1
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Scheschonk L, Nilsen AML, Bischof K, Jueterbock A. Chloroplast DNA methylation in the kelp Saccharina latissima is determined by origin and possibly influenced by cultivation. Evol Appl 2024; 17:e13744. [PMID: 38962361 PMCID: PMC11219511 DOI: 10.1111/eva.13744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 05/21/2024] [Accepted: 06/11/2024] [Indexed: 07/05/2024] Open
Abstract
DNA cytosine methylation is an important epigenetic mechanism in genomic DNA. In most land plants, it is absent in the chloroplast DNA. We detected methylation in the chloroplast DNA of the kelp Saccharina latissima, a non-model macroalgal species of high ecological and economic importance. Since the functional role of the chloroplast methylome is yet largely unknown, this fundamental research assessed the chloroplast DNA cytosine methylation in wild and laboratory raised kelp from different climatic origins (High-Arctic at 79° N, and temperate at 54° N), and in laboratory samples from these origins raised at different temperatures (5, 10 and 15°C). Results suggest genome-wide differences in methylated sites and methylation level between the origins, while rearing temperature had only weak effects on the chloroplast methylome. Our findings point at the importance of matching conditions to origin in restoration and cultivation processes to be valid even on plastid level.
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Affiliation(s)
| | - Anne M. L. Nilsen
- Algal and Microbial Biotechnology Division, Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Kai Bischof
- University of Bremen, Marine Botany & MARUMBremenGermany
| | - Alexander Jueterbock
- Algal and Microbial Biotechnology Division, Faculty of Biosciences and AquacultureNord UniversityBodøNorway
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2
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Harkess A, Bewick AJ, Lu Z, Fourounjian P, Michael TP, Schmitz RJ, Meyers BC. The unusual predominance of maintenance DNA methylation in Spirodela polyrhiza. G3 (BETHESDA, MD.) 2024; 14:jkae004. [PMID: 38190722 PMCID: PMC10989885 DOI: 10.1093/g3journal/jkae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/28/2023] [Accepted: 11/06/2023] [Indexed: 01/10/2024]
Abstract
Duckweeds are among the fastest reproducing plants, able to clonally divide at exponential rates. However, the genetic and epigenetic impact of clonality on plant genomes is poorly understood. 5-methylcytosine (5mC) is a modified base often described as necessary for the proper regulation of certain genes and transposons and for the maintenance of genome integrity in plants. However, the extent of this dogma is limited by the current phylogenetic sampling of land plant species diversity. Here we analyzed DNA methylomes, small RNAs, mRNA-seq, and H3K9me2 histone modification for Spirodela polyrhiza. S. polyrhiza has lost highly conserved genes involved in de novo methylation of DNA at sites often associated with repetitive DNA, and within genes, however, symmetrical DNA methylation and heterochromatin are maintained during cell division at certain transposons and repeats. Consequently, small RNAs that normally guide methylation to silence repetitive DNA like retrotransposons are diminished. Despite the loss of a highly conserved methylation pathway, and the reduction of small RNAs that normally target repetitive DNA, transposons have not proliferated in the genome, perhaps due in part to the rapid, clonal growth lifestyle of duckweeds.
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Affiliation(s)
- Alex Harkess
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Adam J Bewick
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Zefu Lu
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Paul Fourounjian
- Waksman Institute of Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Todd P Michael
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
- Division of Plant Sciences, University of Missouri—Columbia, Columbia, MO 65211, USA
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3
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Sammarco I, Díez Rodríguez B, Galanti D, Nunn A, Becker C, Bossdorf O, Münzbergová Z, Latzel V. DNA methylation in the wild: epigenetic transgenerational inheritance can mediate adaptation in clones of wild strawberry (Fragaria vesca). THE NEW PHYTOLOGIST 2024; 241:1621-1635. [PMID: 38058250 DOI: 10.1111/nph.19464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
Due to the accelerating climate change, it is crucial to understand how plants adapt to rapid environmental changes. Such adaptation may be mediated by epigenetic mechanisms like DNA methylation, which could heritably alter phenotypes without changing the DNA sequence, especially across clonal generations. However, we are still missing robust evidence of the adaptive potential of DNA methylation in wild clonal populations. Here, we studied genetic, epigenetic and transcriptomic variation of Fragaria vesca, a predominantly clonally reproducing herb. We examined samples from 21 natural populations across three climatically distinct geographic regions, as well as clones of the same individuals grown in a common garden. We found that epigenetic variation was partly associated with climate of origin, particularly in non-CG contexts. Importantly, a large proportion of this variation was heritable across clonal generations. Additionally, a subset of these epigenetic changes affected the expression of genes mainly involved in plant growth and responses to pathogen and abiotic stress. These findings highlight the potential influence of epigenetic changes on phenotypic traits. Our findings indicate that variation in DNA methylation, which can be environmentally inducible and heritable, may enable clonal plant populations to adjust to their environmental conditions even in the absence of genetic adaptation.
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Affiliation(s)
- Iris Sammarco
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
| | - Bárbara Díez Rodríguez
- Natural Resources and Climate Area, CARTIF Technology Centre, Parque Tecnológico de Boecillo, parc. 205, 47151, Boecillo, Valladolid, Spain
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch Strasse 8, D-35043, Marburg, Germany
- Department of Forest Genetics, Albert-Ludwigs-Universität Freiburg, Bertoldstraße 17, 79098, Freiburg i. Br., Germany
| | - Dario Galanti
- Royal Botanic Gardens, Kew, Richmond, UK
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
| | - Adam Nunn
- ecSeq Bioinformatics GmbH, Sternwartenstraße 29, 04103, Saxony, Germany
- Department of Computer Science, University of Leipzig, Härtelstraße 16-18, Leipzig, 04107, Germany
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr Bohr-Gasse 3, 1030, Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig Maximilians University Munich, Grosshaderner Str. 2-4, 82152, Martinsried, Germany
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
| | - Zuzana Münzbergová
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01, Prague, Czechia
| | - Vít Latzel
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czechia
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4
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Zhu J, Wang Y, Wang Q, Li B, Wang X, Zhou X, Zhang H, Xu W, Li S, Wang L. The combination of DNA methylation and positive regulation of anthocyanin biosynthesis by MYB and bHLH transcription factors contributes to the petal blotch formation in Xibei tree peony. HORTICULTURE RESEARCH 2023; 10:uhad100. [PMID: 37427034 PMCID: PMC10327543 DOI: 10.1093/hr/uhad100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 05/05/2023] [Indexed: 07/11/2023]
Abstract
Xibei tree peony is a distinctive cultivar group that features red-purple blotches in petals. Interestingly, the pigmentations of blotches and non-blotches are largely independent of one another. The underlying molecular mechanism had attracted lots of attention from investigators, but was still uncertain. Our present work demonstrates the factors that are closely related to blotch formation in Paeonia rockii 'Shu Sheng Peng Mo'. Non-blotch pigmentation is prevented by the silencing of anthocyanin structural genes, among which PrF3H, PrDFR, and PrANS are the three major genes. We characterized two R2R3-MYBs as the key transcription factors that control the early and late anthocyanin biosynthetic pathways. PrMYBa1, which belongs to MYB subgroup 7 (SG7) was found to activate the early biosynthetic gene (EBG) PrF3H by interacting with SG5 member PrMYBa2 to form an 'MM' complex. The SG6 member PrMYBa3 interacts with two SG5 (IIIf) bHLHs to synergistically activate the late biosynthetic genes (LBGs) PrDFR and PrANS, which is essential for anthocyanin accumulation in petal blotches. The comparison of methylation levels of the PrANS and PrF3H promoters between blotch and non-blotch indicated a correlation between hypermethylation and gene silencing. The methylation dynamics of PrANS promoter during flower development revealed a potential early demethylating reaction, which may have contributed to the particular expression of PrANS solely in the blotch area. We suggest that the formation of petal blotch may be highly associated with the cooperation of transcriptional activation and DNA methylation of structural gene promoters.
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Affiliation(s)
- Jin Zhu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yizhou Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianyu Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohan Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xian Zhou
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hechen Zhang
- Horticulture Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Wenzhong Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanshan Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangsheng Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Cadavid IC, Balbinott N, Margis R. Beyond transcription factors: more regulatory layers affecting soybean gene expression under abiotic stress. Genet Mol Biol 2023; 46:e20220166. [PMID: 36706026 PMCID: PMC9881580 DOI: 10.1590/1678-4685-gmb-2022-0166] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/18/2022] [Indexed: 01/28/2023] Open
Abstract
Abiotic stresses such as nutritional imbalance, salt, light intensity, and high and low temperatures negatively affect plant growth and development. Through the course of evolution, plants developed multiple mechanisms to cope with environmental variations, such as physiological, morphological, and molecular adaptations. Epigenetic regulation, transcription factor activity, and post-transcriptional regulation operated by RNA molecules are mechanisms associated with gene expression regulation under stress. Epigenetic regulation, including histone and DNA covalent modifications, triggers chromatin remodeling and changes the accessibility of transcription machinery leading to alterations in gene activity and plant homeostasis responses. Soybean is a legume widely produced and whose productivity is deeply affected by abiotic stresses. Many studies explored how soybean faces stress to identify key elements and improve productivity through breeding and genetic engineering. This review summarizes recent progress in soybean gene expression regulation through epigenetic modifications and circRNAs pathways, and points out the knowledge gaps that are important to study by the scientific community. It focuses on epigenetic factors participating in soybean abiotic stress responses, and chromatin modifications in response to stressful environments and draws attention to the regulatory potential of circular RNA in post-transcriptional processing.
