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Pulido M, Casacuberta JM. Transposable element evolution in plant genome ecosystems. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102418. [PMID: 37459733 DOI: 10.1016/j.pbi.2023.102418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/22/2023] [Accepted: 06/20/2023] [Indexed: 09/18/2023]
Abstract
The relationship of transposable elements (TEs) with their host genomes has usually been seen as an arms race between TEs and their host genomes. Consequently, TEs are supposed to amplify by bursts of transposition, when the TE escapes host surveillance, followed by long periods of TE quiescence and efficient host control. Recent data obtained from an increasing number of assembled plant genomes and resequencing population datasets show that TE dynamics is more complex and varies among TE families and their host genomes. This variation ranges from large genomes that accommodate large TE populations to genomes that are very active in TE elimination, and from inconspicuous elements with very low activity to elements with high transposition and elimination rates. The dynamics of each TE family results from a long history of interaction with the host in a genome populated by many other TE families, very much like an evolving ecosystem.
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Affiliation(s)
- Marc Pulido
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain.
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2
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Liu P, Cuerda-Gil D, Shahid S, Slotkin RK. The Epigenetic Control of the Transposable Element Life Cycle in Plant Genomes and Beyond. Annu Rev Genet 2022; 56:63-87. [DOI: 10.1146/annurev-genet-072920-015534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Within the life cycle of a living organism, another life cycle exists for the selfish genome inhabitants, which are called transposable elements (TEs). These mobile sequences invade, duplicate, amplify, and diversify within a genome, increasing the genome's size and generating new mutations. Cells act to defend their genome, but rather than permanently destroying TEs, they use chromatin-level repression and epigenetic inheritance to silence TE activity. This level of silencing is ephemeral and reversible, leading to a dynamic equilibrium between TE suppression and reactivation within a host genome. The coexistence of the TE and host genome can also lead to the domestication of the TE to serve in host genome evolution and function. In this review, we describe the life cycle of a TE, with emphasis on how epigenetic regulation is harnessed to control TEs for host genome stability and innovation.
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Affiliation(s)
- Peng Liu
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Diego Cuerda-Gil
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
- Graduate Program in the Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Saima Shahid
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - R. Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
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Gu X, Su Y, Wang T. 转座元件对植物基因组进化、表观遗传和适应性的作用. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements. BIOLOGY 2021; 10:biology10090896. [PMID: 34571773 PMCID: PMC8465862 DOI: 10.3390/biology10090896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 11/22/2022]
Abstract
Simple Summary Transposable elements (TEs) are DNA sequences that are, or were, able to move (transpose) within the genome of a single cell. They were first discovered by Barbara McClintock while working on maize, and they make up a large fraction of the genome. Transpositions can result in mutations and they can alter the genome size. Cells regulate the activity of TEs using a variety of mechanisms, such as chemical modifications of DNA and small RNAs. Machine learning (ML) is an interdisciplinary subject that studies computer algorithms that can improve through experience and by the use of data. ML has been successfully applied to a variety of problems in bioinformatics and has exhibited favorable precision and speed. Here, we provide a systematic and guided review on the ML and bioinformatic methods and tools that are used for the analysis of the regulation of TEs. Abstract Transposable elements (TEs, or mobile genetic elements, MGEs) are ubiquitous genetic elements that make up a substantial proportion of the genome of many species. The recent growing interest in understanding the evolution and function of TEs has revealed that TEs play a dual role in genome evolution, development, disease, and drug resistance. Cells regulate TE expression against uncontrolled activity that can lead to developmental defects and disease, using multiple strategies, such as DNA chemical modification, small RNA (sRNA) silencing, chromatin modification, as well as sequence-specific repressors. Advancements in bioinformatics and machine learning approaches are increasingly contributing to the analysis of the regulation mechanisms. A plethora of tools and machine learning approaches have been developed for prediction, annotation, and expression profiling of sRNAs, for methylation analysis of TEs, as well as for genome-wide methylation analysis through bisulfite sequencing data. In this review, we provide a guided overview of the bioinformatic and machine learning state of the art of fields closely associated with TE regulation and function.
