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Zou LH, Zhu B, Chen Y, Lu Y, Ramkrishnan M, Xu C, Zhou X, Ding Y, Cho J, Zhou M. Genetic and epigenetic reprogramming in response to internal and external cues by induced transposon mobilization in Moso bamboo. THE NEW PHYTOLOGIST 2024. [PMID: 39238152 DOI: 10.1111/nph.20107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 08/21/2024] [Indexed: 09/07/2024]
Abstract
Long terminal repeat retroelements (LTR-REs) have profound effects on DNA methylation and gene regulation. Despite the vast abundance of LTR-REs in the genome of Moso bamboo (Phyllostachys edulis), an industrial crop in underdeveloped countries, their precise implication of the LTR-RE mobility in stress response and development remains unknown. We investigated the RNA and DNA products of LTR-REs in Moso bamboo under various developmental stages and stressful conditions. Surprisingly, our analyses identified thousands of active LTR-REs, particularly those located near genes involved in stress response and developmental regulation. These genes adjacent to active LTR-REs exhibited an increased expression under stress and are associated with reduced DNA methylation that is likely affected by the induced LTR-REs. Moreover, the analyses of simultaneous mapping of insertions and DNA methylation showed that the LTR-REs effectively alter the epigenetic status of the genomic regions where they inserted, and concomitantly their transcriptional competence which might impact the stress resilience and growth of the host. Our work unveils the unusually strong LTR-RE mobility in Moso bamboo and its close association with (epi)genetic changes, which supports the co-evolution of the parasitic DNAs and host genome in attaining stress tolerance and developmental robustness.
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Affiliation(s)
- Long-Hai Zou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Bailiang Zhu
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Yaxin Chen
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Yaping Lu
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Muthusamy Ramkrishnan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Chao Xu
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Xiaohong Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Yiqian Ding
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Jungnam Cho
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
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Fan W, Wang L, Chu J, Li H, Kim EY, Cho J. Tracing Mobile DNAs: From Molecular to Population Scales. FRONTIERS IN PLANT SCIENCE 2022; 13:837378. [PMID: 35178063 PMCID: PMC8843828 DOI: 10.3389/fpls.2022.837378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Transposable elements (TEs, transposons) are mobile DNAs that are prevalent in most eukaryotic genomes. In plants, their mobility has vastly contributed to genetic diversity which is essential for adaptive changes and evolution of a species. Such mobile nature of transposon has been also actively exploited in plant science research by generating genetic mutants in non-model plant systems. On the other hand, transposon mobilization can bring about detrimental effects to host genomes and they are therefore mostly silenced by the epigenetic mechanisms. TEs have been studied as major silencing targets and acted a main feature in the remarkable growth of the plant epigenetics field. Despite the importance of transposon in plant biology and biotechnology, their mobilization and the underlying mechanisms are largely left unanswered. This is mainly because of the sequence repetitiveness of transposons, which makes their detection and analyses difficult and complicated. Recently, some attempts have been made to develop new experimental methods detecting active transposons and their mobilization behavior. These techniques reveal TE mobility in various levels, including the molecular, cellular, organismal and population scales. In this review, we will highlight the novel technical approaches in the study of mobile genetic elements and discuss how these techniques impacted on the advancement of transposon research and broadened our understanding of plant genome plasticity.
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Affiliation(s)
- Wenwen Fan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ling Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Chu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Eun Yu Kim
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Chinese Academy of Sciences, Shanghai, China
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Epigenetic Modifications in Plant Development and Reproduction. EPIGENOMES 2021; 5:epigenomes5040025. [PMID: 34968249 PMCID: PMC8715465 DOI: 10.3390/epigenomes5040025] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 01/27/2023] Open
Abstract
Plants are exposed to highly fluctuating effects of light, temperature, weather conditions, and many other environmental factors throughout their life. As sessile organisms, unlike animals, they are unable to escape, hide, or even change their position. Therefore, the growth and development of plants are largely determined by interaction with the external environment. The success of this interaction depends on the ability of the phenotype plasticity, which is largely determined by epigenetic regulation. In addition to how environmental factors can change the patterns of genes expression, epigenetic regulation determines how genetic expression changes during the differentiation of one cell type into another and how patterns of gene expression are passed from one cell to its descendants. Thus, one genome can generate many ‘epigenomes’. Epigenetic modifications acquire special significance during the formation of gametes and plant reproduction when epigenetic marks are eliminated during meiosis and early embryogenesis and later reappear. However, during asexual plant reproduction, when meiosis is absent or suspended, epigenetic modifications that have arisen in the parental sporophyte can be transmitted to the next clonal generation practically unchanged. In plants that reproduce sexually and asexually, epigenetic variability has different adaptive significance. In asexuals, epigenetic regulation is of particular importance for imparting plasticity to the phenotype when, apart from mutations, the genotype remains unchanged for many generations of individuals. Of particular interest is the question of the possibility of transferring acquired epigenetic memory to future generations and its potential role for natural selection and evolution. All these issues will be discussed to some extent in this review.
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Lizamore D, Bicknell R, Winefield C. Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus. BMC Genomics 2021; 22:676. [PMID: 34544372 PMCID: PMC8454084 DOI: 10.1186/s12864-021-07973-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 09/03/2021] [Indexed: 11/10/2022] Open
Abstract
Background Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour are the result of genetic changes caused by transposable elements. Additionally, epiallele formation may play a role in determining geo-specific (‘terroir’) differences in grapes and thus ultimately in wine. This genomic plasticity might be co-opted for crop improvement via somatic embryogenesis, but that depends on a species-specific understanding of the epigenetic regulation of transposable element (TE) expression and silencing in these cultures. For this reason, we used whole-genome bisulphite sequencing, mRNA sequencing and small RNA sequencing to study the epigenetic status and expression of TEs in embryogenic callus, in comparison with leaf tissue. Results We found that compared with leaf tissue, grapevine embryogenic callus cultures accumulate relatively high genome-wide CHH methylation, particularly across heterochromatic regions. This de novo methylation is associated with an abundance of transcripts from highly replicated TE families, as well as corresponding 24 nt heterochromatic siRNAs. Methylation in the TE-specific CHG context was relatively low over TEs located within genes, and the expression of TE loci within genes was highly correlated with the expression of those genes. Conclusions This multi-‘omics analysis of grapevine embryogenic callus in comparison with leaf tissues reveals a high level of genome-wide transcription of TEs accompanied by RNA-dependent DNA methylation of these sequences in trans. This provides insight into the genomic conditions underlying somaclonal variation and epiallele formation in plants regenerated from embryogenic cultures, which is an important consideration when using these tissues for plant propagation and genetic improvement. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07973-9.
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Affiliation(s)
| | - Ross Bicknell
- Plant and Food Research Ltd, Lincoln, Canterbury, New Zealand
| | - Chris Winefield
- Department Wine, Food and Molecular Biosciences, Lincoln University, Canterbury, New Zealand.
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RNA-directed DNA methylation prevents rapid and heritable reversal of transposon silencing under heat stress in Zea mays. PLoS Genet 2021; 17:e1009326. [PMID: 34125827 PMCID: PMC8224964 DOI: 10.1371/journal.pgen.1009326] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 06/24/2021] [Accepted: 05/28/2021] [Indexed: 12/12/2022] Open
Abstract
In large complex plant genomes, RNA-directed DNA methylation (RdDM) ensures that epigenetic silencing is maintained at the boundary between genes and flanking transposable elements. In maize, RdDM is dependent on Mediator of Paramutation1 (Mop1), a gene encoding a putative RNA dependent RNA polymerase. Here we show that although RdDM is essential for the maintenance of DNA methylation of a silenced MuDR transposon in maize, a loss of that methylation does not result in a restoration of activity. Instead, heritable maintenance of silencing is maintained by histone modifications. At one terminal inverted repeat (TIR) of this element, heritable silencing is mediated via histone H3 lysine 9 dimethylation (H3K9me2), and histone H3 lysine 27 dimethylation (H3K27me2), even in the absence of DNA methylation. At the second TIR, heritable silencing is mediated by histone H3 lysine 27 trimethylation (H3K27me3), a mark normally associated with somatically inherited gene silencing. We find that a brief exposure of high temperature in a mop1 mutant rapidly reverses both of these modifications in conjunction with a loss of transcriptional silencing. These reversals are heritable, even in mop1 wild-type progeny in which methylation is restored at both TIRs. These observations suggest that DNA methylation is neither necessary to maintain silencing, nor is it sufficient to initiate silencing once has been reversed. However, given that heritable reactivation only occurs in a mop1 mutant background, these observations suggest that DNA methylation is required to buffer the effects of environmental stress on transposable elements. Most plant genomes are mostly transposable elements (TEs), most of which are held in check by modifications of both DNA and histones. The bulk of silenced TEs are associated with methylated DNA and histone H3 lysine 9 dimethylation (H3K9me2). In contrast, epigenetically silenced genes are often associated with histone lysine 27 trimethylation (H3K27me3). Although stress can affect each of these modifications, plants are generally competent to rapidly reset them following that stress. Here we demonstrate that although DNA methylation is not required to maintain silencing of the MuDR element, it is essential for preventing heat-induced, stable and heritable changes in both H3K9me2 and H3K27me3 at this element, and for concomitant changes in transcriptional activity. These finding suggest that RdDM acts to buffer the effects of heat on silenced transposable elements, and that a loss of DNA methylation under conditions of stress can have profound and long-lasting effects on epigenetic silencing in maize.
