ArticleMolecular biology and evolution2018
Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 62 citations in OpenAlex.
- Repeated drought induces a reproducible DNA methylation response associated with gene expression inbioRxiv : the preprint server for biology · 2026Article
- Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources.Genome research · 2026Article
- Centromeric retrotransposons shape chromosomal evolution beyond pericentromeric regions.Mobile DNA · 2026Article
- Transposable elements as drivers of genome evolution in Drosophila virilis.Nucleic acids research · 2026Article
- Connecting Epigenetic and Genetic Diversity of LTR Retrotransposons in Sunflower (Plants (Basel, Switzerland) · 2026Article
- Climate-Resilient Crops: Integrating AI, Multi-Omics, and Advanced Phenotyping to Address Global Agricultural and Societal Challenges.Plants (Basel, Switzerland) · 2025Review
- The epigenetics effects of transposable elements are genomic context dependent and not restricted to gene silencing in Drosophila.Genome biology · 2025Article
- Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis.Genome biology · 2025Article
- Transposon Dynamics Drive Genome Evolution and Regulate Genetic Mechanisms of Agronomic Traits in Cotton.Plants (Basel, Switzerland) · 2025Article
- Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms.Molecular biology and evolution · 2024Review
- Construction and analysis of telomere-to-telomere genomes for 2 sweet oranges: Longhuihong and Newhall (Citrus sinensis).GigaScience · 2024Article
- Activation characteristics of Ty3-retrotransposons after spaceflight and genetic stability of insertion sites in rice progeny.Frontiers in plant science · 2024Article
- Evolutionary insights into 3D genome organization and epigenetic landscape ofLife science alliance · 2024Article
- Chromosomal-level genome assembly of the high-quality Xian/Indica rice (Oryza sativa L.) Xiangyaxiangzhan.BMC plant biology · 2023Article
- Off-target piRNA gene silencing in Drosophila melanogaster rescued by a transposable element insertion.PLoS genetics · 2023Article
- Methylation in the CHH Context Allows to Predict Recombination in Rice.International journal of molecular sciences · 2022Article
- Species-specific chromatin landscape determines how transposable elements shape genome evolution.eLife · 2022Article
- Characterization of Transposon-Derived Accessible Chromatin Regions in Rice (International journal of molecular sciences · 2022Article
- Whole-genome DNA methylation patterns ofPlant direct · 2022Article
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Plant genomes contain numerous transposable elements (TEs), and many hypotheses on the evolutionary drivers that restrict TE activity have been postulated. Few models, however, have focused on the evolutionary epigenomic interaction between the plant host and its TE. The host genome recruits epigenetic factors, such as methylation, to silence TEs but methylation can spread beyond the TE sequence and influence the expression of nearby host genes. In this study, we investigated this epigenetic trade-off between TE and proximal host gene silencing by studying the epigenomic regulation of repressing long terminal repeat (LTR) retrotransposons (RTs) in Oryza sativa. Results showed significant evidence of methylation spreading originating from the LTR-RT sequences, and the extent of spreading was dependent on five factors: 1) LTR-RT family, 2) time since the LTR-RT insertion, 3) recombination rate of the LTR-RT region, 4) level of LTR-RT sequence methylation, and 5) chromosomal location. Methylation spreading had negative effects by reducing host gene expression, but only on host genes with LTR-RT inserted in its introns. Our results also suggested high levels of LTR-RT methylation might have a role in suppressing TE-mediated deleterious ectopic recombination. In the end, despite the methylation spreading, no strong epigenetic trade-off was detected and majority of LTR-RT may have only minor epigenetic effects on nearby host genes.
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