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Affiliation(s)
- Isabel Cristina Cadavid
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre, Brazil
| | - Natalia Balbinott
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Porto Alegre, Brazil
| | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre, Brazil.,Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Porto Alegre, Brazil.,Universidade Federal do Rio Grande do Sul, Departamento de Biofisica, Porto Alegre, Brazil
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6
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Saha D, Shaw AK, Datta S, Mitra J, Kar G. DNA hypomethylation is the plausible driver of heat stress adaptation in Linum usitatissimum. PHYSIOLOGIA PLANTARUM 2022; 174:e13689. [PMID: 35462427 DOI: 10.1111/ppl.13689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/31/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Heat stress has a significant impact on the climatic adaptation of flax, a cool-season economic crop. Genome-wide DNA methylation patterns are crucial for understanding how flax cultivars respond to heat adversities. It is worth noting that the DNA methylome in flax has yet to be investigated at the nucleotide level. Although heat stress above 40°C caused oxidative damage in flax leaves, 5-azacytidine, a hypomethylating agent, reduced this effect by 15%-24%. Differences in the expression of the LuMET1 (DNA methyltransferase) gene suggested that DNA methylation/demethylation may play a major role in the flax heat stress response. Thus, whole-genome bisulfite sequencing-derived DNA methylation profiles in flax, with or without heat stress and 5-azaC, were developed and analyzed here. In response to heat stress, a high percentage of significant differentially methylated regions (DMRs), particularly hypomethylated DMRs, were identified in the CHH nucleotide sequence context (H = A/T/C). Some of these DMRs overlapped with transposable element insertions. The majority of DMRs were discovered in intergenic regions, but several DMR loci were also found near genes relevant to heat stress response and epigenetic processes. These DMRs, in particular, are linked to CpG islands, implying a possible role in promoter methylation and gene silencing. The DMRs discovered in this study are crucial for understanding and identifying the key players in heat stress response in flax, which will help in developing climate-smart flax varieties.
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Affiliation(s)
- Dipnarayan Saha
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
| | - Arun Kumar Shaw
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
| | - Subhojit Datta
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
| | - Jiban Mitra
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
| | - Gouranga Kar
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, India
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7
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Inhibitors of DNA Methylation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:471-513. [DOI: 10.1007/978-3-031-11454-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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DNA methylation and histone modifications induced by abiotic stressors in plants. Genes Genomics 2021; 44:279-297. [PMID: 34837631 DOI: 10.1007/s13258-021-01191-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 11/14/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND A review of research shows that methylation in plants is more complex and sophisticated than in microorganisms and animals. Overall, studies on the effects of abiotic stress on epigenetic modifications in plants are still scarce and limited to few species. Epigenetic regulation of plant responses to environmental stresses has not been elucidated. This study summarizes key effects of abiotic stressors on DNA methylation and histone modifications in plants. DISCUSSION Plant DNA methylation and histone modifications in responses to abiotic stressors varied and depended on the type and level of stress, plant tissues, age, and species. A critical analysis of the literature available revealed that 44% of the epigenetic modifications induced by abiotic stressors in plants involved DNA hypomethylation, 40% DNA hypermethylation, and 16% histone modification. The epigenetic changes in plants might be underestimated since most authors used methods such as methylation-sensitive amplification polymorphism (MSAP), High performance liquid chromatography (HPLC), and immunolabeling that are less sensitive compared to bisulfite sequencing and single-base resolution methylome analyses. More over, mechanisms underlying epigenetic changes in plants have not yet been determined since most reports showed only the level or/and distribution of DNA methylation and histone modifications. CONCLUSIONS Various epigenetic mechanisms are involved in response to abiotic stressors, and several of them are still unknown. Integrated analysis of the changes in the genome by omic approaches should help to identify novel components underlying mechanisms involved in DNA methylation and histone modifications associated with plant response to environmental stressors.
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Osadchuk K, Cheng CL, Irish EE. The integration of leaf-derived signals sets the timing of vegetative phase change in maize, a process coordinated by epigenetic remodeling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 312:111035. [PMID: 34620439 DOI: 10.1016/j.plantsci.2021.111035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/02/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
After germination, the maize shoot proceeds through a series of developmental stages before flowering. The first transition occurs during the vegetative phase where the shoot matures from the juvenile to the adult phase, called vegetative phase change (VPC). In maize, both phases exhibit easily-scored morphological characteristics, facilitating the elucidation of molecular mechanisms directing the characteristic gene expression patterns and resulting physiological features of each phase. miR156 expression is high during the juvenile phase, suppressing expression of squamosa promoter binding proteins/SBP-like transcription factors and miR172. The decline in miR156 and subsequent increase in miR172 expression marks the transition into the adult phase, where miR172 represses transcripts that confer juvenile traits. Leaf-derived signals attenuate miR156 expression and thus the duration of the juvenile phase. As found in other species, VPC in maize utilizes signals that consist of hormones, stress, and sugar to direct epigenetic modifiers. In this review we identify the intersection of leaf-derived signaling with components that contribute to the epigenetic changes which may, in turn, manage the distinct global gene expression patterns of each phase. In maize, published research regarding chromatin remodeling during VPC is minimal. Therefore, we identified epigenetic regulators in the maize genome and, using published gene expression data and research from other plant species, identify VPC candidates.
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Affiliation(s)
- Krista Osadchuk
- 129 E. Jefferson Street, Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Chi-Lien Cheng
- 129 E. Jefferson Street, Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Erin E Irish
- 129 E. Jefferson Street, Department of Biology, University of Iowa, Iowa City, IA, USA.
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10
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Weiner AKM, Cerón-Romero MA, Yan Y, Katz LA. Phylogenomics of the Epigenetic Toolkit Reveals Punctate Retention of Genes across Eukaryotes. Genome Biol Evol 2021; 12:2196-2210. [PMID: 33049043 DOI: 10.1093/gbe/evaa198] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2020] [Indexed: 12/17/2022] Open
Abstract
Epigenetic processes in eukaryotes play important roles through regulation of gene expression, chromatin structure, and genome rearrangements. The roles of chromatin modification (e.g., DNA methylation and histone modification) and non-protein-coding RNAs have been well studied in animals and plants. With the exception of a few model organisms (e.g., Saccharomyces and Plasmodium), much less is known about epigenetic toolkits across the remainder of the eukaryotic tree of life. Even with limited data, previous work suggested the existence of an ancient epigenetic toolkit in the last eukaryotic common ancestor. We use PhyloToL, our taxon-rich phylogenomic pipeline, to detect homologs of epigenetic genes and evaluate their macroevolutionary patterns among eukaryotes. In addition to data from GenBank, we increase taxon sampling from understudied clades of SAR (Stramenopila, Alveolata, and Rhizaria) and Amoebozoa by adding new single-cell transcriptomes from ciliates, foraminifera, and testate amoebae. We focus on 118 gene families, 94 involved in chromatin modification and 24 involved in non-protein-coding RNA processes based on the epigenetics literature. Our results indicate 1) the presence of a large number of epigenetic gene families in the last eukaryotic common ancestor; 2) differential conservation among major eukaryotic clades, with a notable paucity of genes within Excavata; and 3) punctate distribution of epigenetic gene families between species consistent with rapid evolution leading to gene loss. Together these data demonstrate the power of taxon-rich phylogenomic studies for illuminating evolutionary patterns at scales of >1 billion years of evolution and suggest that macroevolutionary phenomena, such as genome conflict, have shaped the evolution of the eukaryotic epigenetic toolkit.
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Affiliation(s)
- Agnes K M Weiner
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Mario A Cerón-Romero
- Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst
| | - Ying Yan
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst
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11
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Kang DR, Zhu Y, Li SL, Ai PH, Khan MA, Ding HX, Wang Y, Wang ZC. Transcriptome analysis of differentially expressed genes in chrysanthemum MET1 RNA interference lines. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1455-1468. [PMID: 34366589 PMCID: PMC8295425 DOI: 10.1007/s12298-021-01022-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 05/14/2023]
Abstract
UNLABELLED DNA methylation is the most important epigenetic modification involved in many essential biological processes. MET1 is one of DNA methyltransferases that affect the level of methylation in the entire genome. To explore the effect of MET1 gene silencing on gene expression profile of Chrysanthemum × morifolium 'Zijingling'. The stem section and leaves at the young stage were taken for transcriptome sequencing. MET1-RNAi leaves had 8 differentially expressed genes while 156 differentially expressed genes were observed in MET1-RNAi stem compared with control leaves and stem. These genes encode many key proteins in plant biological processes, such as transcription factors, signal transduction mechanisms, secondary metabolite synthesis, transport and catabolism and interaction. In general, 34.58% of the differentially expressed genes in leaves and stems were affected by the reduction of the MET1 gene. The differentially expressed genes in stem and leaves of transgenic plants went through significant changes. We found adequate amount of candidate genes associated with flowering, however, the number of genes with significant differences between transgenic and control lines was not too high. Several flowering related genes were screened out for gene expression verification and all of them were obseved as consistent with transcriptome data. These candidate genes may play important role in flowering variation of chrysanthemum. This study reveals the mechanism of CmMET1 interference on the growth and development of chrysanthemum at the transcriptional level, which provides the basis for further research on the epigenetic regulation mechanism in flower induction and development. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01022-1.
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Affiliation(s)
- Dong-ru Kang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Yi Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Shuai-lei Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Peng-hui Ai
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Muhammad Ayoub Khan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Hong-xu Ding
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Ying Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Zi-cheng Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
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12
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Genome-Wide Variation in DNA Methylation Predicts Variation in Leaf Traits in an Ecosystem-Foundational Oak Species. FORESTS 2021. [DOI: 10.3390/f12050569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Epigenetic modifications such as DNA methylation are a potential mechanism for trees to respond to changing environments. However, it remains controversial the extent to which DNA methylation impacts ecologically important traits that influence fitness. In this study, we used reduced-representation bisulfite sequencing to associate genomic and epigenomic variation with seven phenotypic traits related to growth, leaf function, and disease susceptibility in 160 valley oak (Quercus lobata) saplings planted across two common gardens in California. We found that DNA methylation was associated with a significant fraction of phenotypic variance in plant height, leaf lobedness, powdery mildew infection, and trichome density. Two of the seven traits were significantly associated with DNA methylation in the CG context, three traits were significantly associated with CHG methylation, and two traits were significantly associated with CHH methylation. Notably, controlling for genomic variation in SNPs generally reduced the amount of trait variation explained by DNA methylation. Our results suggest that DNA methylation may serve as a useful biomarker to predict phenotypic variation in trees, though it remains unclear the degree to which DNA methylation is a causal mechanism driving phenotypic variation in forest tree species.