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Liu L, Wang T. Male gametophyte development in flowering plants: A story of quarantine and sacrifice. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153365. [PMID: 33548696 DOI: 10.1016/j.jplph.2021.153365] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/06/2021] [Accepted: 01/06/2021] [Indexed: 05/19/2023]
Abstract
Over 160 years ago, scientists made the first microscopic observations of angiosperm pollen. Unlike in animals, male meiosis in angiosperms produces a haploid microspore that undergoes one asymmetric division to form a vegetative cell and a generative cell. These two cells have distinct fates: the vegetative cell exits the cell cycle and elongates to form a tip-growing pollen tube; the generative cell divides once more in the pollen grain or within the growing pollen tube to form a pair of sperm cells. The concept that male germ cells are less active than the vegetative cell came from biochemical analyses and pollen structure anatomy early in the last century and is supported by the pollen transcriptome data of the last decade. However, the mechanism of how and when the transcriptional repression in male germ cells occurs is still not fully understood. In this review, we provide a brief account of the cytological and metabolic differentiation between the vegetative cell and male germ cells, with emphasis on the role of temporary callose walls, dynamic nuclear pore density, transcription repression, and histone variants. We further discuss the intercellular movement of small interfering RNA (siRNA) derived from transposable elements (TEs) and reexamine the function of TE expression in male germ cells.
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Affiliation(s)
- Lingtong Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Tai Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China.
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Kirov I, Omarov M, Merkulov P, Dudnikov M, Gvaramiya S, Kolganova E, Komakhin R, Karlov G, Soloviev A. Genomic and Transcriptomic Survey Provides New Insight into the Organization and Transposition Activity of Highly Expressed LTR Retrotransposons of Sunflower ( Helianthus annuus L.). Int J Mol Sci 2020; 21:E9331. [PMID: 33297579 PMCID: PMC7730604 DOI: 10.3390/ijms21239331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 12/21/2022] Open
Abstract
LTR retrotransposons (RTEs) play a crucial role in plant genome evolution and adaptation. Although RTEs are generally silenced in somatic plant tissues under non-stressed conditions, some expressed RTEs (exRTEs) escape genome defense mechanisms. As our understanding of exRTE organization in plants is rudimentary, we systematically surveyed the genomic and transcriptomic organization and mobilome (transposition) activity of sunflower (Helianthus annuus L.) exRTEs. We identified 44 transcribed RTEs in the sunflower genome and demonstrated their distinct genomic features: more recent insertion time, longer open reading frame (ORF) length, and smaller distance to neighboring genes. We showed that GAG-encoding ORFs are present at significantly higher frequencies in exRTEs, compared with non-expressed RTEs. Most exRTEs exhibit variation in copy number among sunflower cultivars and one exRTE Gagarin produces extrachromosomal circular DNA in seedling, demonstrating recent and ongoing transposition activity. Nanopore direct RNA sequencing of full-length RTE RNA revealed complex patterns of alternative splicing in RTE RNAs, resulting in isoforms that carry ORFs for distinct RTE proteins. Together, our study demonstrates that tens of expressed sunflower RTEs with specific genomic organization shape the hidden layer of the transcriptome, pointing to the evolution of specific strategies that circumvent existing genome defense mechanisms.
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Affiliation(s)
- Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia
| | - Murad Omarov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
- Faculty of Computer Science, National Research University Higher School of Economics, Pokrovsky Boulvar 11, 109028 Moscow, Russia
| | - Pavel Merkulov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
| | - Maxim Dudnikov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia
| | - Sofya Gvaramiya
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
| | - Elizaveta Kolganova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
| | - Roman Komakhin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
| | - Gennady Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
| | - Alexander Soloviev
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
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Benoit M. In the Transcripts: Long-Read Transcriptomics Enables a Novel Type of Transposable Element Annotation in Plants. THE PLANT CELL 2020; 32:2661-2662. [PMID: 32665309 PMCID: PMC7474303 DOI: 10.1105/tpc.20.00523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Matthias Benoit
- Howard Hughes Medical InstituteCold Spring Harbor LaboratoryCold Spring Harbor, New York
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Panda K, Slotkin RK. Long-Read cDNA Sequencing Enables a "Gene-Like" Transcript Annotation of Transposable Elements. THE PLANT CELL 2020; 32:2687-2698. [PMID: 32647069 PMCID: PMC7474280 DOI: 10.1105/tpc.20.00115] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/11/2020] [Accepted: 06/25/2020] [Indexed: 05/05/2023]
Abstract
Transcript-based annotations of genes facilitate both genome-wide analyses and detailed single-locus research. In contrast, transposable element (TE) annotations are rudimentary, consisting of information only on TE location and type. The repetitiveness and limited annotation of TEs prevent the ability to distinguish between potentially functional expressed elements and degraded copies. To improve genome-wide TE bioinformatics, we performed long-read sequencing of cDNAs from Arabidopsis (Arabidopsis thaliana) lines deficient in multiple layers of TE repression. These uniquely mapping transcripts were used to identify the set of TEs able to generate polyadenylated RNAs and create a new transcript-based annotation of TEs that we have layered upon the existing high-quality community standard annotation. We used this annotation to reduce the bioinformatic complexity associated with multimapping reads from short-read RNA sequencing experiments, and we show that this improvement is expanded in a TE-rich genome such as maize (Zea mays). Our TE annotation also enables the testing of specific standing hypotheses in the TE field. We demonstrate that inaccurate TE splicing does not trigger small RNA production, and the cell more strongly targets DNA methylation to TEs that have the potential to make mRNAs. This work provides a transcript-based TE annotation for Arabidopsis and maize, which serves as a blueprint to reduce the bioinformatic complexity associated with repetitive TEs in any organism.
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Affiliation(s)
- Kaushik Panda
- Donald Danforth Plant Science Center, St. Louis, 63132 Missouri
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, 63132 Missouri
- Division of Biological Sciences, University of Missouri, Columbia, 63132 Missouri
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Nieto Feliner G, Casacuberta J, Wendel JF. Genomics of Evolutionary Novelty in Hybrids and Polyploids. Front Genet 2020; 11:792. [PMID: 32849797 PMCID: PMC7399645 DOI: 10.3389/fgene.2020.00792] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/03/2020] [Indexed: 12/15/2022] Open
Abstract
It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically recognized as significant in speciation and adaptation, recognition of the importance of interspecific gene flow has dramatically increased during the genomics era, concomitant with an unending flood of empirical examples, with or without genome doubling. Interspecific gene flow is thus increasingly thought to lead to evolutionary innovation and diversification, via adaptive introgression, homoploid hybrid speciation and allopolyploid speciation. Less well understood, however, are the suite of genetic and genomic mechanisms set in motion by the merger of differentiated genomes, and the temporal scale over which recombinational complexity mediated by gene flow might be expressed and exposed to natural selection. We focus on these issues here, considering the types of molecular genetic and genomic processes that might be set in motion by the saltational event of genome merger between two diverged species, either with or without genome doubling, and how these various processes can contribute to novel phenotypes. Genetic mechanisms include the infusion of new alleles and the genesis of novel structural variation including translocations and inversions, homoeologous exchanges, transposable element mobilization and novel insertional effects, presence-absence variation and copy number variation. Polyploidy generates massive transcriptomic and regulatory alteration, presumably set in motion by disrupted stoichiometries of regulatory factors, small RNAs and other genome interactions that cascade from single-gene expression change up through entire networks of transformed regulatory modules. We highlight both these novel combinatorial possibilities and the range of temporal scales over which such complexity might be generated, and thus exposed to natural selection and drift.
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Affiliation(s)
- Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico, CSIC, Madrid, Spain
| | - Josep Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Barcelona, Spain
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
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Wang D, Zhang J, Zuo T, Zhao M, Lisch D, Peterson T. Small RNA-Mediated De Novo Silencing of Ac/Ds Transposons Is Initiated by Alternative Transposition in Maize. Genetics 2020; 215:393-406. [PMID: 32317287 PMCID: PMC7268987 DOI: 10.1534/genetics.120.303264] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 04/15/2020] [Indexed: 12/26/2022] Open
Abstract
Although transposable elements (TEs) comprise a major fraction of many higher eukaryotic genomes, most TEs are silenced by host defense mechanisms. The means by which otherwise active TEs are recognized and silenced remains poorly understood. Here we analyzed two independent cases of spontaneous silencing of the active maize Ac/Ds transposon system. This silencing is initiated by alternative transposition, a type of aberrant transposition event that engages the termini of two nearby separate TEs. Alternative transposition during DNA replication can generate Composite Insertions that contain inverted duplications of the transposon sequences. We show that the inverted duplications of two Composite Insertions are transcribed to produce double-stranded RNAs that trigger the production of two distinct classes of small interfering RNAs: a 24-nt class complementary to the TE terminal inverted repeats and noncoding subterminal regions, and a 21- to 22-nt class corresponding to the TE transcribed regions. Plants containing these small interfering RNA-generating Composite Insertions exhibit decreased levels of Ac transcript and heritable repression of Ac/Ds transposition. Further, we demonstrate that Composite Insertions can heritably silence otherwise active elements in trans This study documents the first case of transposon silencing induced by alternative transposition and may represent a general initiating mechanism for silencing of DNA transposons.
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Affiliation(s)
- Dafang Wang
- Division of Math and Sciences, Delta State University, Cleveland, Mississippi 38733-0001
| | - Jianbo Zhang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011-3260
| | - Tao Zuo
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011-3260
| | - Meixia Zhao
- Department of Biology, Miami University, Oxford, Ohio 45056
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Thomas Peterson
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011-3260
- Department of Agronomy, Iowa State University, Ames, Iowa 50011-3260
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Burgess D, Li H, Zhao M, Kim SY, Lisch D. Silencing of Mutator Elements in Maize Involves Distinct Populations of Small RNAs and Distinct Patterns of DNA Methylation. Genetics 2020; 215:379-391. [PMID: 32229532 PMCID: PMC7268996 DOI: 10.1534/genetics.120.303033] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/24/2020] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) are a ubiquitous feature of plant genomes. Because of the threat they post to genome integrity, most TEs are epigenetically silenced. However, even closely related plant species often have dramatically different populations of TEs, suggesting periodic rounds of activity and silencing. Here, we show that the process of de novo methylation of an active element in maize involves two distinct pathways, one of which is directly implicated in causing epigenetic silencing and one of which is the result of that silencing. Epigenetic changes involve changes in gene expression that can be heritably transmitted to daughter cells in the absence of changes in DNA sequence. Epigenetics has been implicated in phenomena as diverse as development, stress response, and carcinogenesis. A significant challenge facing those interested in investigating epigenetic phenomena is determining causal relationships between DNA methylation, specific classes of small RNAs, and associated changes in gene expression. Because they are the primary targets of epigenetic silencing in plants and, when active, are often targeted for de novo silencing, TEs represent a valuable source of information about these relationships. We use a naturally occurring system in which a single TE can be heritably silenced by a single derivative of that TE. By using this system it is possible to unravel causal relationships between different size classes of small RNAs, patterns of DNA methylation, and heritable silencing. Here, we show that the long terminal inverted repeats within Zea mays MuDR transposons are targeted by distinct classes of small RNAs during epigenetic silencing that are dependent on distinct silencing pathways, only one of which is associated with transcriptional silencing of the transposon. Further, these small RNAs target distinct regions of the terminal inverted repeats, resulting in different patterns of cytosine methylation with different functional consequences with respect to epigenetic silencing and the heritability of that silencing.