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Ebaid H, Abdel-Salam B, Alhazza I, Al-Tamimi J, Hassan I, Rady A, Mashaly A, Mahmoud A, Sammour R. Samsum ant venom modulates the immune response and redox status at the acute toxic dose in vivo. J Venom Anim Toxins Incl Trop Dis 2019; 25:e20190020. [PMID: 31839800 PMCID: PMC6892565 DOI: 10.1590/1678-9199-jvatitd-2019-0020] [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: 05/16/2019] [Accepted: 11/05/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Ant venoms express surface molecules that participate in antigen presentation involving pro- and anti-inflammatory cytokines. This work aims to investigate the expression of MHC-II, CD80 and CD86 on the polymorphonuclear cells (PMNs) in rats injected with samsum ant venom (SAV). METHODS Rats were divided into three groups - control, SAV-treated (intraperitoneal route, 600 μg/kg), and SAV-treated (subcutaneous route, 600 μg/kg). After five doses, animals were euthanized and samples collected for analysis. RESULTS The subcutaneous SAV-trated rats presented decreased levels of glutathione with increased cholesterol and triglyceride levels. Intraperitoneal SAV-treated animals displayed significantly reduced concentrations of both IFN-γ and IL-17 in comparison with the control group. However, intraperitoneal and subcutaneous SAV-treated rats were able to upregulate the expressions of MHC-II, CD80 and CD86 on PMNs in comparison with the control respectively. The histological examination showed severe lymphocyte depletion in the splenic white pulp of the intraperitoneal SAV-injected rats. CONCLUSION Stimulation of PMNs by SAV leads to upregulation of MHC-II, CD 80, and CD 86, which plays critical roles in antigen presentation and consequently proliferation of T-cells. Subcutaneous route was more efficient than intraperitoneal by elevating MHC-II, CD80 and CD86 expression, disturbing oxidative stability and increasing lipogram concentration.
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Affiliation(s)
- Hossam Ebaid
- Department of Zoology, College of Science, King Saud University,
Riyadh 11451, Saudi Arabia
| | - Bahaa Abdel-Salam
- Department of Biology, College of Science and Humanities in
El-Quwiaya, 11961, Shaqra University, Saudi Arabia
| | - Ibrahim Alhazza
- Department of Zoology, College of Science, King Saud University,
Riyadh 11451, Saudi Arabia
| | - Jameel Al-Tamimi
- Department of Zoology, College of Science, King Saud University,
Riyadh 11451, Saudi Arabia
| | - Iftekhar Hassan
- Department of Zoology, College of Science, King Saud University,
Riyadh 11451, Saudi Arabia
| | - Ahmed Rady
- Department of Zoology, College of Science, King Saud University,
Riyadh 11451, Saudi Arabia
| | - Ashraf Mashaly
- Department of Zoology, College of Science, King Saud University,
Riyadh 11451, Saudi Arabia
| | - Ahmed Mahmoud
- Department of Zoology, College of Science, King Saud University,
Riyadh 11451, Saudi Arabia
| | - Reda Sammour
- Department of Zoology, College of Science, King Saud University,
Riyadh 11451, Saudi Arabia
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Abstract
One of the central goals in biology is to understand how and how much of the phenotype of an organism is encoded in its genome. Although many genes that are crucial for organismal processes have been identified, much less is known about the genetic bases underlying quantitative phenotypic differences in natural populations. We discuss the fundamental gap between the large body of knowledge generated over the past decades by experimental genetics in the laboratory and what is needed to understand the genotype-to-phenotype problem on a broader scale. We argue that systems genetics, a combination of systems biology and the study of natural variation using quantitative genetics, will help to address this problem. We present major advances in these two mostly disconnected areas that have increased our understanding of the developmental processes of flowering time control and root growth. We conclude by illustrating and discussing the efforts that have been made toward systems genetics specifically in plants.
