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Kirov I. Toward Transgene-Free Transposon-Mediated Biological Mutagenesis for Plant Breeding. Int J Mol Sci 2023; 24:17054. [PMID: 38069377 PMCID: PMC10706983 DOI: 10.3390/ijms242317054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Genetic diversity is a key factor for plant breeding. The birth of novel genic and genomic variants is also crucial for plant adaptation in nature. Therefore, the genomes of almost all living organisms possess natural mutagenic mechanisms. Transposable elements (TEs) are a major mutagenic force driving genetic diversity in wild plants and modern crops. The relatively rare TE transposition activity during the thousand-year crop domestication process has led to the phenotypic diversity of many cultivated species. The utilization of TE mutagenesis by artificial and transient acceleration of their activity in a controlled mode is an attractive foundation for a novel type of mutagenesis called TE-mediated biological mutagenesis. Here, I focus on TEs as mutagenic sources for plant breeding and discuss existing and emerging transgene-free approaches for TE activation in plants. Furthermore, I also review the non-randomness of TE insertions in a plant genome and the molecular and epigenetic factors involved in shaping TE insertion preferences. Additionally, I discuss the molecular mechanisms that prevent TE transpositions in germline plant cells (e.g., meiocytes, pollen, egg and embryo cells, and shoot apical meristem), thereby reducing the chances of TE insertion inheritance. Knowledge of these mechanisms can expand the TE activation toolbox using novel gene targeting approaches. Finally, the challenges and future perspectives of plant populations with induced novel TE insertions (iTE plant collections) are discussed.
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Affiliation(s)
- Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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2
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Dziegielewski W, Ziolkowski PA. License to Regulate: Noncoding RNA Special Agents in Plant Meiosis and Reproduction. Front Plant Sci 2021; 12:662185. [PMID: 34489987 PMCID: PMC8418119 DOI: 10.3389/fpls.2021.662185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
The complexity of the subcellular processes that take place during meiosis requires a significant remodeling of cellular metabolism and dynamic changes in the organization of chromosomes and the cytoskeleton. Recently, investigations of meiotic transcriptomes have revealed additional noncoding RNA factors (ncRNAs) that directly or indirectly influence the course of meiosis. Plant meiosis is the point at which almost all known noncoding RNA-dependent regulatory pathways meet to influence diverse processes related to cell functioning and division. ncRNAs have been shown to prevent transposon reactivation, create germline-specific DNA methylation patterns, and affect the expression of meiosis-specific genes. They can also influence chromosome-level processes, including the stimulation of chromosome condensation, the definition of centromeric chromatin, and perhaps even the regulation of meiotic recombination. In many cases, our understanding of the mechanisms underlying these processes remains limited. In this review, we will examine how the different functions of each type of ncRNA have been adopted in plants, devoting attention to both well-studied examples and other possible functions about which we can only speculate for now. We will also briefly discuss the most important challenges in the investigation of ncRNAs in plant meiosis.
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Affiliation(s)
| | - Piotr A. Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
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3
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Debladis E, Lee TF, Huang YJ, Lu JH, Mathioni SM, Carpentier MC, Llauro C, Pierron D, Mieulet D, Guiderdoni E, Chen PY, Meyers BC, Panaud O, Lasserre E. Construction and characterization of a knock-down RNA interference line of OsNRPD1 in rice ( Oryza sativa ssp japonica cv Nipponbare). Philos Trans R Soc Lond B Biol Sci 2020; 375:20190338. [PMID: 32075556 DOI: 10.1098/rstb.2019.0338] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In plants, RNA-directed DNA methylation (RdDM) is a silencing mechanism relying on the production of 24-nt small interfering RNAs (siRNAs) by RNA POLYMERASE IV (Pol IV) to trigger methylation and inactivation of transposable elements (TEs). We present the construction and characterization of osnrpd1, a knock-down RNA interference line of OsNRPD1 gene that encodes the largest subunit of Pol IV in rice (Oryza sativa ssp japonica cv Nipponbare). We show that osnrpd1 displays a lower accumulation of OsNRPD1 transcripts, associated with an overall reduction of 24-nt siRNAs and DNA methylation level in all three contexts, CG, CHG and CHH. We uncovered new insertions of known active TEs, the LTR retrotransposons Tos17 and Lullaby and the long interspersed nuclear element-type retrotransposon Karma. However, we did not observe any clear developmental phenotype, contrary to what was expected for a mutant severely affected in RdDM. In addition, despite the presence of many putatively functional TEs in the rice genome, we found no evidence of in planta global reactivation of transposition. This knock-down of OsNRPD1 likely led to a weakly affected line, with no effect on development and a limited effect on transposition. We discuss the possibility that a knock-out mutation of OsNRPD1 would cause sterility in rice. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
- Emilie Debladis
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France
| | - Tzuu-Fen Lee
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Yan-Jiun Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Jui-Hsien Lu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | | | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France
| | - Christel Llauro
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France
| | - Davy Pierron
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France
| | | | | | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - 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
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Institut Universitaire de France, Paris, France
| | - Eric Lasserre
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France
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Diezma‐Navas L, Pérez‐González A, Artaza H, Alonso L, Caro E, Llave C, Ruiz‐Ferrer V. Crosstalk between epigenetic silencing and infection by tobacco rattle virus in Arabidopsis. Mol Plant Pathol 2019; 20:1439-1452. [PMID: 31274236 PMCID: PMC6792132 DOI: 10.1111/mpp.12850] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
DNA methylation is an important epigenetic mechanism for controlling innate immunity against microbial pathogens in plants. Little is known, however, about the manner in which viral infections interact with DNA methylation pathways. Here we investigate the crosstalk between epigenetic silencing and viral infections in Arabidopsis inflorescences. We found that tobacco rattle virus (TRV) causes changes in the expression of key transcriptional gene silencing factors with RNA-directed DNA methylation activities that coincide with changes in methylation at the whole genome level. Viral susceptibility/resistance was altered in DNA (de)methylation-deficient mutants, suggesting that DNA methylation is an important regulatory system controlling TRV proliferation. We further show that several transposable elements (TEs) underwent transcriptional activation during TRV infection, and that TE regulation likely involved both DNA methylation-dependent and -independent mechanisms. We identified a cluster of disease resistance genes regulated by DNA methylation in infected plants that were enriched for TEs in their promoters. Interestingly, TEs and nearby resistance genes were co-regulated in TRV-infected DNA (de)methylation mutants. Our study shows that DNA methylation contributes to modulate the outcome of viral infections in Arabidopsis, and opens up new possibilities for exploring the role of TE regulation in antiviral defence.