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Affiliation(s)
- Diane Burgess
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Hong Li
- Bayer US, Crop Science, Chesterfield, Missouri 63017
| | - Meixia Zhao
- Department of Biology, Miami University, Oxford, Ohio 45056
| | - Sang Yeol Kim
- US Department of Agriculture, Agricultural Research Service, Urbana, Illinois 61801
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
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13
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Warman C, Panda K, Vejlupkova Z, Hokin S, Unger-Wallace E, Cole RA, Chettoor AM, Jiang D, Vollbrecht E, Evans MMS, Slotkin RK, Fowler JE. High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements. PLoS Genet 2020; 16:e1008462. [PMID: 32236090 PMCID: PMC7112179 DOI: 10.1371/journal.pgen.1008462] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/27/2020] [Indexed: 12/20/2022] Open
Abstract
In flowering plants, gene expression in the haploid male gametophyte (pollen) is essential for sperm delivery and double fertilization. Pollen also undergoes dynamic epigenetic regulation of expression from transposable elements (TEs), but how this process interacts with gene expression is not clearly understood. To explore relationships among these processes, we quantified transcript levels in four male reproductive stages of maize (tassel primordia, microspores, mature pollen, and sperm cells) via RNA-seq. We found that, in contrast with vegetative cell-limited TE expression in Arabidopsis pollen, TE transcripts in maize accumulate as early as the microspore stage and are also present in sperm cells. Intriguingly, coordinate expression was observed between highly expressed protein-coding genes and their neighboring TEs, specifically in mature pollen and sperm cells. To investigate a potential relationship between elevated gene transcript level and pollen function, we measured the fitness cost (male-specific transmission defect) of GFP-tagged coding sequence insertion mutations in over 50 genes identified as highly expressed in the pollen vegetative cell, sperm cell, or seedling (as a sporophytic control). Insertions in seedling genes or sperm cell genes (with one exception) exhibited no difference from the expected 1:1 transmission ratio. In contrast, insertions in over 20% of vegetative cell genes were associated with significant reductions in fitness, showing a positive correlation of transcript level with non-Mendelian segregation when mutant. Insertions in maize gamete expressed2 (Zm gex2), the sole sperm cell gene with measured contributions to fitness, also triggered seed defects when crossed as a male, indicating a conserved role in double fertilization, given the similar phenotype previously demonstrated for the Arabidopsis ortholog GEX2. Overall, our study demonstrates a developmentally programmed and coordinated transcriptional activation of TEs and genes in pollen, and further identifies maize pollen as a model in which transcriptomic data have predictive value for quantitative phenotypes.
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Affiliation(s)
- Cedar Warman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Kaushik Panda
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Zuzana Vejlupkova
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Sam Hokin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
| | - Erica Unger-Wallace
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Rex A. Cole
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Antony M. Chettoor
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
| | - Duo Jiang
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
| | - Erik Vollbrecht
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
- Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, United States of America
- Interdepartmental Genetics, Iowa State University, Ames, Iowa, United States of America
| | - Matthew M. S. Evans
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
| | - R. Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - John E. Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
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14
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Zhao D, Hamilton JP, Vaillancourt B, Zhang W, Eizenga GC, Cui Y, Jiang J, Buell CR, Jiang N. The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum. Nucleic Acids Res 2019; 46:2380-2397. [PMID: 29365184 PMCID: PMC5861414 DOI: 10.1093/nar/gky025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/18/2018] [Indexed: 12/11/2022] Open
Abstract
Acquisition and rearrangement of host genes by transposable elements (TEs) is an important mechanism to increase gene diversity as exemplified by the ∼3000 Pack-Mutator-like TEs in the rice genome which have acquired gene sequences (Pack-MULEs), yet remain enigmatic. To identify signatures of functioning Pack-MULEs and Pack-MULE evolution, we generated transcriptome, translatome, and epigenome datasets and compared Pack-MULEs to genes and other TE families. Approximately 40% of Pack-MULEs were transcribed with 9% having translation evidence, clearly distinguishing them from other TEs. Pack-MULEs exhibited a unique expression profile associated with specificity in reproductive tissues that may be associated with seed traits. Expressed Pack-MULEs resemble regular protein-coding genes as exhibited by a low level of DNA methylation, association with active histone marks and DNase I hypersensitive sites, and an absence of repressive histone marks, suggesting that a substantial fraction of Pack-MULEs are potentially functional in vivo. Interestingly, the expression capacity of Pack-MULEs is independent of the local genomic environment, and the insertion and expression of Pack-MULEs may have altered the local chromosomal expression pattern as well as counteracted the impact of recombination on chromosomal base composition, which has profound consequences on the evolution of chromosome structure.
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Affiliation(s)
- Dongyan Zhao
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Wenli Zhang
- Department of Horticulture, University of Wisconsin, Madison, WI 53705, USA.,State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Georgia C Eizenga
- USDA-ARS Dale Bumpers National Rice Research Center, 2890 Highway 130 East, Stuttgart, AR 72160, USA
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA
| | - Jiming Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI 48824, USA
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15
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Sanchez DH, Gaubert H, Yang W. Evidence of developmental escape from transcriptional gene silencing in MESSI retrotransposons. THE NEW PHYTOLOGIST 2019; 223:950-964. [PMID: 31063594 DOI: 10.1111/nph.15896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/12/2019] [Indexed: 05/04/2023]
Abstract
Transposable elements (TEs) are ubiquitous genomic features. 'Copy-and-paste' long-terminal-repeat (LTR) retrotransposons have been particularly successful during evolution of the plant kingdom, representing a substantial proportion of genomes. For survival in copious numbers, these TEs may have evolved replicative mobilization strategies that circumvented hosts' epigenetic silencing. Stressful circumstances are known to trigger the majority of known mobilizing plant retrotransposons, leading to the idea that most are activated by environmental signals. However, previous research revealed that plant developmental programs include steps of silencing relaxation, suggesting that developmental signals may also be of importance for thriving parasitic elements. Here, we uncover an unusual family of giant LTR retrotransposons from the Solanum clade, named MESSI, with transcriptional competence in shoot apical meristems of tomato. Despite being recognized and targeted by the host epigenetic surveillance, this family is activated in specific meristematic areas fundamental for plant shoot development, which are involved in meristem formation and maintenance. Our work provides initial evidence that some retrotransposons may evolve developmentally associated escape strategies to overcome transcriptional gene silencing in vegetative tissues contributing to the host's next generation. This implies that not only environmental but also developmental signals could be exploited by selfish elements for survival within the plant kingdom.
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Affiliation(s)
- Diego H Sanchez
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR, UK
| | - Hervé Gaubert
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR, UK
| | - Weibing Yang
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR, UK
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16
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He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife 2019; 8:42530. [PMID: 31135340 PMCID: PMC6594752 DOI: 10.7554/elife.42530] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/26/2019] [Indexed: 01/09/2023] Open
Abstract
Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell - vegetative cell (VC) - of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation.
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Affiliation(s)
- Shengbo He
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Martin Vickers
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Jingyi Zhang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
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17
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Retrotransposon expression in response to in vitro inoculation with two fungal pathogens of Scots pine (Pinus sylvestris L.). BMC Res Notes 2019; 12:243. [PMID: 31036050 PMCID: PMC6489336 DOI: 10.1186/s13104-019-4275-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 04/22/2019] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Conifer genomes show high genetic diversity in intergenic regions that contain diverse sets of transposable elements with dominating long terminal repeat (LTR) retrotransposons (RE). Transcription of RE in response to environmental stimuli could produce various types of regulatory non-coding RNAs, but global genomic methylation changes could result in a coincidental expression of normally silent genomic regions. Expression of several RE families was evaluated in Scots pine seedlings after controlled inoculations with two fungal species that exhibit different modes of pathogenicity (necrotrophic and likely biotrophic); data compared to the overall RE distribution in genome. Recognition of regulatory non-coding RNA involved in host-pathogen interplay could be valuable in understanding defence mechanisms of perennial plants. RESULTS In the case of necrotrophic fungi Heterobasidion annosum (HA), short activation followed by restriction of RE expression was revealed after inoculation and during the spread of the pathogen. After inoculation with Lophodermium seditiosum (LS), an early increase in RE expression was revealed with the spread of the pathogen and subsequent transcription rise in all seedlings. Our observations indicate that in the complex plant genome multiple RE families constitutively express in response to pathogen invasion and these sequences could undergo regulation related to host response or pathogen influence.