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13
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Gouda G, Gupta MK, Donde R, Sabarinathan S, Vadde R, Behera L, Mohapatra T. Computational Epigenetics in Rice Research. APPLICATIONS OF BIOINFORMATICS IN RICE RESEARCH 2021:113-140. [DOI: 10.1007/978-981-16-3997-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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14
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Eckert S, Herden J, Stift M, Joshi J, van Kleunen M. Manipulation of cytosine methylation does not remove latitudinal clines in two invasive goldenrod species in Central Europe. Mol Ecol 2020; 30:222-236. [PMID: 33150604 DOI: 10.1111/mec.15722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/03/2020] [Accepted: 10/23/2020] [Indexed: 12/23/2022]
Abstract
Invasive species frequently differentiate phenotypically in novel environments within a few generations, often even with limited genetic variation. For the invasive plants Solidago canadensis and S. gigantea, we tested whether such differentiation might have occurred through heritable epigenetic changes in cytosine methylation. In a 2-year common-garden experiment, we grew plants from seeds collected along a latitudinal gradient in their non-native Central European range to test for trait differentiation and whether differentiation disappeared when seeds were treated with the demethylation agent zebularine. Microsatellite markers revealed no population structure along the latitudinal gradient in S. canadensis, but three genetic clusters in S. gigantea. Solidago canadensis showed latitudinal clines in flowering phenology and growth. In S. gigantea, the number of clonal offspring decreased with latitude. Although zebularine had a significant effect on early growth, probably through effects on cytosine methylation, latitudinal clines remained (or even got stronger) in plants raised from seeds treated with zebularine. Thus, our experiment provides no evidence that epigenetic mechanisms by selective cytosine methylation contribute to the observed phenotypic differentiation in invasive goldenrods in Central Europe.
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Affiliation(s)
- Silvia Eckert
- Biodiversity Research/Systematic Botany, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jasmin Herden
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Marc Stift
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Jasmin Joshi
- Biodiversity Research/Systematic Botany, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,Institute for Landscape and Open Space, Eastern Switzerland University of Applied Sciences, Rapperswil, Switzerland.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Mark van Kleunen
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany.,Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
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15
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Zuo S, Shi G, Fan J, Fan B, Zhang X, Liu S, Hao Y, Wei Z, Zhou X, Feng S. Identification of adhesion-associated DNA methylation patterns in the peripheral nervous system. Exp Ther Med 2020; 21:48. [PMID: 33273976 PMCID: PMC7706384 DOI: 10.3892/etm.2020.9479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/26/2020] [Indexed: 11/06/2022] Open
Abstract
Schwann cells are unique glial cells in the peripheral nervous system. These cells provide a range of cytokines and nutritional factors to maintain axons and support axonal regeneration. However, little is known concerning adhesion-associated epigenetic changes that occur in Schwann cells after peripheral nerve injury (PNI). In the present study, adhesion-associated DNA methylation biomarkers were assessed between normal and injury peripheral nerve. Specifically, normal Schwann cells (NSCs) and activated Schwann cells (ASCs) were obtained from adult Wistar rats. After the Schwann cells were identified, proliferation and adhesion assays were used to assess differences between NSCs and ASCs. Methylated DNA immunoprecipitation-sequencing and bioinformatics analysis were used to identify and analyze the differentially methylated genes. Reverse transcription-quantitative PCR was performed to assess the expression levels of adhesion-associated genes. In the present study, the proliferation and adhesion assays demonstrated that ASCs had a more robust proliferative activity and adhesion compared with NSCs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to identify methylation-associated biological processes and signaling pathways. Protein-protein interaction network analysis revealed that Fyn, Efna1, Jak2, Vav3, Flt4, Epha7, Crk, Kitlg, Ctnnb1 and Ptpn11 were potential markers for Schwann cell adhesion. The expression levels of several adhesion-associated genes, such as vinculin, BCAR1 scaffold protein, collagen type XVIII α1 chain and integrin subunit β6, in ASCs were altered compared with those in NSCs. The current study analyzed adhesion-associated DNA methylation patterns of Schwann cells and identified candidate genes that may potentially regulate Schwann cell adhesion in Wistar rats before and after PNI.
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Affiliation(s)
- Shanhuai Zuo
- Department of Radiology, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Guidong Shi
- Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China.,International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Jianchao Fan
- Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China.,International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Baoyou Fan
- Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China.,International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Xiaolei Zhang
- Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China.,International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Shen Liu
- Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China.,International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Yan Hao
- Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China.,International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Zhijian Wei
- Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China.,International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Xianhu Zhou
- Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China.,International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Shiqing Feng
- Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China.,International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
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16
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Genitoni J, Vassaux D, Delaunay A, Citerne S, Portillo Lemus L, Etienne MP, Renault D, Stoeckel S, Barloy D, Maury S. Hypomethylation of the aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala mimics the adaptive transition into the terrestrial morphotype. PHYSIOLOGIA PLANTARUM 2020; 170:280-298. [PMID: 32623739 DOI: 10.1111/ppl.13162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 06/17/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
Ongoing global changes affect ecosystems and open up new opportunities for biological invasion. The ability of invasive species to rapidly adapt to new environments represents a relevant model for studying short-term adaptation mechanisms. The aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala, is classified as harmful in European rivers. In French wet meadows, this species has shown a rapid transition from aquatic to terrestrial environments with emergence of two distinct morphotypes in 5 years. To understand the heritable mechanisms involved in adjustment to such a new environment, we investigate both genetic and epigenetic as possible sources of flexibility involved in this fast terrestrial transition. We found a low overall genetic differentiation between the two morphotypes arguing against the possibility that terrestrial morphotype emerged from a new adaptive genetic capacity. Artificial hypomethylation was induced on both morphotypes to assess the epigenetic hypothesis. We analyzed global DNA methylation, morphological changes, phytohormones and metabolite profiles of both morphotype responses in both aquatic and terrestrial conditions in shoot and root tissues. Hypomethylation significantly affected morphological variables, phytohormone levels and the amount of some metabolites. The effects of hypomethylation depended on morphotypes, conditions and plant tissues, which highlighted differences among the morphotypes and their plasticity. Using a correlative integrative approach, we showed that hypomethylation of the aquatic morphotype mimicked the characteristics of the terrestrial morphotype. Our data suggest that DNA methylation rather than a new adaptive genetic capacity is playing a key role in L. grandiflora subsp. hexapetala plasticity during its rapid aquatic to terrestrial transition.
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Affiliation(s)
- Julien Genitoni
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC1328 INRA, Université d'Orléans, Orléans, 45067, France
| | - Danièle Vassaux
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
| | - Alain Delaunay
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC1328 INRA, Université d'Orléans, Orléans, 45067, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Luis Portillo Lemus
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
| | - Marie-Pierre Etienne
- Institut Agro, CNRS, Université Rennes, IRMAR (Institut de Recherche Mathématique de Rennes) - UMR 6625, Rennes, F-35000, France
| | - David Renault
- UMR CNRS 6553 EcoBio, University of Rennes 1, Rennes, France
- Institut Universitaire de France, 1 rue Descartes, Paris, France
| | - Solenn Stoeckel
- IGEPP, INRAE, Institut Agro, Université Rennes, Le Rheu, 35653, France
| | - Dominique Barloy
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, 35042, France
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), EA1207 USC1328 INRA, Université d'Orléans, Orléans, 45067, France
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Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations. Int J Mol Sci 2020; 21:ijms21186700. [PMID: 32933168 PMCID: PMC7556024 DOI: 10.3390/ijms21186700] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/04/2020] [Accepted: 09/09/2020] [Indexed: 12/13/2022] Open
Abstract
Brachypodium distachyon (Brachypodium) is a non-domesticated model grass species that can be used to test if variation in genetic sequence or methylation are linked to environmental differences. To assess this, we collected seeds from 12 sites within five climatically distinct regions of Turkey. Seeds from each region were grown under standardized growth conditions in the UK to preserve methylated sequence variation. At six weeks following germination, leaves were sampled and assessed for genomic and DNA methylation variation. In a follow-up experiment, phenomic approaches were used to describe plant growth and drought responses. Genome sequencing and population structure analysis suggested three ancestral clusters across the Mediterranean, two of which were geographically separated in Turkey into coastal and central subpopulations. Phenotypic analyses showed that the coastal subpopulation tended to exhibit relatively delayed flowering and the central, increased drought tolerance as indicated by reduced yellowing. Genome-wide methylation analyses in GpC, CHG and CHH contexts also showed variation which aligned with the separation into coastal and central subpopulations. The climate niche modelling of both subpopulations showed a significant influence from the “Precipitation in the Driest Quarter” on the central subpopulation and “Temperature of the Coldest Month” on the coastal subpopulation. Our work demonstrates genetic diversity and variation in DNA methylation in Turkish accessions of Brachypodium that may be associated with climate variables and the molecular basis of which will feature in ongoing analyses.