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Affiliation(s)
- Takehiko Ogura
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria;
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria;
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Kabelitz T, Brzezinka K, Friedrich T, Górka M, Graf A, Kappel C, Bäurle I. A JUMONJI Protein with E3 Ligase and Histone H3 Binding Activities Affects Transposon Silencing in Arabidopsis. PLANT PHYSIOLOGY 2016; 171:344-58. [PMID: 26979329 PMCID: PMC4854677 DOI: 10.1104/pp.15.01688] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/14/2016] [Indexed: 05/07/2023]
Abstract
Transposable elements (TEs) make up a large proportion of eukaryotic genomes. As their mobilization creates genetic variation that threatens genome integrity, TEs are epigenetically silenced through several pathways, and this may spread to neighboring sequences. JUMONJI (JMJ) proteins can function as antisilencing factors and prevent silencing of genes next to TEs Whether TE silencing is counterbalanced by the activity of antisilencing factors is still unclear. Here, we characterize JMJ24 as a regulator of TE silencing. We show that loss of JMJ24 results in increased silencing of the DNA transposon AtMu1c, while overexpression of JMJ24 reduces silencing. JMJ24 has a JumonjiC (JmjC) domain and two RING domains. JMJ24 autoubiquitinates in vitro, demonstrating E3 ligase activity of the RING domain(s). JMJ24-JmjC binds the N-terminal tail of histone H3, and full-length JMJ24 binds histone H3 in vivo. JMJ24 activity is anticorrelated with histone H3 Lys 9 dimethylation (H3K9me2) levels at AtMu1c Double mutant analyses with epigenetic silencing mutants suggest that JMJ24 antagonizes histone H3K9me2 and requires H3K9 methyltransferases for its activity on AtMu1c Genome-wide transcriptome analysis indicates that JMJ24 affects silencing at additional TEs Our results suggest that the JmjC domain of JMJ24 has lost demethylase activity but has been retained as a binding domain for histone H3. This is in line with phylogenetic analyses indicating that JMJ24 (with the mutated JmjC domain) is widely conserved in angiosperms. Taken together, this study assigns a role in TE silencing to a conserved JmjC-domain protein with E3 ligase activity, but no demethylase activity.
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Affiliation(s)
- Tina Kabelitz
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany (T.K., K.B., T.F., C.K., I.B.); andMax-Planck-Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (M.G., A.G.)
| | - Krzysztof Brzezinka
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany (T.K., K.B., T.F., C.K., I.B.); andMax-Planck-Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (M.G., A.G.)
| | - Thomas Friedrich
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany (T.K., K.B., T.F., C.K., I.B.); andMax-Planck-Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (M.G., A.G.)
| | - Michał Górka
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany (T.K., K.B., T.F., C.K., I.B.); andMax-Planck-Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (M.G., A.G.)
| | - Alexander Graf
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany (T.K., K.B., T.F., C.K., I.B.); andMax-Planck-Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (M.G., A.G.)
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany (T.K., K.B., T.F., C.K., I.B.); andMax-Planck-Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (M.G., A.G.)
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany (T.K., K.B., T.F., C.K., I.B.); andMax-Planck-Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (M.G., A.G.)
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Sigman MJ, Slotkin RK. The First Rule of Plant Transposable Element Silencing: Location, Location, Location. THE PLANT CELL 2016; 28:304-13. [PMID: 26869697 PMCID: PMC4790875 DOI: 10.1105/tpc.15.00869] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/18/2015] [Accepted: 02/10/2016] [Indexed: 05/18/2023]
Abstract
Transposable elements (TEs) are mobile units of DNA that comprise large portions of plant genomes. Besides creating mutations via transposition and contributing to genome size, TEs play key roles in chromosome architecture and gene regulation. TE activity is repressed by overlapping mechanisms of chromatin condensation, epigenetic transcriptional silencing, and targeting by small interfering RNAs. The specific regulation of different TEs, as well as their different roles in chromosome architecture and gene regulation, is specified by where on the chromosome the TE is located: near a gene, within a gene, in a pericentromere/TE island, or at the centromere core. In this Review, we investigate the silencing mechanisms responsible for inhibiting TE activity for each of these chromosomal contexts, emphasizing that chromosomal location is the first rule dictating the specific regulation of each TE.