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18
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Pierron F, Daffe G, Lambert P, Couture P, Baudrimont M. Retrotransposon methylation and activity in wild fish (A. anguilla): A matter of size. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 245:494-503. [PMID: 30458379 DOI: 10.1016/j.envpol.2018.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 06/09/2023]
Abstract
Understanding how organisms cope with global change is a major question in many fields of biology. Mainly, understanding the molecular mechanisms supporting rapid phenotypic changes of organisms in response to stress and linking stress-induced molecular events to adaptive or adverse outcomes at the individual or population levels remain a major challenge in evolutionary biology, ecology or ecotoxicology. In this view, the present study aimed to test (i) whether environmental factors, especially pollutants, can trigger changes in the activity of retrotransposons (RTs) in wild fish and (ii) if changes in RT DNA methylation or transcription levels can be linked to modifications at the individual level. RTs are genetic elements that have the ability to replicate and integrate elsewhere in the genome. Although RTs are mainly quiescent during normal development, they can be experimentally activated under life-threatening conditions, affecting the fitness of their host. Wild eels were collected in four sampling sites presenting differing levels of contamination. The methylation level and the transcriptional activity of two RTs and two genes involved in development and cell differentiation were analyzed in fish liver in addition to the determination of fish contaminants levels and diverse growth and morphometric indices. An up-regulation of RTs associated to lower methylation levels and lower growth indices were observed in highly contaminated fish. Our results suggest that RT activation in fish experiencing stress conditions could have both detrimental and beneficial implications, affecting fish growth but promoting resistance to environmental stressors such as pollutants.
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Affiliation(s)
| | - Guillemine Daffe
- CNRS, Université de Bordeaux, Observatoire Aquitain des Sciences de l'Univers, UMS 2567 POREA, Allée Geoffroy Saint Hilaire, F-33615, Pessac, France
| | - Patrick Lambert
- Institut National de Recherche en Sciences et Technologies pour l'Environnement et l'Agriculture (IRSTEA), équipe Poissons Migrateurs Amphihalins (PMA), Cestas, France
| | - Patrice Couture
- Institut national de La Recherche Scientifique (INRS), Centre Eau Terre Environnement, 490 rue de La Couronne, Québec, QC G1K 9A9, Canada
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19
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Ni JZ, Kalinava N, Mendoza SG, Gu SG. The spatial and temporal dynamics of nuclear RNAi-targeted retrotransposon transcripts in Caenorhabditis elegans. Development 2018; 145:dev167346. [PMID: 30254142 PMCID: PMC6215403 DOI: 10.1242/dev.167346] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 09/17/2018] [Indexed: 02/03/2023]
Abstract
Nuclear RNA interference provides a unique approach to the study of RNA-mediated transgenerational epigenetic inheritance. A paradox in the field is that expression of target loci is necessary for the initiation and maintenance of their silencing. How expression and repression are coordinated during animal development is poorly understood. To resolve this gap, we took imaging, deep-sequencing and genetic approaches towards delineating the developmental regulation and subcellular localization of RNA transcripts of two representative endogenous targets, the LTR retrotransposons Cer3 and Cer8. By examining wild-type worms and a collection of mutant strains, we found that the expression and silencing cycle of Cer3 and Cer8 is coupled with embryonic and germline development. Strikingly, endogenous targets exhibit a hallmark of nuclear enrichment of their RNA transcripts. In addition, germline and somatic repressions of Cer3 have different genetic requirements for three heterochromatin enzymes, MET-2, SET-25 and SET-32, in conjunction with the nuclear Argonaute protein HRDE-1. These results provide the first comprehensive cellular and developmental characterization of nuclear RNAi activities throughout the animal reproductive cycle.
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Affiliation(s)
- Julie Zhouli Ni
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Natallia Kalinava
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sofia Galindo Mendoza
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sam Guoping Gu
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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20
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Shaping Plant Adaptability, Genome Structure and Gene Expression through Transposable Element Epigenetic Control: Focus on Methylation. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8090180] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In plants, transposable elements (TEs) represent a large fraction of the genome, with potential to alter gene expression and produce genomic rearrangements. Epigenetic control of TEs is often used to stop unrestricted movement of TEs that would result in detrimental effects due to insertion in essential genes. The current review focuses on the effects of methylation on TEs and their genomic context, and how this type of epigenetic control affects plant adaptability when plants are faced with different stresses and changes. TEs mobilize in response to stress elicitors, including biotic and abiotic cues, but also developmental transitions and ‘genome shock’ events like polyploidization. These events transitionally lift TE repression, allowing TEs to move to new genomic locations. When TEs fall close to genes, silencing through methylation can spread to nearby genes, resulting in lower gene expression. The presence of TEs in gene promoter regions can also confer stress inducibility modulated through alternative methylation and demethylation of the TE. Bursts of transposition triggered by events of genomic shock can increase genome size and account for differences seen during polyploidization or species divergence. Finally, TEs have evolved several mechanisms to suppress their own repression, including the use of microRNAs to control genes that promote methylation. The interplay between silencing, transient TE activation, and purifying selection allows the genome to use TEs as a reservoir of potential beneficial modifications but also keeps TEs under control to stop uncontrolled detrimental transposition.
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21
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Anderson SN, Zynda GJ, Song J, Han Z, Vaughn MW, Li Q, Springer NM. Subtle Perturbations of the Maize Methylome Reveal Genes and Transposons Silenced by Chromomethylase or RNA-Directed DNA Methylation Pathways. G3 (BETHESDA, MD.) 2018; 8:1921-1932. [PMID: 29618467 PMCID: PMC5982821 DOI: 10.1534/g3.118.200284] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/03/2018] [Indexed: 01/17/2023]
Abstract
DNA methylation is a chromatin modification that can provide epigenetic regulation of gene and transposon expression. Plants utilize several pathways to establish and maintain DNA methylation in specific sequence contexts. The chromomethylase (CMT) genes maintain CHG (where H = A, C or T) methylation. The RNA-directed DNA methylation (RdDM) pathway is important for CHH methylation. Transcriptome analysis was performed in a collection of Zea mays lines carrying mutant alleles for CMT or RdDM-associated genes. While the majority of the transcriptome was not affected, we identified sets of genes and transposon families sensitive to context-specific decreases in DNA methylation in mutant lines. Many of the genes that are up-regulated in CMT mutant lines have high levels of CHG methylation, while genes that are differentially expressed in RdDM mutants are enriched for having nearby mCHH islands, implicating context-specific DNA methylation in the regulation of expression for a small number of genes. Many genes regulated by CMTs exhibit natural variation for DNA methylation and transcript abundance in a panel of diverse inbred lines. Transposon families with differential expression in the mutant genotypes show few defining features, though several families up-regulated in RdDM mutants show enriched expression in endosperm tissue, highlighting the potential importance for this pathway during reproduction. Taken together, our findings suggest that while the number of genes and transposon families whose expression is reproducibly affected by mild perturbations in context-specific methylation is small, there are distinct patterns for loci impacted by RdDM and CMT mutants.
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Affiliation(s)
- Sarah N Anderson
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108
| | - Gregory J Zynda
- Texas Advanced Computing Center, University of Texas, Austin, TX 78758
| | - Jawon Song
- Texas Advanced Computing Center, University of Texas, Austin, TX 78758
| | - Zhaoxue Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Matthew W Vaughn
- Texas Advanced Computing Center, University of Texas, Austin, TX 78758
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108
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22
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Cerbin S, Jiang N. Duplication of host genes by transposable elements. Curr Opin Genet Dev 2018; 49:63-69. [PMID: 29571044 DOI: 10.1016/j.gde.2018.03.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/07/2018] [Accepted: 03/08/2018] [Indexed: 12/12/2022]
Abstract
The availability of large amounts of genomic and transcriptome sequences have allowed systematic surveys about the host gene sequences that have been duplicated by transposable elements. It is now clear that all super-families of transposons are capable of duplicating genes or gene fragments, and such incidents have been detected in a wide spectrum of organisms. Emerging evidence suggests that a considerable portion of them function as coding or non-coding sequences, driving innovations at molecular and phenotypic levels. Interestingly, the duplication events not only have to occur in the reproductive tissues to become heritable, but the duplicated copies are also preferentially expressed in those tissues. As a result, reproductive tissues may serve as the 'incubator' for genes generated by transposable elements.
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Affiliation(s)
- Stefan Cerbin
- Department of Horticulture, 1066 Bogue Street, Michigan State University, East Lansing, MI 48824, USA
| | - Ning Jiang
- Department of Horticulture, 1066 Bogue Street, Michigan State University, East Lansing, MI 48824, USA.
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23
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Lang D, Ullrich KK, Murat F, Fuchs J, Jenkins J, Haas FB, Piednoel M, Gundlach H, Van Bel M, Meyberg R, Vives C, Morata J, Symeonidi A, Hiss M, Muchero W, Kamisugi Y, Saleh O, Blanc G, Decker EL, van Gessel N, Grimwood J, Hayes RD, Graham SW, Gunter LE, McDaniel SF, Hoernstein SNW, Larsson A, Li FW, Perroud PF, Phillips J, Ranjan P, Rokshar DS, Rothfels CJ, Schneider L, Shu S, Stevenson DW, Thümmler F, Tillich M, Villarreal Aguilar JC, Widiez T, Wong GKS, Wymore A, Zhang Y, Zimmer AD, Quatrano RS, Mayer KFX, Goodstein D, Casacuberta JM, Vandepoele K, Reski R, Cuming AC, Tuskan GA, Maumus F, Salse J, Schmutz J, Rensing SA. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:515-533. [PMID: 29237241 DOI: 10.1111/tpj.13801] [Citation(s) in RCA: 260] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/20/2017] [Accepted: 11/24/2017] [Indexed: 05/18/2023]
Abstract
The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
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Affiliation(s)
- Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Florent Murat
- INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, OT Gatersleben, D-06466, Stadt Seeland, Germany
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Mathieu Piednoel
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829, Cologne, Germany
| | - Heidrun Gundlach
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Michiel Van Bel
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Cristina Vives
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Jordi Morata
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | | | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Omar Saleh
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Guillaume Blanc
- Structural and Genomic Information Laboratory (IGS), Aix-Marseille Université, CNRS, UMR 7256 (IMM FR 3479), Marseille, France
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Lee E Gunter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stuart F McDaniel
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Sebastian N W Hoernstein
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Anders Larsson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | | | | | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Daniel S Rokshar
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720-2465, USA
| | - Lucas Schneider
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Shengqiang Shu
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Fritz Thümmler
- Vertis Biotechnologie AG, Lise-Meitner-Str. 30, 85354, Freising, Germany
| | - Michael Tillich
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam-Golm, Germany
| | | | - Thomas Widiez
- Department of Plant Biology, University of Geneva, Sciences III, Geneva 4, CH-1211, Switzerland
- Department of Plant Biology & Pathology Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Ann Wymore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yong Zhang
- Shenzhen Huahan Gene Life Technology Co. Ltd, Shenzhen, China
| | - Andreas D Zimmer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Ralph S Quatrano
- Department of Biology, Washington University, St. Louis, MO, USA
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
- WZW, Technical University Munich, Munich, Germany
| | | | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Klaas Vandepoele
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Jérome Salse
- INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany
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24
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Nakajima K. Be my baby: patterning toward plant germ cells. CURRENT OPINION IN PLANT BIOLOGY 2018; 41:110-115. [PMID: 29223127 DOI: 10.1016/j.pbi.2017.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 05/28/2023]
Abstract
In flowering plants, germ cells are formed via tightly coordinated patterning processes that facilitate specification of spore mother cells and meiosis during sporogenesis, as well as functional differentiation of germ cells in gametogenesis. Studies using the conventional Arabidopsis system and the newly emerged bryophyte system have revealed novel interactions between regulatory factors that restrict the number of spore mother cells, and evolutionarily conserved factors that promote germ cell differentiation. This short review summarizes recent advances in our understanding of the cellular events that lead to the formation of germ cells in plants, and highlights questions that remain to be addressed in the field.
