filtering steps to account for genetic linkage and lineage relations between Arabidopsis accessions, as well as transitive covariance as possible confounding factors. We show that upon appropriate filtering, correlated mutations prove indeed informative with regard to molecular interactions, and furthermore, appear to reflect on chromosomal interactions. Our study demonstrates that the concept of correlated mutations can also be applied successfully to within-species sequence variation and establishes a promising approach to help unravel the complex molecular interactions in A. thaliana and other species with broad sequence information.
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Affiliation(s)
- Laura Perlaza-Jiménez
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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Shen Y, Zhang J, Liu Y, Liu S, Liu Z, Duan Z, Wang Z, Zhu B, Guo YL, Tian Z. DNA methylation footprints during soybean domestication and improvement. Genome Biol 2018; 19:128. [PMID: 30201012 PMCID: PMC6130073 DOI: 10.1186/s13059-018-1516-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/22/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In addition to genetic variation, epigenetic variation plays an important role in determining various biological processes. The importance of natural genetic variation to crop domestication and improvement has been widely investigated. However, the contribution of epigenetic variation in crop domestication at population level has rarely been explored. RESULTS To understand the impact of epigenetics on crop domestication, we investigate the variation of DNA methylation during soybean domestication and improvement by whole-genome bisulfite sequencing of 45 soybean accessions, including wild soybeans, landraces, and cultivars. Through methylomic analysis, we identify 5412 differentially methylated regions (DMRs). These DMRs exhibit characters distinct from those of genetically selected regions. In particular, they have significantly higher genetic diversity. Association analyses suggest only 22.54% of DMRs can be explained by local genetic variations. Intriguingly, genes in the DMRs that are not associated with any genetic variation are enriched in carbohydrate metabolism pathways. CONCLUSIONS This study provides a valuable map of DNA methylation across diverse accessions and dissects the relationship between DNA methylation variation and genetic variation during soybean domestication, thus expanding our understanding of soybean domestication and improvement.
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Affiliation(s)
- Yanting Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Jixiang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Zhi Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Zheng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Baoge Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
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48
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Partial maintenance of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation. Proc Natl Acad Sci U S A 2018; 115:E9145-E9152. [PMID: 30201727 PMCID: PMC6166847 DOI: 10.1073/pnas.1805371115] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
While clonally propagated individuals should share identical genomes, there is often substantial phenotypic variation among them. Both genetic and epigenetic modifications induced during regeneration have been associated with this phenomenon. Here we investigated the fate of the epigenome after asexual propagation by generating clonal individuals from differentiated somatic cells through the manipulation of a zygotic transcription factor. We found that phenotypic novelty in clonal progeny was linked to epigenetic imprints that reflect the organ used for regeneration. Some of these organ-specific imprints can be maintained during the cloning process and subsequent rounds of meiosis. Our findings are fundamental for understanding the significance of epigenetic variability arising from asexual reproduction and have significant implications for future biotechnological applications. Plants differ from animals in their capability to easily regenerate fertile adult individuals from terminally differentiated cells. This unique developmental plasticity is commonly observed in nature, where many species can reproduce asexually through the ectopic initiation of organogenic or embryogenic developmental programs. While organ-specific epigenetic marks are not passed on during sexual reproduction, the fate of epigenetic marks during asexual reproduction and the implications for clonal progeny remain unclear. Here we report that organ-specific epigenetic imprints in Arabidopsis thaliana can be partially maintained during asexual propagation from somatic cells in which a zygotic program is artificially induced. The altered marks are inherited even over multiple rounds of sexual reproduction, becoming fixed in hybrids and resulting in heritable molecular and physiological phenotypes that depend on the identity of the founder tissue. Consequently, clonal plants display distinct interactions with beneficial and pathogenic microorganisms. Our results demonstrate how novel phenotypic variation in plants can be unlocked through altered inheritance of epigenetic marks upon asexual propagation.
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49
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Chen X, Schï Nberger B, Menz J, Ludewig U. Plasticity of DNA methylation and gene expression under zinc deficiency in Arabidopsis roots. PLANT & CELL PHYSIOLOGY 2018; 59:1790-1802. [PMID: 29800330 DOI: 10.1093/pcp/pcy100] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 05/10/2018] [Indexed: 05/24/2023]
Abstract
DNA methylation is a heritable chromatin modification that maintains chromosome stability, regulates transposon silencing and appears to be involved in gene expression in response to environmental conditions. Environmental stress alters DNA methylation patterns that are correlated with gene expression differences. Here, genome-wide differential DNA methylation was identified upon prolonged zinc (Zn) deficiency, leading to hypo- and hypermethylated chromosomal regions. Preferential CpG methylation changes occurred in gene promoters and gene bodies, but did not overlap with transcriptional start sites. Methylation changes were also prominent in transposable elements. In contrast, non-CpG methylation differences were exclusively found in promoters of protein-coding genes and in transposable elements. Strongly Zn deficiency-induced genes and their promoters were mostly non-methylated, irrespective of Zn supply. Differential DNA methylation in the CpG and CHG, but not in the CHH context, was found close to a few up-regulated Zn deficiency genes. However, the transcriptional Zn deficiency response in roots appeared little correlated with associated DNA methylation changes in promoters or gene bodies. Furthermore, under Zn deficiency, developmental defects were identified in an Arabidopsis mutant lacking non-CpG methylation. The root methylome thus responds specifically to a micronutrient deficiency and is important for efficient Zn utilization at low availability, but the relationship of differential methylation and differentially expressed genes is surprisingly poor.
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Affiliation(s)
- Xiaochao Chen
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr. 20, Stuttgart, Germany
| | - Brigitte Schï Nberger
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr. 20, Stuttgart, Germany
| | - Jochen Menz
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr. 20, Stuttgart, Germany
| | - Uwe Ludewig
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr. 20, Stuttgart, Germany
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50
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Ganguly DR, Crisp PA, Eichten SR, Pogson BJ. Maintenance of pre-existing DNA methylation states through recurring excess-light stress. PLANT, CELL & ENVIRONMENT 2018; 41:1657-1672. [PMID: 29707792 DOI: 10.1111/pce.13324] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 05/23/2023]
Abstract
The capacity for plant stress priming and memory and the notion of this being underpinned by DNA methylation-mediated memory is an appealing hypothesis for which there is mixed evidence. We previously established a lack of drought-induced methylome variation in Arabidopsis thaliana (Arabidopsis); however, this was tied to only minor observations of physiological memory. There are numerous independent observations demonstrating that photoprotective mechanisms, induced by excess-light stress, can lead to robust programmable changes in newly developing leaf tissues. Although key signalling molecules and transcription factors are known to promote this priming signal, an untested question is the potential involvement of chromatin marks towards the maintenance of light stress acclimation, or memory. Thus, we systematically tested our previous hypothesis of a stress-resistant methylome using a recurring excess-light stress, then analysing new, emerging, and existing tissues. The DNA methylome showed negligible stress-associated variation, with the vast majority attributable to stochastic differences. Yet, photoacclimation was evident through enhanced photosystem II performance in exposed tissues, and nonphotochemical quenching and fluorescence decline ratio showed evidence of mitotic transmission. Thus, we have observed physiological acclimation in new and emerging tissues in the absence of substantive DNA methylome changes.
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Affiliation(s)
- Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Division of Plant Sciences, Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - Peter A Crisp
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Division of Plant Sciences, Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Division of Plant Sciences, Research School of Biology, Australian National University, Acton, ACT 2601, Australia
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