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18
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Pereira WJ, Pappas MDCR, Grattapaglia D, Pappas GJ. A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing. PLoS One 2020; 15:e0233800. [PMID: 32497070 PMCID: PMC7272069 DOI: 10.1371/journal.pone.0233800] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/12/2020] [Indexed: 12/14/2022] Open
Abstract
Several studies suggest the relation of DNA methylation to diseases in humans and important phenotypes in plants drawing attention to this epigenetic mark as an important source of variability. In the last decades, several methodologies were developed to assess the methylation state of a genome. However, there is still a lack of affordable and precise methods for genome wide analysis in large sample size studies. Methyl sensitive double digestion MS-DArT sequencing method emerges as a promising alternative for methylation profiling. We developed a computational pipeline for the identification of DNA methylation using MS-DArT-seq data and carried out a pilot study using the Eucalyptus grandis tree sequenced for the species reference genome. Using a statistic framework as in differential expression analysis, 72,515 genomic sites were investigated and 5,846 methylated sites identified, several tissue specific, distributed along the species 11 chromosomes. We highlight a bias towards identification of DNA methylation in genic regions and the identification of 2,783 genes and 842 transposons containing methylated sites. Comparison with WGBS, DNA sequencing after treatment with bisulfite, data demonstrated a precision rate higher than 95% for our approach. The availability of a reference genome is useful for determining the genomic context of methylated sites but not imperative, making this approach suitable for any species. Our approach provides a cost effective, broad and reliable examination of DNA methylation profile on MspI/HpaII restriction sites, is fully reproducible and the source code is available on GitHub (https://github.com/wendelljpereira/ms-dart-seq).
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Affiliation(s)
| | | | - Dario Grattapaglia
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Georgios Joannis Pappas
- Department of Cell Biology, University of Brasília, Brasília, Distrito Federal, Brazil
- * E-mail:
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19
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Pereira WJ, Pappas MDCR, Grattapaglia D, Pappas GJ. A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing. PLoS One 2020; 15:e0233800. [PMID: 32497070 DOI: 10.1371/journal.pone.00233800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/12/2020] [Indexed: 05/27/2023] Open
Abstract
Several studies suggest the relation of DNA methylation to diseases in humans and important phenotypes in plants drawing attention to this epigenetic mark as an important source of variability. In the last decades, several methodologies were developed to assess the methylation state of a genome. However, there is still a lack of affordable and precise methods for genome wide analysis in large sample size studies. Methyl sensitive double digestion MS-DArT sequencing method emerges as a promising alternative for methylation profiling. We developed a computational pipeline for the identification of DNA methylation using MS-DArT-seq data and carried out a pilot study using the Eucalyptus grandis tree sequenced for the species reference genome. Using a statistic framework as in differential expression analysis, 72,515 genomic sites were investigated and 5,846 methylated sites identified, several tissue specific, distributed along the species 11 chromosomes. We highlight a bias towards identification of DNA methylation in genic regions and the identification of 2,783 genes and 842 transposons containing methylated sites. Comparison with WGBS, DNA sequencing after treatment with bisulfite, data demonstrated a precision rate higher than 95% for our approach. The availability of a reference genome is useful for determining the genomic context of methylated sites but not imperative, making this approach suitable for any species. Our approach provides a cost effective, broad and reliable examination of DNA methylation profile on MspI/HpaII restriction sites, is fully reproducible and the source code is available on GitHub (https://github.com/wendelljpereira/ms-dart-seq).
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Affiliation(s)
| | | | - Dario Grattapaglia
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
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20
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Divergent DNA Methylation Signatures of Juvenile Seedlings, Grafts and Adult Apple Trees. EPIGENOMES 2020; 4:epigenomes4010004. [PMID: 34968238 PMCID: PMC8594697 DOI: 10.3390/epigenomes4010004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/16/2020] [Accepted: 02/27/2020] [Indexed: 12/17/2022] Open
Abstract
The vast majority of previous studies on epigenetics in plants have centered on the study of inheritance of DNA methylation patterns in annual plants. In contrast, perennial plants may have the ability to accumulate changes in DNA methylation patterns over numerous years. However, currently little is known about long-lived perennial and clonally reproducing plants that may have evolved different DNA methylation inheritance mechanisms as compared to annual plants. To study the transmission of DNA methylation patterns in a perennial plant, we used apple (Malus domestica) as a model plant. First, we investigated the inheritance of DNA methylation patterns during sexual reproduction in apple by comparing DNA methylation patterns of mature trees to juvenile seedlings resulting from selfing. While we did not observe a drastic genome-wide change in DNA methylation levels, we found clear variations in DNA methylation patterns localized in regions enriched for genes involved in photosynthesis. Using transcriptomics, we also observed that genes involved in this pathway were overexpressed in seedlings. To assess how DNA methylation patterns are transmitted during clonal propagation we then compared global DNA methylation of a newly grafted tree to its mature donor tree. We identified significant, albeit weak DNA methylation changes resulting from grafting. Overall, we found that a majority of DNA methylation patterns from the mature donor tree are transmitted to newly grafted plants, however with detectable specific local differences. Both the epigenomic and transcriptomic data indicate that grafted plants are at an intermediate phase between an adult tree and seedling and inherit part of the epigenomic history of their donor tree.
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21
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Gardiner LJ. Understanding DNA Methylation Patterns in Wheat. Methods Mol Biol 2020; 2093:33-46. [PMID: 32088887 DOI: 10.1007/978-1-0716-0179-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The bread wheat genome is large (17 Gb), allohexaploid, and highly repetitive (80-90% of the genome), which makes genomic and epigenomic analyses expensive to conduct and a challenge to analyze. Here we provide an overview of recent bioinformatic and experimental methods that have been developed to understand DNA methylation patterns in the complex polyploid genome of wheat.
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Tatineni S, Sato S, Nersesian N, Alexander J, Quach T, Graybosch RA, Clemente TE. Transgenic Wheat Harboring an RNAi Element Confers Dual Resistance Against Synergistically Interacting Wheat Streak Mosaic Virus and Triticum Mosaic Virus. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:108-122. [PMID: 31687913 DOI: 10.1094/mpmi-10-19-0275-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Wheat streak mosaic virus (WSMV) and triticum mosaic virus (TriMV) are economically important viruses of wheat (Triticum aestivum L.), causing significant yield losses in the Great Plains region of the United States. These two viruses are transmitted by wheat curl mites, which often leads to mixed infections with synergistic interaction in grower fields that exacerbates yield losses. Development of dual-resistant wheat lines would provide effective control of these two viruses. In this study, a genetic resistance strategy employing an RNA interference (RNAi) approach was implemented by assembling a hairpin element composed of a 202-bp (404-bp in total) stem sequence of the NIb (replicase) gene from each of WSMV and TriMV in tandem and of an intron sequence in the loop. The derived RNAi element was cloned into a binary vector and was used to transform spring wheat genotype CB037. Phenotyping of T1 lineages across eight independent transgenic events for resistance revealed that i) two of the transgenic events provided resistance to WSMV and TriMV, ii) four events provided resistance to either WSMV or TriMV, and iii) no resistance was found in two other events. T2 populations derived from the two events classified as dual-resistant were subsequently monitored for stability of the resistance phenotype through the T4 generation. The resistance phenotype in these events was temperature-dependent, with a complete dual resistance at temperatures ≥25°C and an increasingly susceptible response at temperatures below 25°C. Northern blot hybridization of total RNA from transgenic wheat revealed that virus-specific small RNAs (vsRNAs) accumulated progressively with an increase in temperature, with no detectable levels of vsRNA accumulation at 20°C. Thus, the resistance phenotype of wheat harboring an RNAi element was correlated with accumulation of vsRNAs, and the generation of vsRNAs can be used as a molecular marker for the prediction of resistant phenotypes of transgenic plants at a specific temperature.
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Affiliation(s)
- Satyanarayana Tatineni
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
| | - Shirley Sato
- Center for Biotechnology, University of Nebraska-Lincoln
| | | | | | - Truyen Quach
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln
| | | | - Tom Elmo Clemente
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln
- Center for Plant Science Innovation, University of Nebraska-Lincoln
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Vyse K, Faivre L, Romich M, Pagter M, Schubert D, Hincha DK, Zuther E. Transcriptional and Post-Transcriptional Regulation and Transcriptional Memory of Chromatin Regulators in Response to Low Temperature. FRONTIERS IN PLANT SCIENCE 2020; 11:39. [PMID: 32117378 PMCID: PMC7020257 DOI: 10.3389/fpls.2020.00039] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/13/2020] [Indexed: 05/04/2023]
Abstract
Chromatin regulation ensures stable repression of stress-inducible genes under non-stress conditions and transcriptional activation and memory of stress-related genes after stress exposure. However, there is only limited knowledge on how chromatin genes are regulated at the transcriptional and post-transcriptional level upon stress exposure and relief from stress. We reveal that the repressive modification histone H3 lysine 27 trimethylation (H3K27me3) targets genes which are quickly activated upon cold exposure, however, H3K27me3 is not necessarily lost during a longer time in the cold. In addition, we have set-up a quantitative reverse transcription polymerase chain reaction-based platform for high-throughput transcriptional profiling of a large set of chromatin genes. We find that the expression of many of these genes is regulated by cold. In addition, we reveal an induction of several DNA and histone demethylase genes and certain histone variants after plants have been shifted back to ambient temperature (deacclimation), suggesting a role in the memory of cold acclimation. We also re-analyze large scale transcriptomic datasets for transcriptional regulation and alternative splicing (AS) of chromatin genes, uncovering an unexpected level of regulation of these genes, particularly at the splicing level. This includes several vernalization regulating genes whose AS may result in cold-regulated protein diversity. Overall, we provide a profiling platform for the analysis of chromatin regulatory genes and integrative analyses of their regulation, suggesting a dynamic regulation of key chromatin genes in response to low temperature stress.