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Affiliation(s)
- Keiji Nakajima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
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25
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Annacondia ML, Magerøy MH, Martinez G. Stress response regulation by epigenetic mechanisms: changing of the guards. PHYSIOLOGIA PLANTARUM 2018; 162:239-250. [PMID: 29080251 DOI: 10.1111/ppl.12662] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/25/2017] [Accepted: 10/25/2017] [Indexed: 05/23/2023]
Abstract
Plants are sessile organisms that lack a specialized immune system to cope with biotic and abiotic stress. Instead, plants have complex regulatory networks that determine the appropriate distribution of resources between the developmental and the defense programs. In the last years, epigenetic regulation of repeats and gene expression has evolved as an important player in the transcriptional regulation of stress-related genes. Here, we review the current knowledge about how different stresses interact with different levels of epigenetic control of the genome. Moreover, we analyze the different examples of transgenerational epigenetic inheritance and connect them with the known features of genome epigenetic regulation. Although yet to be explored, the interplay between epigenetics and stress resistance seems to be a relevant and dynamic player of the interaction of plants with their environments.
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Affiliation(s)
- Maria Luz Annacondia
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | | | - German Martinez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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26
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Kalendar R, Amenov A, Daniyarov A. Use of retrotransposon-derived genetic markers to analyse genomic variability in plants. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 46:15-29. [PMID: 30939255 DOI: 10.1071/fp18098] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/23/2018] [Indexed: 06/09/2023]
Abstract
Transposable elements (TEs) are common mobile genetic elements comprising several classes and making up the majority of eukaryotic genomes. The movement and accumulation of TEs has been a major force shaping the genes and genomes of most organisms. Most eukaryotic genomes are dominated by retrotransposons and minimal DNA transposon accumulation. The 'copy and paste' lifecycle of replicative transposition produces new genome insertions without excising the original element. Horizontal TE transfer among lineages is rare. TEs represent a reservoir of potential genomic instability and RNA-level toxicity. Many TEs appear static and nonfunctional, but some are capable of replicating and mobilising to new positions, and somatic transposition events have been observed. The overall structure of retrotransposons and the domains responsible for the phases of their replication are highly conserved in all eukaryotes. TEs are important drivers of species diversity and exhibit great variety in their structure, size and transposition mechanisms, making them important putative actors in evolution. Because TEs are abundant in plant genomes, various applications have been developed to exploit polymorphisms in TE insertion patterns, including conventional or anchored PCR, and quantitative or digital PCR with primers for the 5' or 3' junction. Alternatively, the retrotransposon junction can be mapped using high-throughput next-generation sequencing and bioinformatics. With these applications, TE insertions can be rapidly, easily and accurately identified, or new TE insertions can be found. This review provides an overview of the TE-based applications developed for plant species and assesses the contributions of TEs to the analysis of plants' genetic diversity.
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Affiliation(s)
- Ruslan Kalendar
- Department of Agricultural Sciences, PO Box 27 (Latokartanonkaari 5), FI-00014 University of Helsinki, Helsinki, Finland
| | - Asset Amenov
- RSE 'National Center for Biotechnology', 13/5 Kurgalzhynskoye Road, Astana, 010000, Kazakhstan
| | - Asset Daniyarov
- RSE 'National Center for Biotechnology', 13/5 Kurgalzhynskoye Road, Astana, 010000, Kazakhstan
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27
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Dukowic-Schulze S, Liu C, Chen C. Not just gene expression: 3D implications of chromatin modifications during sexual plant reproduction. PLANT CELL REPORTS 2018; 37:11-16. [PMID: 29032424 DOI: 10.1007/s00299-017-2222-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/05/2017] [Indexed: 06/07/2023]
Abstract
DNA methylation and histone modifications are epigenetic changes on a DNA molecule that alter the three-dimensional (3D) structure locally as well as globally, impacting chromatin looping and packaging on a larger scale. Epigenetic marks thus inform higher-order chromosome organization and placement in the nucleus. Conventional epigenetic marks are joined by chromatin modifiers like cohesins, condensins and membrane-anchoring complexes to support particularly 3D chromosome organization. The most popular consequences of epigenetic modifications are gene expression changes, but chromatin modifications have implications beyond this, particularly in actively dividing cells and during sexual reproduction. In this opinion paper, we will focus on epigenetic mechanisms and chromatin modifications during meiosis as part of plant sexual reproduction where 3D management of chromosomes and re-organization of chromatin are defining features and prime tasks in reproductive cells, not limited to modulating gene expression. Meiotic chromosome organization, pairing and synapsis of homologous chromosomes as well as distribution of meiotic double-strand breaks and resulting crossovers are presumably highly influenced by epigenetic mechanisms. Special mobile small RNAs have been described in anthers, where these so-called phasiRNAs seem to direct DNA methylation in meiotic cells. Intriguingly, many of the mentioned developmental processes make use of epigenetic changes and small RNAs in a manner other than gene expression changes. Widening our approaches and opening our mind to thinking three-dimensionally regarding epigenetics in plant development holds high promise for new discoveries and could give us a boost for further knowledge.
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Affiliation(s)
- Stefanie Dukowic-Schulze
- Department of Horticultural Science, University of Minnesota, Alderman Hall, 1970 Folwell Avenue, Saint Paul, MN, 55108, USA
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, Alderman Hall, 1970 Folwell Avenue, Saint Paul, MN, 55108, USA.
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28
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Abstract
Previously believed to be mere random degradation products, tRNA-derived small RNAs have been lately connected to a series of functions that include, surprisingly, genome protection against retrotransposons. tRNAs have been known for a long time to be involved in the replication cycle of retroviruses, pararetroviruses and retrotransposons as primers of their reverse transcription. tRNA-derived small RNAs, as functional small RNAs or as mere tRNA degradation products, have emerged as important players in the regulation of genic transcription. Nevertheless, the involvement of functional sRNAs derived from tRNA transcripts in transposon posttranscriptional control is a regulatory layer that remained elusive until now. Here I review the recent discoveries in the field that connect tRNA-derived small RNAs and retrotransposon control.
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Affiliation(s)
- German Martinez
- a Department of Plant Biology , Swedish University of Agricultural Sciences and Linnean Center for Plant Biology , Uppsala , Sweden
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29
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Martinez G, Choudury SG, Slotkin RK. tRNA-derived small RNAs target transposable element transcripts. Nucleic Acids Res 2017; 45:5142-5152. [PMID: 28335016 PMCID: PMC5605234 DOI: 10.1093/nar/gkx103] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/06/2017] [Indexed: 12/19/2022] Open
Abstract
tRNA-derived RNA fragments (tRFs) are 18–26 nucleotide small RNAs that are not random degradation products, but are rather specifically cleaved from mature tRNA transcripts. Abundant in stressed or viral-infected cells, the function and potential targets of tRFs are not known. We identified that in the unstressed wild-type male gamete containing pollen of flowering plants, and analogous reproductive structure in non-flowering plant species, tRFs accumulate to high levels. In the reference plant Arabidopsis thaliana, tRFs are processed by Dicer-like 1 and incorporated into Argonaute1 (AGO1), akin to a microRNA. We utilized the fact that many plant small RNAs direct cleavage of their target transcripts to demonstrate that the tRF–AGO1 complex acts to specifically target and cleave endogenous transposable element (TE) mRNAs produced from transcriptionally active TEs. The data presented here demonstrate that tRFs are bona-fide regulatory microRNA-like small RNAs involved in the regulation of genome stability through the targeting of TE transcripts.
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Affiliation(s)
- German Martinez
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, Columbus, 43210 OH, USA.,Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, 75007 Uppsala, Sweden
| | - Sarah G Choudury
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, Columbus, 43210 OH, USA.,Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, 43210 OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, 43210 OH, USA
| | - R Keith Slotkin
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, Columbus, 43210 OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, 43210 OH, USA
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30
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Martinez G, Köhler C. Role of small RNAs in epigenetic reprogramming during plant sexual reproduction. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:22-28. [PMID: 28088028 DOI: 10.1016/j.pbi.2016.12.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/29/2016] [Indexed: 05/07/2023]
Abstract
Sexual reproduction, the formation of a new individual from specialized reproductive cells after fertilization, involves the precise orchestration of different developmental and genomic processes. These processes are to a large extent governed by small RNAs (sRNAs) that either belong to the class of micro RNAs (miRNAs) or small-interfering RNAs (siRNAs). The latter are derived from transposable elements (TEs) and involved in genome defense and transgenerational inheritance of heterochromatin identity, ensuring genome stability. Remarkably, male and female gametophytes employ sRNAs to ensure reproductive success, but the underlying processes of their formation and action differ. Here, we review current advances in the field concerning the roles of sRNAs during flowering plant (angiosperm) reproduction and pinpoint where further research is required to solve open questions.