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Affiliation(s)
- Meredith J Sigman
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
| | - R Keith Slotkin
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
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9
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Mozgová I, Köhler C, Gaudin V, Hennig L. The many faces of plant chromatin: Meeting summary of the 4th European workshop on plant chromatin 2015, Uppsala, Sweden. Epigenetics 2015; 10:1084-90. [PMID: 26646904 DOI: 10.1080/15592294.2015.1106674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In June 2015, the fourth European Workshop on Plant Chromatin took place in Uppsala, Sweden, bringing together 80 researchers studying various aspects of plant chromatin and epigenetics. The intricate relationships between plant chromatin dynamics and gene expression change, chromatin organization within the plant cell nucleus, and the impact of chromatin structure on plant development were discussed. Among the main highlights of the meeting were an ever-growing list of newly identified players in chromatin structure establishment and the development of novel tools and approaches to foster our understanding of chromatin-mediated gene regulation, taking into account the context of the plant cell nucleus and its architecture. In this report, we summarize some of the main advances and prospects of plant chromatin research presented at this meeting.
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Affiliation(s)
- Iva Mozgová
- a Department of Plant Biology ; Uppsala BioCenter; Swedish University of Agricultural Sciences and Linnean Center for Plant Biology ; Uppsala , Sweden
| | - Claudia Köhler
- a Department of Plant Biology ; Uppsala BioCenter; Swedish University of Agricultural Sciences and Linnean Center for Plant Biology ; Uppsala , Sweden
| | - Valérie Gaudin
- b INRA-AgroParisTech; Institut Jean-Pierre Bourgin ; Versailles , France
| | - Lars Hennig
- a Department of Plant Biology ; Uppsala BioCenter; Swedish University of Agricultural Sciences and Linnean Center for Plant Biology ; Uppsala , Sweden
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10
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Lämke J, Brzezinka K, Altmann S, Bäurle I. A hit-and-run heat shock factor governs sustained histone methylation and transcriptional stress memory. EMBO J 2015; 35:162-75. [PMID: 26657708 DOI: 10.15252/embj.201592593] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/13/2015] [Indexed: 01/19/2023] Open
Abstract
In nature, plants often encounter chronic or recurring stressful conditions. Recent results indicate that plants can remember a past exposure to stress to be better prepared for a future stress incident. However, the molecular basis of this is poorly understood. Here, we report the involvement of chromatin modifications in the maintenance of acquired thermotolerance (heat stress [HS] memory). HS memory is associated with the accumulation of histone H3 lysine 4 di- and trimethylation at memory-related loci. This accumulation outlasts their transcriptional activity and marks them as recently transcriptionally active. High accumulation of H3K4 methylation is associated with hyper-induction of gene expression upon a recurring HS. This transcriptional memory and the sustained accumulation of H3K4 methylation depend on HSFA2, a transcription factor that is required for HS memory, but not initial heat responses. Interestingly, HSFA2 associates with memory-related loci transiently during the early stages following HS. In summary, we show that transcriptional memory after HS is associated with sustained H3K4 hyper-methylation and depends on a hit-and-run transcription factor, thus providing a molecular framework for HS memory.
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Affiliation(s)
- Jörn Lämke
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Krzysztof Brzezinka
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Simone Altmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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11
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Kabelitz T, Bäurle I. Get the jump - Do 3'UTRs protect transposable elements from silencing? Mob Genet Elements 2015; 5:51-54. [PMID: 26442184 DOI: 10.1080/2159256x.2015.1052179] [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: 01/06/2015] [Revised: 04/29/2015] [Accepted: 05/08/2015] [Indexed: 12/26/2022] Open
Abstract
Eukaryotic genomes contain large numbers of transposable elements and repetitive sequences that are subjected to silencing through epigenetic mechanisms. These involve primarily DNA methylation, chromatin modifications and small RNA. It is known that these transposable elements can affect the expression of neighboring genes; however, little is known about how transposable element silencing depends on the general chromosomal environment at the insertion site. Taking advantage of the vast genomic resources available in Arabidopsis thaliana, a recent report begins to unravel these interactions by identifying insertion sites of one specific MULE element, AtMu1c across the A. thaliana lineage. Among over 30 insertion sites analyzed, a correlation between the loss of epigenetic silencing and the insertion into the 3'end of protein coding genes was found. Here, we discuss details, implications and potential mechanisms of these findings that may be applicable to a much wider set of transposable elements and across diverse species.
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Affiliation(s)
- Tina Kabelitz
- Institute for Biochemistry and Biology; University of Potsdam ; Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology; University of Potsdam ; Potsdam, Germany
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12
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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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