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Affiliation(s)
- Kora Vyse
- Central Infrastructure Group Genomics and Transcript Profiling, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Léa Faivre
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Melissa Romich
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Majken Pagter
- Department of Chemistry and Bioscience, Aalborg University, Aalborg East, Denmark
| | - Daniel Schubert
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- *Correspondence: Daniel Schubert, ; Ellen Zuther,
| | - Dirk K. Hincha
- Central Infrastructure Group Genomics and Transcript Profiling, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Ellen Zuther
- Central Infrastructure Group Genomics and Transcript Profiling, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- *Correspondence: Daniel Schubert, ; Ellen Zuther,
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Susceptibility of Winter Wheat and Triticale to Yellow Rust Influenced by Complex Interactions between Vernalisation, Temperature, Plant Growth Stage and Pathogen Race. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy10010013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Environmental factors influence the disease susceptibility of crop plants. In this study, we established an experimental system to investigate the effects of vernalisation, temperature and plant growth stage on the susceptibility of winter wheat and winter triticale to Puccinia striiformis, the causal agent of yellow (stripe) rust. Two temperature regimes: standard (18 °C day/12 °C night) and low (12 °C day/6 °C night), vernalised and non-vernalised seedlings, vernalised adult plants and two pathogen races were investigated. At low temperatures, vernalisation reduced the susceptibility of seedlings exposed to the ‘Warrior’ race, while this was only the case for five out of eight varieties exposed to the ‘Kranich’ race. Changing from standard to low temperature resulted in increased susceptibility of non-vernalised seedlings of seven varieties inoculated with the ‘Warrior’ race and five varieties inoculated with the ‘Kranich’ race. Increased susceptibility at low temperature was also detected for several varieties at the adult plant growth stage. Comparisons between vernalised seedlings and adult plants revealed an effect of plant growth stage on disease susceptibility (e.g., Adult Plant Resistance) in five varieties at standard temperature for the ‘Warrior’ race and in five and four varieties at standard and low temperature respectively, for the ‘Kranich’ race. The complex and unpredictable interactions between environment and pathogen influencing yellow rust susceptibility of individual varieties stress the importance of phenotyping for disease resistance under different environmental conditions and pathogen populations. The environmental impact on rust susceptibility should also be taken into account in early-warning systems targeting wheat and triticale breeding programmes and growers.
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25
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Sun SS, Zhou XJ, Li ZZ, Song HY, Long ZC, Fu PC. Intra-individual heteroplasmy in the Gentiana tongolensis plastid genome (Gentianaceae). PeerJ 2019; 7:e8025. [PMID: 31799070 PMCID: PMC6884991 DOI: 10.7717/peerj.8025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 10/11/2019] [Indexed: 11/20/2022] Open
Abstract
Chloroplasts are typically inherited from the female parent and are haploid in most angiosperms, but rare intra-individual heteroplasmy in plastid genomes has been reported in plants. Here, we report an example of plastome heteroplasmy and its characteristics in Gentiana tongolensis (Gentianaceae). The plastid genome of G. tongolensis is 145,757 bp in size and is missing parts of petD gene when compared with other Gentiana species. A total of 112 single nucleotide polymorphisms (SNPs) and 31 indels with frequencies of more than 2% were detected in the plastid genome, and most were located in protein coding regions. Most sites with SNP frequencies of more than 10% were located in six genes in the LSC region. After verification via cloning and Sanger sequencing at three loci, heteroplasmy was identified in different individuals. The cause of heteroplasmy at the nucleotide level in plastome of G. tongolensis is unclear from the present data, although biparental plastid inheritance and transfer of plastid DNA seem to be most likely. This study implies that botanists should reconsider the heredity and evolution of chloroplasts and be cautious with using chloroplasts as genetic markers, especially in Gentiana.
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Affiliation(s)
- Shan-Shan Sun
- College of Life Science, Luoyang Normal University, Luoyang, Henan, People’s Republic of China
| | - Xiao-Jun Zhou
- College of Life Science, Luoyang Normal University, Luoyang, Henan, People’s Republic of China
| | - Zhi-Zhong Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Hong-Yang Song
- College of Life Science, Luoyang Normal University, Luoyang, Henan, People’s Republic of China
| | - Zhi-Cheng Long
- HostGene. Co. Ltd., Wuhan, Hubei, People’s Republic of China
| | - Peng-Cheng Fu
- College of Life Science, Luoyang Normal University, Luoyang, Henan, People’s Republic of China
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Weighill D, Tschaplinski TJ, Tuskan GA, Jacobson D. Data Integration in Poplar: 'Omics Layers and Integration Strategies. Front Genet 2019; 10:874. [PMID: 31608114 PMCID: PMC6773870 DOI: 10.3389/fgene.2019.00874] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 08/20/2019] [Indexed: 12/20/2022] Open
Abstract
Populus trichocarpa is an important biofuel feedstock that has been the target of extensive research and is emerging as a model organism for plants, especially woody perennials. This research has generated several large ‘omics datasets. However, only few studies in Populus have attempted to integrate various data types. This review will summarize various ‘omics data layers, focusing on their application in Populus species. Subsequently, network and signal processing techniques for the integration and analysis of these data types will be discussed, with particular reference to examples in Populus.
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Affiliation(s)
- Deborah Weighill
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Timothy J Tschaplinski
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Daniel Jacobson
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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Banerjee AK, Guo W, Huang Y. Genetic and epigenetic regulation of phenotypic variation in invasive plants – linking research trends towards a unified framework. NEOBIOTA 2019. [DOI: 10.3897/neobiota.49.33723] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Phenotypic variation in the introduced range of an invasive species can be modified by genetic variation, environmental conditions and their interaction, as well as stochastic events like genetic drift. Recent studies found that epigenetic modifications may also contribute to phenotypic variation being independent of genetic changes. Despite gaining profound ecological insights from empirical studies, understanding the relative contributions of these molecular mechanisms behind phenotypic variation has received little attention for invasive plant species in particular.
This review therefore aimed at summarizing and synthesizing information on the genetic and epigenetic basis of phenotypic variation of alien invasive plants in the introduced range and their evolutionary consequences. Transgenerational inheritance of epigenetic modifications was highlighted focusing on its influence on microevolution of the invasive plant species. We presented a comprehensive account of epigenetic regulation of phenotypic variation and its role in plant invasion in the presence of reduced standing genetic variation, inbreeding depression and associated genomic events which have often been observed during introduction and range expansion of an invasive alien species. Finally, taking clues from the studies conducted so far, we proposed a unified framework of future experimental approaches to understand ecological and evolutionary aspects of phenotypic variation. This holistic approach, being aligned to the invasion process in particular (introduction-establishment-spread), was intended to understand the molecular mechanisms of phenotypic variation of an invasive species in its introduced range and to disentangle the effects of standing genetic variation and epigenetic regulation of phenotypic variation.
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Strygina KV, Khlestkina EK. Myc-like transcriptional factors in wheat: structural and functional organization of the subfamily I members. BMC PLANT BIOLOGY 2019; 19:50. [PMID: 30813892 PMCID: PMC6393960 DOI: 10.1186/s12870-019-1639-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
BACKGROUND Myc-like regulatory factors carrying the basic helix-loop-helix (bHLH) domain belong to a large superfamily of transcriptional factors (TFs) present in all eukaryotic kingdoms. In plants, the representatives of this superfamily regulate diverse biological processes including growth and development as well as response to various stresses. As members of the regulatory MBW complexes, they participate in biosynthesis of flavonoids. In wheat, only one member (TaMyc1) of the Myc-like TFs family has been studied, while structural and functional organization of further members remained uncharacterized. From two Myc-subfamilies described recently in the genomes of Triticeae tribe species, we investigated thoroughly the members of the subfamily I which includes the TaMyc1 gene. RESULTS Comparison of the promoter regions of the Myc subfamily I members in wheat suggested their division into two groups (likely homoeologous sets): TaMyc-1 (TaMyc-A1/TaMyc1, TaMyc-B1, TaMyc-D1) and TaMyc-2 (TaMyc-A2 and TaMyc-D2). It was demonstrated that the TaMyc-D1 copy has lost its functionality due to the frame shift mutation. The study of functional features of the other four copies suggested some of them to be involved in the biosynthesis of anthocyanins. In particular, TaMyc-B1 is assumed to be a co-regulator of the gene TaC1-A1 (encoding R2R3-Myb factor) in the MBW regulatory complex activating anthocyanin synthesis in wheat coleoptile. The mRNA levels of the TaMyc-A1, TaMyc-B1, TaMyc-A2 and TaMyc-D2 genes increased significantly in wheat seedlings exposed to osmotic stress. Salinity stress induced expression of TaMyc-B1 and TaMyc-A2, while TaMyc-A1 was repressed. CONCLUSIONS The features of the structural and functional organization of the members of subfamily I of Myc-like TFs in wheat were determined. Myc-like co-regulator (TaMyc-B1) of anthocyanin synthesis in wheat coleoptile was described for the first time. The Myc-encoding genes presumably involved in response to drought and salinity were determined in wheat. The results obtained are important for further manipulations with Myc genes, aimed on increasing wheat adaptability.