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Affiliation(s)
- German Martinez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.
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31
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Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants. PLoS Genet 2017; 13:e1006630. [PMID: 28212378 PMCID: PMC5338827 DOI: 10.1371/journal.pgen.1006630] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 03/06/2017] [Accepted: 02/10/2017] [Indexed: 11/19/2022] Open
Abstract
Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants. This method successfully identified known active retrotransposons in both Arabidopsis and rice material where the epigenome is destabilized. When applying mobilome-seq to developmental stages in wild type rice, we identified PopRice as a highly active retrotransposon producing eccDNA forms in the wild type endosperm. The mobilome-seq strategy opens new routes for the characterization of a yet unexplored fraction of plant genomes.
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32
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Ma W, Gabriel TS, Martis MM, Gursinsky T, Schubert V, Vrána J, Doležel J, Grundlach H, Altschmied L, Scholz U, Himmelbach A, Behrens SE, Banaei-Moghaddam AM, Houben A. Rye B chromosomes encode a functional Argonaute-like protein with in vitro slicer activities similar to its A chromosome paralog. THE NEW PHYTOLOGIST 2017; 213:916-928. [PMID: 27468091 DOI: 10.1111/nph.14110] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/18/2016] [Indexed: 05/21/2023]
Abstract
B chromosomes (Bs) are supernumerary, dispensable parts of the nuclear genome, which appear in many different species of eukaryote. So far, Bs have been considered to be genetically inert elements without any functional genes. Our comparative transcriptome analysis and the detection of active RNA polymerase II (RNAPII) in the proximity of B chromatin demonstrate that the Bs of rye (Secale cereale) contribute to the transcriptome. In total, 1954 and 1218 B-derived transcripts with an open reading frame were expressed in generative and vegetative tissues, respectively. In addition to B-derived transposable element transcripts, a high percentage of short transcripts without detectable similarity to known proteins and gene fragments from A chromosomes (As) were found, suggesting an ongoing gene erosion process. In vitro analysis of the A- and B-encoded AGO4B protein variants demonstrated that both possess RNA slicer activity. These data demonstrate unambiguously the presence of a functional AGO4B gene on Bs and that these Bs carry both functional protein coding genes and pseudogene copies. Thus, B-encoded genes may provide an additional level of gene control and complexity in combination with their related A-located genes. Hence, physiological effects, associated with the presence of Bs, may partly be explained by the activity of B-located (pseudo)genes.
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Affiliation(s)
- Wei Ma
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Tobias Sebastian Gabriel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Mihaela Maria Martis
- Institute of Bioinformatics and Systems Biology/Munich Information Center for Protein Sequences, Helmholtz Center Munich, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- National Bioinformatics Infrastructure Sweden, Department of Clinical and Experimental Medicine, Linköping University, SE-558185, Linköping, Sweden
| | - Torsten Gursinsky
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Faculty of Life Sciences, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Jan Vrána
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Heidrun Grundlach
- Institute of Bioinformatics and Systems Biology/Munich Information Center for Protein Sequences, Helmholtz Center Munich, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Faculty of Life Sciences, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Ali Mohammad Banaei-Moghaddam
- Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, PO Box 13145-1384, Tehran, Iran
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
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33
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Castellano M, Martinez G, Marques MC, Moreno-Romero J, Köhler C, Pallas V, Gomez G. Changes in the DNA methylation pattern of the host male gametophyte of viroid-infected cucumber plants. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5857-5868. [PMID: 27697787 PMCID: PMC5066502 DOI: 10.1093/jxb/erw353] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Eukaryotic organisms exposed to adverse conditions are required to show a certain degree of transcriptional plasticity in order to cope successfully with stress. Epigenetic regulation of the genome is a key regulatory mechanism allowing dynamic changes of the transcriptional status of the plant in response to stress. The Hop stunt viroid (HSVd) induces the demethylation of ribosomal RNA (rRNA) in cucumber (Cucumis sativus) leaves, leading to increasing transcription rates of rRNA. In addition to the clear alterations observed in vegetative tissues, HSVd infection is also associated with drastic changes in gametophyte development. To examine the basis of viroid-induced alterations in reproductive tissues, we analysed the cellular and molecular consequences of HSVd infection in the male gametophyte of cucumber plants. Our results indicate that in the pollen grain, accumulation of HSVd RNA induces a decondensation of the generative nucleus that correlates with a dynamic demethylation of repetitive regions in the cucumber genome that include rRNA genes and transposable elements (TEs). We therefore propose that HSVd infection impairs the epigenetic control of rRNA genes and TEs in gametic cells of cucumber, a phenomenon thus far unknown to occur in this reproductive tissue as a consequence of pathogen infection.
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Affiliation(s)
- Mayte Castellano
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politecnica de Valencia (UPV), CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - German Martinez
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Maria Carmen Marques
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politecnica de Valencia (UPV), CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Jordi Moreno-Romero
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politecnica de Valencia (UPV), CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Gustavo Gomez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politecnica de Valencia (UPV), CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
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34
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Martínez G, Panda K, Köhler C, Slotkin RK. Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell. NATURE PLANTS 2016; 2:16030. [PMID: 27249563 DOI: 10.1038/nplants.2016.30] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 02/04/2016] [Indexed: 05/23/2023]
Abstract
Plant small interfering RNAs (siRNAs) communicate from cell to cell and travel long distances through the vasculature. However, siRNA movement into germ cells has remained controversial, and has gained interest because the terminally differentiated pollen vegetative nurse cell surrounding the sperm cells undergoes a programmed heterochromatin decondensation and transcriptional reactivation of transposable elements (TEs). Transcription of TEs leads to their post-transcriptional degradation into siRNAs, and it has been proposed that the purpose of this TE reactivation is to generate and load TE siRNAs into the sperm cells. Here, we identify the molecular pathway of TE siRNA production in the pollen grain and demonstrate that siRNAs produced from pollen vegetative cell transcripts can silence TE reporters in the sperm cells. Our data demonstrates that TE siRNAs act non-cell-autonomously, inhibiting TE activity in the germ cells and potentially the next generation.
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Affiliation(s)
- Germán Martínez
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, 500 Aronoff Laboratory, 318 West 12th Avenue, Columbus, Ohio 43210, USA
| | - Kaushik Panda
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, 500 Aronoff Laboratory, 318 West 12th Avenue, Columbus, Ohio 43210, USA
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, SE-750 07 Uppsala, Sweden
| | - R Keith Slotkin
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, 500 Aronoff Laboratory, 318 West 12th Avenue, Columbus, Ohio 43210, USA
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Beulé T, Agbessi MD, Dussert S, Jaligot E, Guyot R. Genome-wide analysis of LTR-retrotransposons in oil palm. BMC Genomics 2015; 16:795. [PMID: 26470789 PMCID: PMC4608283 DOI: 10.1186/s12864-015-2023-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/07/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The oil palm (Elaeis guineensis Jacq.) is a major cultivated crop and the world's largest source of edible vegetable oil. The genus Elaeis comprises two species E. guineensis, the commercial African oil palm and E. oleifera, which is used in oil palm genetic breeding. The recent publication of both the African oil palm genome assembly and the first draft sequence of its Latin American relative now allows us to tackle the challenge of understanding the genome composition, structure and evolution of these palm genomes through the annotation of their repeated sequences. METHODS In this study, we identified, annotated and compared Transposable Elements (TE) from the African and Latin American oil palms. In a first step, Transposable Element databases were built through de novo detection in both genome sequences then the TE content of both genomes was estimated. Then putative full-length retrotransposons with Long Terminal Repeats (LTRs) were further identified in the E. guineensis genome for characterization of their structural diversity, copy number and chromosomal distribution. Finally, their relative expression in several tissues was determined through in silico analysis of publicly available transcriptome data. RESULTS Our results reveal a congruence in the transpositional history of LTR retrotransposons between E. oleifera and E. guineensis, especially the Sto-4 family. Also, we have identified and described 583 full-length LTR-retrotransposons in the Elaeis guineensis genome. Our work shows that these elements are most likely no longer mobile and that no recent insertion event has occurred. Moreover, the analysis of chromosomal distribution suggests a preferential insertion of Copia elements in gene-rich regions, whereas Gypsy elements appear to be evenly distributed throughout the genome. CONCLUSIONS Considering the high proportion of LTR retrotransposon in the oil palm genome, our work will contribute to a greater understanding of their impact on genome organization and evolution. Moreover, the knowledge gained from this study constitutes a valuable resource for both the improvement of genome annotation and the investigation of the evolutionary history of palms.
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Affiliation(s)
- Thierry Beulé
- CIRAD, UMR DIADE (IRD, UM), 34394, Montpellier, France.
| | | | | | | | - Romain Guyot
- IRD, UMR IPME (IRD, CIRAD, UM), 34394, Montpellier, France.
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Fultz D, Choudury SG, Slotkin RK. Silencing of active transposable elements in plants. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:67-76. [PMID: 26164237 DOI: 10.1016/j.pbi.2015.05.027] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/20/2015] [Accepted: 05/22/2015] [Indexed: 05/04/2023]
Abstract
In plant genomes the vast majority of transposable elements (TEs) are found in a transcriptionally silenced state that is epigenetically propagated from generation to generation. Although the mechanism of this maintenance of silencing has been well studied, it is now clear that the pathways responsible for maintaining TEs in a silenced state differ from the pathways responsible for initially targeting the TE for silencing. Recently, attention in this field has focused on investigating the molecular mechanisms that initiate and establish TE silencing. Here we review the current models of how TEs are triggered for silencing, the data supporting each model, and the key future questions in this fast moving field.
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Affiliation(s)
- Dalen Fultz
- Department of Molecular Genetics, The Ohio State University, United States
| | - Sarah G Choudury
- Department of Molecular Genetics, The Ohio State University, United States
| | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, United States; Center for RNA Biology, The Ohio State University, United States.