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Affiliation(s)
- Laura Diezma‐Navas
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones BiológicasCSICRamiro de Maeztu 9MadridSpain
- Doctorado en Biotecnología y Recursos Genéticos de Plantas y Microorganismos AsociadosETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid28040MadridSpain
| | - Ana Pérez‐González
- Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Campus de Montegancedo UPM28223Pozuelo de Alarcón, MadridSpain
| | - Haydeé Artaza
- Bionformatic and Statistic Service, Centro de Investigaciones BiológicasCSICRamiro de Maeztu 928040MadridSpain
- Present address:
Department of Clinical ScienceUniversity of Bergen5020BergenNorway
| | - Lola Alonso
- Bionformatic and Statistic Service, Centro de Investigaciones BiológicasCSICRamiro de Maeztu 928040MadridSpain
- Present address:
Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center (CNIO)MadridSpain
| | - Elena Caro
- Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Campus de Montegancedo UPM28223Pozuelo de Alarcón, MadridSpain
| | - César Llave
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones BiológicasCSICRamiro de Maeztu 9MadridSpain
| | - Virginia Ruiz‐Ferrer
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones BiológicasCSICRamiro de Maeztu 9MadridSpain
- Present address:
Department of Plant Physiology, Plant Biotechnology and Molecular Biology Group. Environmental Sciences and Biochemistry SchoolCastilla‐La Mancha UniversityToledoSpain
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Yan H, Bombarely A, Xu B, Frazier TP, Wang C, Chen P, Chen J, Hasing T, Cui C, Zhang X, Zhao B, Huang L. siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass. Biotechnol Biofuels 2018; 11:208. [PMID: 30061930 PMCID: PMC6058383 DOI: 10.1186/s13068-018-1202-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/10/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND Understanding the DNA methylome and its relationship with non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), is essential for elucidating the molecular mechanisms underlying key biological processes in plants. Few studies have examined the functional roles of the DNA methylome in grass species with highly heterozygous polyploid genomes. RESULTS We performed genome-wide DNA methylation profiling in the tetraploid switchgrass (Panicum virgatum L.) cultivar 'Alamo' using bisulfite sequencing. Single-base-resolution methylation patterns were observed in switchgrass leaf and root tissues, which allowed for characterization of the relationship between DNA methylation and mRNA, miRNA, and lncRNA populations. The results of this study revealed that siRNAs positively regulate DNA methylation of the mCHH sites surrounding genes, and that DNA methylation interferes with gene and lncRNA expression in switchgrass. Ninety-six genes covered by differentially methylated regions (DMRs) were annotated by GO analysis as being involved in stimulus-related processes. Functionally, 82% (79/96) of these genes were found to be hypomethylated in switchgrass root tissue. Sequencing analysis of lncRNAs identified two lncRNAs that are potential precursors of miRNAs, which are predicted to target genes that function in cellulose biosynthesis, stress regulation, and stem and root development. CONCLUSIONS This study characterized the DNA methylome in switchgrass and elucidated its relevance to gene and non-coding RNAs. These results provide valuable genomic resources and references that will aid further epigenetic research in this important biofuel crop.
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Affiliation(s)
- Haidong Yan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | | | - Bin Xu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Taylor P. Frazier
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Chengran Wang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Peilin Chen
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Jing Chen
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Tomas Hasing
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | - Chenming Cui
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061 USA
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
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Greaves IK, Eichten SR, Groszmann M, Wang A, Ying H, Peacock WJ, Dennis ES. Twenty-four-nucleotide siRNAs produce heritable trans-chromosomal methylation in F1 Arabidopsis hybrids. Proc Natl Acad Sci U S A 2016; 113:E6895-902. [PMID: 27791153 DOI: 10.1073/pnas.1613623113] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hybrid Arabidopsis plants undergo epigenetic reprogramming producing decreased levels of 24-nt siRNAs and altered patterns of DNA methylation that can affect gene expression. Driving the changes in methylation are the processes trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM). In TCM/TCdM the methylation state of one allele is altered to resemble the other allele. We show that Pol IV-dependent sRNAs are required to establish TCM events. The changes in DNA methylation and the associated changes in sRNA levels in the F1 hybrid can be maintained in subsequent generations and affect hundreds of regions in the F2 epigenome. The inheritance of these altered epigenetic states varies in F2 individuals, resulting in individuals with genetically identical loci displaying different epigenetic states and gene expression profiles. The change in methylation at these regions is associated with the presence of sRNAs. Loci without any sRNA activity can have altered methylation states, suggesting that a sRNA-independent mechanism may also contribute to the altered methylation state of the F1 and F2 generations.
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