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Affiliation(s)
- Ksenia V. Strygina
- Siberian Branch of the Russian Academy of Sciences, Institute of Cytology and Genetics, Lavrentjeva Ave. 10, Novosibirsk, 630090 Russia
| | - Elena K. Khlestkina
- Siberian Branch of the Russian Academy of Sciences, Institute of Cytology and Genetics, Lavrentjeva Ave. 10, Novosibirsk, 630090 Russia
- N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya Str., 42-44, St. Petersburg, 190000 Russia
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Sun L, Alariqi M, Zhu Y, Li J, Li Z, Wang Q, Li Y, Rui H, Zhang X, Jin S. Red fluorescent protein (DsRed2), an ideal reporter for cotton genetic transformation and molecular breeding. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.cj.2018.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Motta-Neto CC, Marques A, Costa GW, Cioffi MB, Bertollo LA, Soares RX, Scortecci KC, Artoni RF, Molina WF. Differential hypomethylation of the repetitive Tol2/Alu-rich sequences in the genome of Bodianus species (Labriformes, Labridae). COMPARATIVE CYTOGENETICS 2018; 12:145-162. [PMID: 29675141 PMCID: PMC5904366 DOI: 10.3897/compcytogen.v12i2.21830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/28/2018] [Indexed: 06/08/2023]
Abstract
Representatives of the order Labriformes show karyotypes of extreme conservatism together with others with high chromosomal diversification. However, the cytological characterization of epigenetic modifications remains unknown for the majority of the species. In the family Labridae, the most abundant fishes on tropical reefs, the genomes of the genus Bodianus Bloch, 1790 have been characterized by the occurrence of a peculiar chromosomal region, here denominated BOD. This region is exceptionally decondensed, heterochromatic, argentophilic, GC-neutral and, in contrast to classical secondary constrictions, shows no signals of hybridization with 18S rDNA probes. In order to characterize the BOD region, the methylation pattern, the distribution of Alu and Tol2 retrotransposons and of 18S and 5S rDNA sites, respectively, were analyzed by Fluorescence In Situ Hybridization (FISH) on metaphase chromosomes of two Bodianus species, B. insularis Gomon & Lubbock, 1980 and B. pulchellus (Poey, 1860). Immunolocalization of the 5-methylcytosine revealed hypermethylated chromosomal regions, dispersed along the entire length of the chromosomes of both species, while the BOD regions exhibited a hypomethylated pattern. Hypomethylation of the BOD region is associated with the precise co-location of Tol2 and Alu elements, suggesting their active participation in the regulatory epigenetic process. This evidence underscores a probable differential methylation action during the cell cycle, as well as the role of Tol2/Alu elements in functional processes of fish genomes.
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Affiliation(s)
- Clóvis C. Motta-Neto
- Center of Biosciences, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Brazil
| | - André Marques
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Gideão W.W.F. Costa
- Center of Biosciences, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Marcelo B. Cioffi
- Department of Genetics and Evolution, Federal University of São Carlos, São Paulo, Brazil
| | - Luiz A.C. Bertollo
- Department of Genetics and Evolution, Federal University of São Carlos, São Paulo, Brazil
| | - Rodrigo X. Soares
- Center of Biosciences, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Kátia C. Scortecci
- Center of Biosciences, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Roberto F. Artoni
- Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Wagner F. Molina
- Center of Biosciences, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Brazil
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Alonso C, Pérez R, Bazaga P, Medrano M, Herrera CM. Within-plant variation in seed size and inflorescence fecundity is associated with epigenetic mosaicism in the shrub Lavandula latifolia (Lamiaceae). ANNALS OF BOTANY 2018; 121:153-160. [PMID: 29186299 PMCID: PMC5786237 DOI: 10.1093/aob/mcx140] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 11/02/2017] [Indexed: 05/30/2023]
Abstract
BACKGROUND AND AIMS Sub-individual variation in traits of homologous structures has multiple ecological consequences for individuals and populations. Assessing the evolutionary significance of such effects requires an improved knowledge of the mechanisms underlying within-plant phenotypic heterogeneity. The hypothesis that continuous within-plant variation in some phenotypic traits can be associated with epigenetic mosaicism was examined. METHODS Fifteen individuals of the long-lived, evergreen Mediterranean shrub Lavandula latifolia were studied. Five widely spaced 'modules', each consisting of a single inflorescence plus all its subtending basal leaves, were collected from each shrub. Genomic DNA was extracted from leaf samples and genome-wide cytosine methylation determined by reversed phase high-performance liquid chromatography (HPLC) with spectrofluorimetric detection. The number and mean mass of seeds produced were determined for each inflorescence. An assessment was made of whether (1) leaves from different modules in the same plant differed significantly in global DNA cytosine methylation, and (2) mosaicism in cytosine methylation contributed to explain variation across modules in number and size of seeds. KEY RESULTS Leaves from different modules in the same plant differed in global DNA cytosine methylation. The magnitude of epigenetic mosaicism was substantial, as the variance in DNA methylation among modules of the same shrub was greater than the variance between individuals. Number and mean mass of seeds produced by individual inflorescences varied within plants and were quadratically related to cytosine methylation of subtending leaves, with an optimum at an intermediate methylation level (approx. 25 %). CONCLUSIONS The results support a causal link between global cytosine methylation of leaves in a module and the size and numbers of seeds produced by the associated inflorescence. It is proposed that variation in global DNA methylation within L. latifolia shrubs may result from the concerted action of plant sectoriality and differential exposure of different plant parts to some environmental factor(s) with a capacity to induce durable epigenetic changes.
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Affiliation(s)
- Conchita Alonso
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio, Sevilla, Spain
| | - Ricardo Pérez
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de La Cartuja, CSIC-US, Avda. Américo Vespucio, Sevilla, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio, Sevilla, Spain
| | - Mónica Medrano
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio, Sevilla, Spain
| | - Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio, Sevilla, Spain
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Liu H, Zhang H, Dong YX, Hao YJ, Zhang XS. DNA METHYLTRANSFERASE1-mediated shoot regeneration is regulated by cytokinin-induced cell cycle in Arabidopsis. THE NEW PHYTOLOGIST 2018; 217:219-232. [PMID: 28960381 DOI: 10.1111/nph.14814] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/19/2017] [Indexed: 05/22/2023]
Abstract
DNA methylation plays a critical role in diverse biological processes of plants. Arabidopsis DNA METHYLTRANSFERASE1 (MET1) represses shoot regeneration by inhibiting WUSCHEL (WUS) expression, which is essential for shoot initiation. However, the upstream signals regulating MET1 expression during this process are unclear. We analyzed the signals regulating MET1 expression using a number of established strategies, such as genetic analysis, confocal microscopy, quantitative real-time PCR and chromatin immunoprecipitation. MET1 expression patterns underwent dynamic changes with the initiation of WUS during shoot regeneration. The cell cycle regulator E2FA was characterized as an upstream factor directly promoting MET1 expression. Moreover, cytokinin promoted MET1 expression partially by enhancing CYCD3 expression. Our findings reveal that MET1-mediated shoot regeneration is regulated by the cytokinin-induced cell cycle, and provide new insights into the regulation of DNA methylation in shoot regeneration.
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Affiliation(s)
- Hui Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Hui Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Yu Xiu Dong
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Yu Jin Hao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
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Li D, Lei Z, Xue J, Zhou G, Hang Y, Sun X. Regulation of FATTY ACID ELONGATION1 expression and production in Brassica oleracea and Capsella rubella. PLANTA 2017; 246:763-778. [PMID: 28674753 DOI: 10.1007/s00425-017-2731-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
The contribution of variations in coding regions or promoters to the changes in FAE1 expression levels have be quantified and compared in parallel by specifically designed swapping constructs. FATTY ACID ELONGATION1 (FAE1) is a key gene in control of erucic acid synthesis in plant seeds. The expression of FAE1 genes in Brassica oleracea and Capsella rubella, representatives of high and low erucic acid species, respectively, was characterized to provide insight into the regulation of very long-chain fatty-acid biosynthesis in seeds. Virtually, no methylation was detected either in B. oleracea or in C. rubella, suggesting that modification of promoter methylation might not be a predominant mechanism. Swapping constructs were specifically designed to quantify and compare the contribution of variations in coding regions or promoters to the changes in FAE1 expression levels in parallel. A significantly higher fold change in erucic acid content was observed when swapping coding regions rather than when swapping promoters, indicating that the coding region is a major determinant of the catalytic power of β-ketoacyl-CoA synthase proteins. Common motifs have been proposed as essential for the preservation of basic gene expression patterns, such as seed-specific expression. However, the occurrence of variation in common cis-elements or the presence of species-specific cis-elements might be plausible mechanisms for changes in the expression levels in different organisms. In addition, conflicting observations in previous reports associated with FAE1 expression are discussed, and we suggest that caution should be taken when selecting a plant transformation vector and in interpreting the results obtained from vectors carrying the CaMV 35S promoter.
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Affiliation(s)
- Dinghong Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China
| | - Zhao Lei
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China
| | - Jiayu Xue
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China
| | - Guangcan Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China
| | - Yueyu Hang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China
| | - Xiaoqin Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1 Qianhu Houcun, Nanjing, 210014, Jiangsu, China.
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Haak DC, Fukao T, Grene R, Hua Z, Ivanov R, Perrella G, Li S. Multilevel Regulation of Abiotic Stress Responses in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1564. [PMID: 29033955 PMCID: PMC5627039 DOI: 10.3389/fpls.2017.01564] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/28/2017] [Indexed: 05/18/2023]
Abstract
The sessile lifestyle of plants requires them to cope with stresses in situ. Plants overcome abiotic stresses by altering structure/morphology, and in some extreme conditions, by compressing the life cycle to survive the stresses in the form of seeds. Genetic and molecular studies have uncovered complex regulatory processes that coordinate stress adaptation and tolerance in plants, which are integrated at various levels. Investigating natural variation in stress responses has provided important insights into the evolutionary processes that shape the integrated regulation of adaptation and tolerance. This review primarily focuses on the current understanding of how transcriptional, post-transcriptional, post-translational, and epigenetic processes along with genetic variation orchestrate stress responses in plants. We also discuss the current and future development of computational tools to identify biologically meaningful factors from high dimensional, genome-scale data and construct the signaling networks consisting of these components.