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Cerveau N, Gilbert C, Liu C, Garrett RA, Grève P, Bouchon D, Cordaux R. Genomic context drives transcription of insertion sequences in the bacterial endosymbiont Wolbachia wVulC. Gene 2015; 564:81-6. [PMID: 25813874 DOI: 10.1016/j.gene.2015.03.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 03/19/2015] [Accepted: 03/20/2015] [Indexed: 11/24/2022]
Abstract
Transposable elements (TEs) are DNA pieces that are present in almost all the living world at variable genomic density. Due to their mobility and density, TEs are involved in a large array of genomic modifications. In eukaryotes, TE expression has been studied in detail in several species. In prokaryotes, studies of IS expression are generally linked to particular copies that induce a modification of neighboring gene expression. Here we investigated global patterns of IS transcription in the Alphaproteobacterial endosymbiont Wolbachia wVulC, using both RT-PCR and bioinformatic analyses. We detected several transcriptional promoters in all IS groups. Nevertheless, only one of the potentially functional IS groups possesses a promoter located upstream of the transposase gene, that could lead up to the production of a functional protein. We found that the majority of IS groups are expressed whatever their functional status. RT-PCR analyses indicate that the transcription of two IS groups lacking internal promoters upstream of the transposase start codon may be driven by the genomic environment. We confirmed this observation with the transcription analysis of individual copies of one IS group. These results suggest that the genomic environment is important for IS expression and it could explain, at least partly, copy number variability of the various IS groups present in the wVulC genome and, more generally, in bacterial genomes.
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Affiliation(s)
- Nicolas Cerveau
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpin, 86073 Poitiers Cedex 9, France
| | - Clément Gilbert
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpin, 86073 Poitiers Cedex 9, France
| | - Chao Liu
- Department of Biology, University of Copenhagen, 2200N Copenhagen, Denmark
| | - Roger A Garrett
- Department of Biology, University of Copenhagen, 2200N Copenhagen, Denmark
| | - Pierre Grève
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpin, 86073 Poitiers Cedex 9, France
| | - Didier Bouchon
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpin, 86073 Poitiers Cedex 9, France
| | - Richard Cordaux
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpin, 86073 Poitiers Cedex 9, France.
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Grandbastien MA. LTR retrotransposons, handy hitchhikers of plant regulation and stress response. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:403-16. [DOI: 10.1016/j.bbagrm.2014.07.017] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 11/30/2022]
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FT-like proteins induce transposon silencing in the shoot apex during floral induction in rice. Proc Natl Acad Sci U S A 2015; 112:E901-10. [PMID: 25675495 DOI: 10.1073/pnas.1417623112] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Floral induction is a crucial developmental step in higher plants. Florigen, a mobile floral activator that is synthesized in the leaf and transported to the shoot apex, was recently identified as a protein encoded by FLOWERING LOCUS T (FT) and its orthologs; the rice florigen is Heading date 3a (Hd3a) protein. The 14-3-3 proteins mediate the interaction of Hd3a with the transcription factor OsFD1 to form a ternary structure called the florigen activation complex on the promoter of OsMADS15, a rice APETALA1 ortholog. However, crucial information, including the spatiotemporal overlap among FT-like proteins and the components of florigen activation complex and downstream genes, remains unclear. Here, we confirm that Hd3a coexists, in the same regions of the rice shoot apex, with the other components of the florigen activation complex and its transcriptional targets. Unexpectedly, however, RNA-sequencing analysis of shoot apex from wild-type and RNA-interference plants depleted of florigen activity revealed that 4,379 transposable elements (TEs; 58% of all classifiable rice TEs) were expressed collectively in the vegetative and reproductive shoot apex. Furthermore, in the reproductive shoot apex, 214 TEs were silenced by florigen. Our results suggest a link between floral induction and regulation of TEs.
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40
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Kawashima T, Berger F. Epigenetic reprogramming in plant sexual reproduction. Nat Rev Genet 2014; 15:613-24. [DOI: 10.1038/nrg3685] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Mirouze M, Vitte C. Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2801-12. [PMID: 24744427 DOI: 10.1093/jxb/eru120] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In the past decade, plant biologists and breeders have developed a growing interest in the field of epigenetics, which is defined as the study of heritable changes in gene expression that cannot be explained by changes in the DNA sequence. Epigenetic marks can be responsive to the environment, and evolve faster than genetic changes. Therefore, epigenetic diversity may represent an unexplored resource of natural variation that could be used in plant breeding programmes. On the other hand, crop genomes are largely populated with transposable elements (TEs) that are efficiently targeted by epigenetic marks, and part of the epigenetic diversity observed might be explained by TE polymorphisms. Characterizing the degree to which TEs influence epigenetic variation in crops is therefore a major goal to better use epigenetic variation. To date, epigenetic analyses have been mainly focused on the model plant Arabidopsis thaliana, and have provided clues on epigenome features, components that silence pathways, and effects of silencing impairment. But to what extent can Arabidopsis be used as a model for the epigenomics of crops? In this review, we discuss the similarities and differences between the epigenomes of Arabidopsis and crops. We explore the relationship between TEs and epigenomes, focusing on TE silencing control and escape, and the impact of TE mobility on epigenomic variation. Finally, we provide insights into challenges to tackle, and future directions to take in the route towards using epigenetic diversity in plant breeding programmes.
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Affiliation(s)
- Marie Mirouze
- Institut de Recherche pour le Développement, UMR232 DIADE Diversité Adaptation et Développement des Plantes, Université Montpellier 2, 911 avenue Agropolis F-34394 Montpellier, France
| | - Clémentine Vitte
- CNRS, UMR de Génétique Végétale, Chemin de Moulon, F-91190 Gif sur Yvette, France
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Candaele J, Demuynck K, Mosoti D, Beemster GT, Inzé D, Nelissen H. Differential methylation during maize leaf growth targets developmentally regulated genes. PLANT PHYSIOLOGY 2014; 164:1350-64. [PMID: 24488968 PMCID: PMC3938625 DOI: 10.1104/pp.113.233312] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 01/28/2014] [Indexed: 05/20/2023]
Abstract
DNA methylation is an important and widespread epigenetic modification in plant genomes, mediated by DNA methyltransferases (DMTs). DNA methylation is known to play a role in genome protection, regulation of gene expression, and splicing and was previously associated with major developmental reprogramming in plants, such as vernalization and transition to flowering. Here, we show that DNA methylation also controls the growth processes of cell division and cell expansion within a growing organ. The maize (Zea mays) leaf offers a great tool to study growth processes, as the cells progressively move through the spatial gradient encompassing the division zone, transition zone, elongation zone, and mature zone. Opposite to de novo DMTs, the maintenance DMTs were transcriptionally regulated throughout the growth zone of the maize leaf, concomitant with differential CCGG methylation levels in the four zones. Surprisingly, the majority of differentially methylated sequences mapped on or close to gene bodies and not to repeat-rich loci. Moreover, especially the 5' and 3' regions of genes, which show overall low methylation levels, underwent differential methylation in a developmental context. Genes involved in processes such as chromatin remodeling, cell cycle progression, and growth regulation, were differentially methylated. The presence of differential methylation located upstream of the gene anticorrelated with transcript expression, while gene body differential methylation was unrelated to the expression level. These data indicate that DNA methylation is correlated with the decision to exit mitotic cell division and to enter cell expansion, which adds a new epigenetic level to the regulation of growth processes.
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Cavrak VV, Lettner N, Jamge S, Kosarewicz A, Bayer LM, Mittelsten Scheid O. How a retrotransposon exploits the plant's heat stress response for its activation. PLoS Genet 2014; 10:e1004115. [PMID: 24497839 PMCID: PMC3907296 DOI: 10.1371/journal.pgen.1004115] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 11/28/2013] [Indexed: 11/18/2022] Open
Abstract
Retrotransposons are major components of plant and animal genomes. They amplify by reverse transcription and reintegration into the host genome but their activity is usually epigenetically silenced. In plants, genomic copies of retrotransposons are typically associated with repressive chromatin modifications installed and maintained by RNA-directed DNA methylation. To escape this tight control, retrotransposons employ various strategies to avoid epigenetic silencing. Here we describe the mechanism developed by ONSEN, an LTR-copia type retrotransposon in Arabidopsis thaliana. ONSEN has acquired a heat-responsive element recognized by plant-derived heat stress defense factors, resulting in transcription and production of full length extrachromosomal DNA under elevated temperatures. Further, the ONSEN promoter is free of CG and CHG sites, and the reduction of DNA methylation at the CHH sites is not sufficient to activate the element. Since dividing cells have a more pronounced heat response, the extrachromosomal ONSEN DNA, capable of reintegrating into the genome, accumulates preferentially in the meristematic tissue of the shoot. The recruitment of a major plant heat shock transcription factor in periods of heat stress exploits the plant's heat stress response to achieve the transposon's activation, making it impossible for the host to respond appropriately to stress without losing control over the invader. Transposons are programmed to amplify within their host genomes. In defense, hosts have evolved mechanisms to impede transposon activation, often by epigenetic transcriptional silencing. A constant and likely unending arms race between host and invader has brought about different strategies to mutually counteract the tricks of the other. Several such strategies are combined in one transposon in the Arabidopsis genome. Its promoter is devoid of symmetric sites necessary for stable maintenance of repressive DNA methylation, and a reduction of methylation at the remaining cytosines does not activate the element. More sophisticated still: its promoter shares a sequence motif with heat stress-responsive plant genes and is recognized by a heat-induced plant transcription factor. Whenever the plants must activate their heat stress defense under high temperatures, the transposon is able to generate new extrachromosomal DNA copies that can potentially integrate into new sites of the genome. In addition, the heat response is especially strong in tissue with dividing cells, which form consequently the largest amount of extrachromosomal transposon copies. We see this as an example of a “wolf in sheep's clothing” strategy, whereby the transposon becomes visible as such only under specific stress conditions of its host.
