ArticleGenome biology and evolution2018
Modeling Interactions between Transposable Elements and the Plant Epigenetic Response: A Surprising Reliance on Element Retention.
Article in Genome biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Cooperation, competition and enforcement in transposon evolution.Nature communications · 2026Article
- Multi-locus models of deleterious epimutation-selection balance and the evolution of recombination modifiers.G3 (Bethesda, Md.) · 2026Article
- Population genomics reveals association of transposable elements variants with climatic adaptation in wild Amur grape.Nature communications · 2026Article
- Exploring the genomic landscape of mites and harnessing MITE insertion polymorphism markers in jute (Corchorus sp.).Scientific reports · 2025Article
- DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions.Communications biology · 2025Article
- Evolutionary Dynamics of Transposable Element Activity and Regulation in the Apennine Yellow-Bellied Toad (Bombina pachypus).Genome biology and evolution · 2025Article
- A review of plant epigenetics through the lens of almond.The plant genome · 2023Review
- Article
- Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defenses.G3 (Bethesda, Md.) · 2021Article
- Perspective: 50 years of plant chromosome biology.Plant physiology · 2021Article
- Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models.Genomics, proteomics & bioinformatics · 2021Article
- Genomic re-assessment of the transposable element landscape of the potato genome.Plant cell reports · 2020Article
- Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes.Genome biology · 2020Article
- Double-edged sword: The evolutionary consequences of the epigenetic silencing of transposable elements.PLoS genetics · 2020Review
- Integrating transposable elements in the 3D genome.Mobile DNA · 2020Article
- Where the Wild Things Are: Transposable Elements as Drivers of Structural and Functional Variations in the Wheat Genome.Frontiers in plant science · 2020Review
- On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements.Genes · 2019Review
- Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes.Mobile DNA · 2019Article
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4 authors.
Funding
Abstract
Transposable elements (TEs) compose the majority of angiosperm DNA. Plants counteract TE activity by silencing them epigenetically. One form of epigenetic silencing requires 21-22 nt small interfering RNAs that act to degrade TE mRNA and may also trigger DNA methylation. DNA methylation is reinforced by a second mechanism, the RNA-dependent DNA methylation (RdDM) pathway. RdDM relies on 24 nt small interfering RNAs and ultimately establishes TEs in a quiescent state. These host factors interact at a systems level, but there have been no system level analyses of their interactions. Here, we define a deterministic model that represents the propagation of active TEs, aspects of the host response and the accumulation of silenced TEs. We describe general properties of the model and also fit it to biological data in order to explore two questions. The first is why two overlapping pathways are maintained, given that both are likely energetically expensive. Under our model, RdDM silenced TEs effectively even when the initiation of silencing was weak. This relationship implies that only a small amount of RNAi is needed to initiate TE silencing, but reinforcement by RdDM is necessary to efficiently counter TE propagation. Second, we investigated the reliance of the host response on rates of TE deletion. The model predicted that low levels of deletion lead to few active TEs, suggesting that silencing is most efficient when methylated TEs are retained in the genome, thereby providing one explanation for the large size of plant genomes.
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