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Affiliation(s)
- David C. Haak
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, BlacksburgVA, United States
| | - Takeshi Fukao
- Department of Crop and Soil Environmental Sciences, Virginia Tech, BlacksburgVA, United States
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, BlacksburgVA, United States
| | - Zhihua Hua
- Department of Environmental and Plant Biology, Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, AthensOH, United States
| | - Rumen Ivanov
- Institut für Botanik, Heinrich-Heine-Universität DüsseldorfDüsseldorf, Germany
| | - Giorgio Perrella
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, United Kingdom
| | - Song Li
- Department of Crop and Soil Environmental Sciences, Virginia Tech, BlacksburgVA, United States
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Bonnot T, Bancel E, Alvarez D, Davanture M, Boudet J, Pailloux M, Zivy M, Ravel C, Martre P. Grain subproteome responses to nitrogen and sulfur supply in diploid wheat Triticum monococcum ssp. monococcum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017. [PMID: 28628250 DOI: 10.1111/tpj.13615] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Wheat grain storage proteins (GSPs) make up most of the protein content of grain and determine flour end-use value. The synthesis and accumulation of GSPs depend highly on nitrogen (N) and sulfur (S) availability and it is important to understand the underlying control mechanisms. Here we studied how the einkorn (Triticum monococcum ssp. monococcum) grain proteome responds to different amounts of N and S supply during grain development. GSP composition at grain maturity was clearly impacted by nutrition treatments, due to early changes in the rate of GSP accumulation during grain filling. Large-scale analysis of the nuclear and albumin-globulin subproteomes during this key developmental phase revealed that the abundance of 203 proteins was significantly modified by the nutrition treatments. Our results showed that the grain proteome was highly affected by perturbation in the N:S balance. S supply strongly increased the rate of accumulation of S-rich α/β-gliadin and γ-gliadin, and the abundance of several other proteins involved in glutathione metabolism. Post-anthesis N supply resulted in the activation of amino acid metabolism at the expense of carbohydrate metabolism and the activation of transport processes including nucleocytoplasmic transit. Protein accumulation networks were analyzed. Several central actors in the response were identified whose variation in abundance was related to variation in the amounts of many other proteins and are thus potentially important for GSP accumulation. This detailed analysis of grain subproteomes provides information on how wheat GSP composition can possibly be controlled in low-level fertilization condition.
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Affiliation(s)
- Titouan Bonnot
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - Emmanuelle Bancel
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - David Alvarez
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - Marlène Davanture
- UMR GQE, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, 91190, France
| | - Julie Boudet
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - Marie Pailloux
- LIMOS, CNRS, Université Blaise Pascal, Aubière, 63173, France
| | - Michel Zivy
- UMR GQE, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, 91190, France
| | - Catherine Ravel
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - Pierre Martre
- UMR GDEC, INRA, Université Clermont Auvergne, 5 chemin de Beaulieu, Clermont-Ferrand, 63039, France
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Qi X, Wang H, Ning Y, Sun H, Jiang J, Chen S, Fang W, Guan Z, Chen F. Genetic diversity and methylation polymorphism analysis of Chrysanthemum nankingense. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2017.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kalinka A, Achrem M, Poter P. The DNA methylation level against the background of the genome size and t-heterochromatin content in some species of the genus Secale L. PeerJ 2017; 5:e2889. [PMID: 28149679 PMCID: PMC5267573 DOI: 10.7717/peerj.2889] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 12/08/2016] [Indexed: 01/05/2023] Open
Abstract
Methylation of cytosine in DNA is one of the most important epigenetic modifications in eukaryotes and plays a crucial role in the regulation of gene activity and the maintenance of genomic integrity. DNA methylation and other epigenetic mechanisms affect the development, differentiation or the response of plants to biotic and abiotic stress. This study compared the level of methylation of cytosines on a global (ELISA) and genomic scale (MSAP) between the species of the genus Secale. We analyzed whether the interspecific variation of cytosine methylation was associated with the size of the genome (C-value) and the content of telomeric heterochromatin. MSAP analysis showed that S. sylvestre was the most distinct species among the studied rye taxa; however, the results clearly indicated that these differences were not statistically significant. The total methylation level of the studied loci was very similar in all taxa and ranged from 60% in S. strictum ssp. africanum to 66% in S. cereale ssp. segetale, which confirmed the lack of significant differences in the sequence methylation pattern between the pairs of rye taxa. The level of global cytosine methylation in the DNA was not significantly associated with the content of t-heterochromatin and did not overlap with the existing taxonomic rye relationships. The highest content of 5-methylcytosine was found in S. cereale ssp. segetale (83%), while very low in S. strictum ssp. strictum (53%), which was significantly different from the methylation state of all taxa, except for S. sylvestre. The other studied taxa of rye had a similar level of methylated cytosine ranging from 66.42% (S. vavilovii) to 74.41% in (S. cereale ssp. afghanicum). The results obtained in this study are evidence that the percentage of methylated cytosine cannot be inferred solely based on the genome size or t-heterochromatin. This is a significantly more complex issue.
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Affiliation(s)
- Anna Kalinka
- Department of Cell Biology, Faculty of Biology, University of Szczecin, Szczecin, Poland; Molecular Biology and Biotechnology Center, Faculty of Biology, University of Szczecin, Szczecin, Poland
| | - Magdalena Achrem
- Department of Cell Biology, Faculty of Biology, University of Szczecin, Szczecin, Poland; Molecular Biology and Biotechnology Center, Faculty of Biology, University of Szczecin, Szczecin, Poland
| | - Paulina Poter
- Department of Cell Biology, Faculty of Biology, University of Szczecin , Szczecin , Poland
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Das A, Datta S, Thakur S, Shukla A, Ansari J, Sujayanand GK, Chaturvedi SK, Kumar PA, Singh NP. Expression of a Chimeric Gene Encoding Insecticidal Crystal Protein Cry1Aabc of Bacillus thuringiensis in Chickpea ( Cicer arietinum L.) Confers Resistance to Gram Pod Borer ( Helicoverpa armigera Hubner.). FRONTIERS IN PLANT SCIENCE 2017; 8:1423. [PMID: 28871265 PMCID: PMC5566580 DOI: 10.3389/fpls.2017.01423] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/31/2017] [Indexed: 05/08/2023]
Abstract
Domain swapping and generation of chimeric insecticidal crystal protein is an emerging area of insect pest management. The lepidopteran insect pest, gram pod borer (Helicoverpa armigera H.) wreaks havoc to chickpea crop affecting production. Lepidopteran insects were reported to be controlled by Bt (cryI) genes. We designed a plant codon optimized chimeric Bt gene (cry1Aabc) using three domains from three different cry1A genes (domains I, II, and III from cry1Aa, cry1Ab, and cry1Ac, respectively) and expressed it under the control of a constitutive promoter in chickpea (cv. DCP92-3) to assess its effect on gram pod borer. A total of six transgenic chickpea shoots were established by grafting into mature fertile plants. The in vitro regenerated (organogenetic) shoots were selected based on antibiotic kanamycin monosulfate (100 mg/L) with transformation efficiency of 0.076%. Three transgenic events were extensively studied based on gene expression pattern and insect mortality across generations. Protein expression in pod walls, immature seeds and leaves (pre- and post-flowering) were estimated and expression in pre-flowering stage was found higher than that of post-flowering. Analysis for the stable integration, expression and insect mortality (detached leaf and whole plant bioassay) led to identification of efficacious transgenic chickpea lines. The chimeric cry1Aabc expressed in chickpea is effective against gram pod borer and generated events can be utilized in transgenic breeding program.
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Affiliation(s)
- Alok Das
- Division of Plant Biotechnology, ICAR-Indian Institute of Pulses ResearchKanpur, India
| | - Subhojit Datta
- Division of Plant Biotechnology, ICAR-Indian Institute of Pulses ResearchKanpur, India
| | - Shallu Thakur
- Division of Plant Biotechnology, ICAR-Indian Institute of Pulses ResearchKanpur, India
| | - Alok Shukla
- Division of Plant Biotechnology, ICAR-Indian Institute of Pulses ResearchKanpur, India
| | - Jamal Ansari
- Division of Plant Biotechnology, ICAR-Indian Institute of Pulses ResearchKanpur, India
| | - G. K. Sujayanand
- Division of Crop Protection, ICAR-Indian Institute of Pulses ResearchKanpur, India
| | - Sushil K. Chaturvedi
- Division of Crop Improvement, ICAR-Indian Institute of Pulses ResearchKanpur, India
| | - P. A. Kumar
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
| | - N. P. Singh
- Division of Plant Biotechnology, ICAR-Indian Institute of Pulses ResearchKanpur, India
- *Correspondence: N. P. Singh,
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Perrella G, Kaiserli E. Light behind the curtain: photoregulation of nuclear architecture and chromatin dynamics in plants. THE NEW PHYTOLOGIST 2016; 212:908-919. [PMID: 27813089 PMCID: PMC5111779 DOI: 10.1111/nph.14269] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/14/2016] [Indexed: 05/24/2023]
Abstract
Light is a powerful stimulus regulating many aspects of plant development and phenotypic plasticity. Plants sense light through the action of specialized photoreceptor protein families that absorb different wavelengths and intensities of light. Recent discoveries in the area of photobiology have uncovered photoreversible changes in nuclear organization correlated with transcriptional regulation patterns that lead to de-etiolation and photoacclimation. Novel signalling components bridging photoreceptor activation with chromatin remodelling and regulation of gene expression have been discovered. Moreover, coregulated gene loci have been shown to relocate to the nuclear periphery in response to light. The study of photoinduced changes in nuclear architecture is a flourishing area leading to major discoveries that will allow us to better understand how highly conserved mechanisms underlying genomic reprogramming are triggered by environmental and endogenous stimuli. This review aims to discuss fundamental and innovative reports demonstrating how light triggers changes in chromatin and nuclear architecture during photomorphogenesis.