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Affiliation(s)
- Vladimir V. Cavrak
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Nicole Lettner
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Suraj Jamge
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Agata Kosarewicz
- Research Institute of Molecular Pathology, Vienna, Austria; and Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna, Austria
| | - Laura Maria Bayer
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
- * E-mail:
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Luo A, Shi C, Zhang L, Sun MX. The expression and roles of parent-of-origin genes in early embryogenesis of angiosperms. FRONTIERS IN PLANT SCIENCE 2014; 5:729. [PMID: 25566300 PMCID: PMC4267172 DOI: 10.3389/fpls.2014.00729] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/01/2014] [Indexed: 05/03/2023]
Abstract
Uniparental transcripts during embryogenesis may arise due to gamete delivery during fertilization or genomic imprinting. Such transcripts have been found in a number of plant species and appear critical for the early development of embryo or endosperm in seeds. Although the regulatory expression mechanism and function of these genes in embryogenesis require further elucidation, recent studies suggest stage-specific and highly dynamic features that might be essential for critical developmental events such as zygotic division and cell fate determination during embryogenesis. Here, we summarize the current work in this field and discuss future research directions.
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Affiliation(s)
- An Luo
- State Key Laboratory of Hybrid Rice, Department of Cell and Developmental Biology, College of Life Sciences, Wuhan UniversityWuhan, China
- College of Life Sciences, Yangtze UniversityJingzhou, China
| | - Ce Shi
- State Key Laboratory of Hybrid Rice, Department of Cell and Developmental Biology, College of Life Sciences, Wuhan UniversityWuhan, China
| | - Liyao Zhang
- State Key Laboratory of Hybrid Rice, Department of Cell and Developmental Biology, College of Life Sciences, Wuhan UniversityWuhan, China
| | - Meng-Xiang Sun
- State Key Laboratory of Hybrid Rice, Department of Cell and Developmental Biology, College of Life Sciences, Wuhan UniversityWuhan, China
- *Correspondence: Meng-Xiang Sun, State Key Laboratory of Hybrid Rice, Department of Cell and Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China e-mail:
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45
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Verhoeven KJF, Preite V. Epigenetic variation in asexually reproducing organisms. Evolution 2013; 68:644-55. [PMID: 24274255 DOI: 10.1111/evo.12320] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/14/2013] [Indexed: 01/10/2023]
Abstract
The role that epigenetic inheritance can play in adaptation may differ between sexuals and asexuals because (1) the dynamics of adaptation differ under sexual and asexual reproduction and the opportunities offered by epigenetic inheritance may affect these dynamics differently; and (2) in asexual reproduction epigenetic reprogramming mechanisms that are associated with meiosis can be bypassed, which could promote the buildup of epigenetic variation in asexuals. Here, we evaluate current evidence for an epigenetic contribution to adaptation in asexuals. We argue that two aspects of epigenetic variation should have particular relevance for asexuals, namely epigenetics-mediated phenotypic plasticity within and between generations, and heritable variation via stochastic epimutations. An evaluation of epigenetic reprogramming mechanisms suggests that some, but not all, forms of asexual reproduction enhance the likelihood of stable transmission of epigenetic marks across generations compared to sexual reproduction. However, direct tests of these predicted sexual-asexual differences are virtually lacking. Stable transmission of DNA methylation, transcriptomes, and phenotypes from parent to clonal offspring are demonstrated in various asexual species, and clonal genotypes from natural populations show habitat-specific DNA methylation. We discuss how these initial observations can be extended to demonstrate an epigenetic contribution to adaptation.
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Affiliation(s)
- Koen J F Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands.
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Anderson SN, Johnson CS, Jones DS, Conrad LJ, Gou X, Russell SD, Sundaresan V. Transcriptomes of isolated Oryza sativa gametes characterized by deep sequencing: evidence for distinct sex-dependent chromatin and epigenetic states before fertilization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:729-41. [PMID: 24215296 DOI: 10.1111/tpj.12336] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/12/2013] [Accepted: 09/19/2013] [Indexed: 05/19/2023]
Abstract
The formation of a zygote by the fusion of egg and sperm involves the two gametic transcriptomes. In flowering plants, the embryo sac embedded within the ovule contains the egg cell, whereas the pollen grain contains two sperm cells inside a supporting vegetative cell. The difficulties of collecting isolated gametes and consequent low recovery of RNA have restricted in-depth analysis of gametic transcriptomes in flowering plants. We isolated living egg cells, sperm cells and pollen vegetative cells from Oryza sativa (rice), and identified transcripts for approximately 36 000 genes by deep sequencing. The three transcriptomes are highly divergent, with about three-quarters of those genes differentially expressed in the different cell types. Distinctive expression profiles were observed for genes involved in chromatin conformation, including an unexpected expression in the sperm cell of genes associated with active chromatin. Furthermore, both the sperm cell and the pollen vegetative cell were deficient in expression of key RNAi components. Differences in gene expression were also observed for genes for hormonal signaling and cell cycle regulation. The egg cell and sperm cell transcriptomes reveal major differences in gene expression to be resolved in the zygote, including pathways affecting chromatin configuration, hormones and cell cycle. The sex-specific differences in the expression of RNAi components suggest that epigenetic silencing in the zygote might act predominantly through female-dependent pathways. More generally, this study provides a detailed gene expression landscape for flowering plant gametes, enabling the identification of specific gametic functions, and their contributions to zygote and seed development.
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Affiliation(s)
- Sarah N Anderson
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
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Schmitz RJ, He Y, Valdés-López O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res 2013; 23:1663-74. [PMID: 23739894 PMCID: PMC3787263 DOI: 10.1101/gr.152538.112] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 06/05/2013] [Indexed: 01/22/2023]
Abstract
Cytosine DNA methylation is one avenue for passing information through cell divisions. Here, we present epigenomic analyses of soybean recombinant inbred lines (RILs) and their parents. Identification of differentially methylated regions (DMRs) revealed that DMRs mostly cosegregated with the genotype from which they were derived, but examples of the uncoupling of genotype and epigenotype were identified. Linkage mapping of methylation states assessed from whole-genome bisulfite sequencing of 83 RILs uncovered widespread evidence for local methylQTL. This epigenomics approach provides a comprehensive study of the patterns and heritability of methylation variants in a complex genetic population over multiple generations, paving the way for understanding how methylation variants contribute to phenotypic variation.
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Affiliation(s)
- Robert J. Schmitz
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Yupeng He
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Bioinformatics Program, University of California at San Diego, La Jolla, California 92093, USA
| | - Oswaldo Valdés-López
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Saad M. Khan
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
- Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA
| | - Trupti Joshi
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
- Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA
- Department of Computer Science, University of Missouri, Columbia, Missouri 65211, USA
- National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211, USA
| | - Mark A. Urich
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Joseph R. Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Brian Diers
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801, USA
| | - Dong Xu
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
- Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA
- Department of Computer Science, University of Missouri, Columbia, Missouri 65211, USA
- National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211, USA
| | - Gary Stacey
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
- National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211, USA
- Divisions of Plant Science and Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
| | - Joseph R. Ecker
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
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Gross SM, Martin JA, Simpson J, Abraham-Juarez MJ, Wang Z, Visel A. De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. BMC Genomics 2013; 14:563. [PMID: 23957668 PMCID: PMC3765226 DOI: 10.1186/1471-2164-14-563] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 08/13/2013] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Agaves are succulent monocotyledonous plants native to xeric environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient form of photosynthesis), and existing technologies for ethanol production, agaves have gained attention both as potential lignocellulosic bioenergy feedstocks and models for exploring plant responses to abiotic stress. However, the lack of comprehensive Agave sequence datasets limits the scope of investigations into the molecular-genetic basis of Agave traits. RESULTS Here, we present comprehensive, high quality de novo transcriptome assemblies of two Agave species, A. tequilana and A. deserti, built from short-read RNA-seq data. Our analyses support completeness and accuracy of the de novo transcriptome assemblies, with each species having a minimum of approximately 35,000 protein-coding genes. Comparison of agave proteomes to those of additional plant species identifies biological functions of gene families displaying sequence divergence in agave species. Additionally, a focus on the transcriptomics of the A. deserti juvenile leaf confirms evolutionary conservation of monocotyledonous leaf physiology and development along the proximal-distal axis. CONCLUSIONS Our work presents a comprehensive transcriptome resource for two Agave species and provides insight into their biology and physiology. These resources are a foundation for further investigation of agave biology and their improvement for bioenergy development.
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Affiliation(s)
- Stephen M Gross
- DOE Joint Genome Institute, Walnut Creek, CA, USA
- Genomics Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jeffrey A Martin
- DOE Joint Genome Institute, Walnut Creek, CA, USA
- Genomics Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - June Simpson
- Department of Genetic Engineering, CINVESTAV, Irapuato, Guanajuato, Mexico
| | | | - Zhong Wang
- DOE Joint Genome Institute, Walnut Creek, CA, USA
- Genomics Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Axel Visel
- DOE Joint Genome Institute, Walnut Creek, CA, USA
- Genomics Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
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Borges F, Calarco JP, Martienssen RA. Reprogramming the epigenome in Arabidopsis pollen. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2013; 77:1-5. [PMID: 23619015 DOI: 10.1101/sqb.2013.77.014969] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Epigenetic reprogramming in Arabidopsis thaliana occurs in developing pollen. The male gametophyte is derived from haploid microspores via two postmeiotic cell divisions to give rise to the gametes (sperm cells, SC) and the vegetative cell (VC). The purification of individual cell types during pollen development coupled with genome-wide DNA methylation analysis and small RNA sequencing has revealed a dynamic regulation of the epigenome during gametogenesis. Interestingly, imprinted loci and previously identified variable epialleles are hypermethylated in the germline; however, their stability after fertilization appears to require targeted demethylation in the neighboring vegetative cell nucleus, possibly by releasing mobile small RNAs that reinforce transcriptional gene silencing and DNA methylation in the gametes. These results have led to a new model for the establishment and transgenerational maintenance of epigenetic marks in flowering plants.
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Affiliation(s)
- F Borges
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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