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Affiliation(s)
- Giorgio Perrella
- Institute of Molecular, Cell and Systems BiologyCollege of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems BiologyCollege of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
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Affiliation(s)
- Sonja Grath
- Department of Biology II, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany; ,
| | - John Parsch
- Department of Biology II, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany; ,
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Wang W, Qin Q, Sun F, Wang Y, Xu D, Li Z, Fu B. Genome-Wide Differences in DNA Methylation Changes in Two Contrasting Rice Genotypes in Response to Drought Conditions. FRONTIERS IN PLANT SCIENCE 2016; 7:1675. [PMID: 27877189 PMCID: PMC5099141 DOI: 10.3389/fpls.2016.01675] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/24/2016] [Indexed: 05/26/2023]
Abstract
Differences in drought stress tolerance within diverse rice genotypes have been attributed to genetic diversity and epigenetic alterations. DNA methylation is an important epigenetic modification that influences diverse biological processes, but its effects on rice drought stress tolerance are poorly understood. In this study, methylated DNA immunoprecipitation sequencing and an Affymetrix GeneChip rice genome array were used to profile the DNA methylation patterns and transcriptomes of the drought-tolerant introgression line DK151 and its drought-sensitive recurrent parent IR64 under drought and control conditions. The introgression of donor genomic DNA induced genome-wide DNA methylation changes in DK151 plants. A total of 1190 differentially methylated regions (DMRs) were detected between the two genotypes under normal growth conditions, and the DMR-associated genes in DK151 plants were mainly related to stress response, programmed cell death, and nutrient reservoir activity, which are implicated to constitutive drought stress tolerance. A comparison of the DNA methylation changes in the two genotypes under drought conditions indicated that DK151 plants have a more stable methylome, with only 92 drought-induced DMRs, than IR64 plants with 506 DMRs. Gene ontology analyses of the DMR-associated genes in drought-stressed plants revealed that changes to the DNA methylation status of genotype-specific genes are associated with the epigenetic regulation of drought stress responses. Transcriptome analysis further helped to identify a set of 12 and 23 DMR-associated genes that were differentially expressed in DK151 and IR64, respectively, under drought stress compared with respective controls. Correlation analysis indicated that DNA methylation has various effects on gene expression, implying that it affects gene expression directly or indirectly through diverse regulatory pathways. Our results indicate that drought-induced alterations to DNA methylation may influence an epigenetic mechanism that regulates the expression of unique genes responsible for drought stress tolerance.
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Affiliation(s)
- Wensheng Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
| | - Qiao Qin
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
| | - Fan Sun
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yinxiao Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
| | - Dandan Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
- College of Agronomy, Anhui Agricultural UniversityHefei, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
- Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural SciencesShenzhen, China
| | - Binying Fu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
- Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural SciencesShenzhen, China
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Zhou Y, Yang Y, Zhou X, Chi Y, Fan B, Chen Z. Structural and Functional Characterization of the VQ Protein Family and VQ Protein Variants from Soybean. Sci Rep 2016; 6:34663. [PMID: 27708406 PMCID: PMC5052590 DOI: 10.1038/srep34663] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/13/2016] [Indexed: 11/09/2022] Open
Abstract
Proteins containing the FxxxVQxhTG or VQ motif interact with WRKY transcription factors. Although VQ proteins have been reported in several plants, knowledge about their structures, functions and evolution is still very limited. Here, we report structural and functional analysis of the VQ protein family from soybean. Like Arabidopsis homologues, soybean VQ proteins bind only Group I and IIc WRKY proteins and a substantial number of their genes are responsive to stress-associated phytohormones. Overexpression of some soybean VQ genes in Arabidopsis had strong effects on plant growth, development, disease resistance and heat tolerance. Phylogenetic analysis, sequence alignment and site-directed mutagenesis revealed that the region immediately upstream of the FxxxVQxhTG motif also affects binding to WRKY proteins. Consistent with a larger WRKY-binding VQ domain, soybean VQ22 protein from cultivated soybean contains a 4-amino acid deletion in the region preceding its VQ motif that completely abolishes its binding to WRKY proteins. By contrast, the 4-amino acid deletion is absent in the VQ22 protein from wild soybean species (Glycine soja). Overexpression of wild soybean VQ22 in cultivated soybean inhibited growth, particularly after cold treatment. Thus, the mutation of soybean VQ22 is associated with advantageous phenotypes and may have been positively selected during evolution.
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Affiliation(s)
- Yuan Zhou
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Yan Yang
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Xinjian Zhou
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Yingjun Chi
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
| | - Baofang Fan
- Department of Botany and Plant Pathology, 915 W. State Street, Purdue University, West Lafayette, IN 47907, USA
| | - Zhixiang Chen
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou, 310058, China
- Department of Botany and Plant Pathology, 915 W. State Street, Purdue University, West Lafayette, IN 47907, USA
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Niederhuth CE, Bewick AJ, Ji L, Alabady MS, Kim KD, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, Egesi C, Schmutz J, Grimwood J, Jackson SA, Springer NM, Schmitz RJ. Widespread natural variation of DNA methylation within angiosperms. Genome Biol 2016; 17:194. [PMID: 27671052 DOI: 10.1101/045880] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/09/2016] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species. RESULTS By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species. CONCLUSIONS These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.
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Affiliation(s)
- Chad E Niederhuth
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Adam J Bewick
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Magdy S Alabady
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Qing Li
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Nicholas A Rohr
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Aditi Rambani
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA
| | - John M Burke
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Joshua A Udall
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Chiedozie Egesi
- National Root Crops Research Institute (NRCRI), Umudike, Km 8 Ikot Ekpene Road, PMB 7006, Umuahia, 440001, Nigeria
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Nathan M Springer
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA.
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Niederhuth CE, Bewick AJ, Ji L, Alabady MS, Kim KD, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, Egesi C, Schmutz J, Grimwood J, Jackson SA, Springer NM, Schmitz RJ. Widespread natural variation of DNA methylation within angiosperms. Genome Biol 2016; 17:194. [PMID: 27671052 PMCID: PMC5037628 DOI: 10.1186/s13059-016-1059-0] [Citation(s) in RCA: 313] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/09/2016] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species. RESULTS By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species. CONCLUSIONS These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.
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Affiliation(s)
- Chad E Niederhuth
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Adam J Bewick
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Magdy S Alabady
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Qing Li
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Nicholas A Rohr
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Aditi Rambani
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA
| | - John M Burke
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Joshua A Udall
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Chiedozie Egesi
- National Root Crops Research Institute (NRCRI), Umudike, Km 8 Ikot Ekpene Road, PMB 7006, Umuahia, 440001, Nigeria
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Nathan M Springer
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA.
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Niederhuth CE, Schmitz RJ. Putting DNA methylation in context: from genomes to gene expression in plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:149-156. [PMID: 27590871 DOI: 10.1016/j.bbagrm.2016.08.009] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 08/20/2016] [Accepted: 08/23/2016] [Indexed: 12/26/2022]
Abstract
Plant DNA methylation is its own language, interpreted by the cell to maintain silencing of transposons, facilitate chromatin structure, and to ensure proper expression of some genes. Just as in any language, context is important. Rather than being a simple "on-off switch", DNA methylation has a range of "meanings" dependent upon the underlying sequence and its location in the genome. Differences in the sequence context of individual sites are established, maintained, and interpreted by differing molecular pathways. Varying patterns of methylation within genes and surrounding sequences are associated with a continuous range of expression differences, from silencing to constitutive expression. These often-subtle differences have been pieced together from years of effort, but have taken off with the advent of methods for assessing methylation across entire genomes. Recognizing these patterns and identifying underlying causes is essential for understanding the function of DNA methylation and its systems-wide contribution to a range of processes in plant genomes. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Chad E Niederhuth
- Department of Genetics, The University of Georgia, Athens, GA, 30602, USA
| | - Robert J Schmitz
- Department of Genetics, The University of Georgia, Athens, GA, 30602, USA.
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Lopez M, Halby L, Arimondo PB. DNA Methyltransferase Inhibitors: Development and Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:431-473. [DOI: 10.1007/978-3-319-43624-1_16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Gardiner LJ, Quinton-Tulloch M, Olohan L, Price J, Hall N, Hall A. A genome-wide survey of DNA methylation in hexaploid wheat. Genome Biol 2015; 16:273. [PMID: 26653535 PMCID: PMC4674939 DOI: 10.1186/s13059-015-0838-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/17/2015] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND DNA methylation is an important mechanism of epigenetic gene expression control that can be passed between generations. Here, we use sodium bisulfite treatment and targeted gene enrichment to study genome-wide methylation across the three sub-genomes of allohexaploid wheat. RESULTS While the majority of methylation is conserved across all three genomes we demonstrate that differential methylation exists between the sub-genomes in approximately equal proportions. We correlate sub-genome-specific promoter methylation with decreased expression levels and show that altered growing temperature has a small effect on methylation state, identifying a small but functionally relevant set of methylated genes. Finally, we demonstrate long-term methylation maintenance using a comparison between the D sub-genome of hexaploid wheat and its progenitor Aegilops tauschii. CONCLUSIONS We show that tri-genome methylation is highly conserved with the diploid wheat progenitor while sub-genome-specific methylation shows more variation.
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Affiliation(s)
- Laura-Jayne Gardiner
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Mark Quinton-Tulloch
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Lisa Olohan
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Jonathan Price
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Anthony Hall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
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Zhang P, Wang J, Geng Y, Dai J, Zhong Y, Chen Z, Zhu K, Wang X, Chen S. MSAP-based analysis of DNA methylation diversity in tobacco exposed to different environments and at different development phases. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Dyachenko OV, Tarlachkov SV, Marinitch DV, Shevchuk TV, Buryanov YI. Expression of exogenous DNA methyltransferases: application in molecular and cell biology. BIOCHEMISTRY (MOSCOW) 2015; 79:77-87. [PMID: 24794723 DOI: 10.1134/s0006297914020011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
DNA methyltransferases might be used as powerful tools for studies in molecular and cell biology due to their ability to recognize and modify nitrogen bases in specific sequences of the genome. Methylation of the eukaryotic genome using exogenous DNA methyltransferases appears to be a promising approach for studies on chromatin structure. Currently, the development of new methods for targeted methylation of specific genetic loci using DNA methyltransferases fused with DNA-binding proteins is especially interesting. In the present review, expression of exogenous DNA methyltransferase for purposes of in vivo analysis of the functional chromatin structure along with investigation of the functional role of DNA methylation in cell processes are discussed, as well as future prospects for application of DNA methyltransferases in epigenetic therapy and in plant selection.
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Affiliation(s)
- O V Dyachenko
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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