ArticleProceedings of the National Academy of Sciences of the United States of America2011
Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 157 papers.
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157 citing papers in PubMed, 323 citations in OpenAlex.
- Repeated drought induces a reproducible DNA methylation response associated with gene expression inbioRxiv : the preprint server for biology · 2026Article
- Transposable elements and their epigenetic modifications mediate gene expression and subgenome dominance in Brassica carinata.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- A chromosome-level genome assembly of Platycladus orientalis and comparative genomics reveal pivotal roles of transposable elements in gene duplication and pseudogenization across gymnosperm giga-genomes.Plant communications · 2026Article
- Centromeric retrotransposons shape chromosomal evolution beyond pericentromeric regions.Mobile DNA · 2026Article
- Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations.Nature plants · 2025Article
- Genome-Wide Identification, Evolutionary Expansion, and Expression Analyses of Aux/IAA Gene Family inBiology · 2025Article
- DNA Methylation and Alternative Splicing Safeguard Genome and Transcriptome After a Retrotransposition Burst inInternational journal of molecular sciences · 2025Article
- Persistent Habitat Instability and Patchiness, Sexual Attraction, Founder Events, Drift and Selection: A Recipe for Rapid Diversification of Orchids.Plants (Basel, Switzerland) · 2025Review
- Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome.Plants (Basel, Switzerland) · 2025Review
- The genomic and epigenomic landscapes of hemizygous genes across crops with contrasting reproductive systems.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Biased Retention of Environment-Responsive Genes Following Genome Fractionation.Molecular biology and evolution · 2024Article
- Reclassification of Botryococcus braunii chemical races into separate species based on a comparative genomics analysis.PloS one · 2024Article
- The lack of negative association between TE load and subgenome dominance in synthesizedProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Selection signatures and population dynamics of transposable elements in lima bean.Communications biology · 2023Article
- Chromosome-Wide Distribution and Characterization of H3K36me3 and H3K27Ac in the Marine Model DiatomPlants (Basel, Switzerland) · 2023Article
- Extracellular vesicles: cross-organismal RNA trafficking in plants, microbes, and mammalian cells.Extracellular vesicles and circulating nucleic acids · 2023Article
- Abundance of Transgene Transcript Variants Associated with Somatically Active TransgenicInternational journal of molecular sciences · 2023Article
- Off-target piRNA gene silencing in Drosophila melanogaster rescued by a transposable element insertion.PLoS genetics · 2023Article
- The creation of autotetraploid provides insights into critical features of DNA methylome changes after genome doubling in water spinach (Frontiers in plant science · 2023Article
- The Heterogeneity in the Landscape of Gene Dominance in Maize is Accompanied by Unique Chromatin Environments.Molecular biology and evolution · 2022Article
97 more citing papers are in PubMed but not listed here.
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6 authors at 2 institutions in 2 countries.
Funding
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Abstract
Transposable elements (TEs) are often the primary determinant of genome size differences among eukaryotes. In plants, the proliferation of TEs is countered through epigenetic silencing mechanisms that prevent mobility. Recent studies using the model plant Arabidopsis thaliana have revealed that methylated TE insertions are often associated with reduced expression of nearby genes, and these insertions may be subject to purifying selection due to this effect. Less is known about the genome-wide patterns of epigenetic silencing of TEs in other plant species. Here, we compare the 24-nt siRNA complement from A. thaliana and a closely related congener with a two- to threefold higher TE copy number, Arabidopsis lyrata. We show that TEs--particularly siRNA-targeted TEs--are associated with reduced gene expression within both species and also with gene expression differences between orthologs. In addition, A. lyrata TEs are targeted by a lower fraction of uniquely matching siRNAs, which are associated with more effective silencing of TE expression. Our results suggest that the efficacy of RNA-directed DNA methylation silencing is lower in A. lyrata, a finding that may shed light on the causes of differential TE proliferation among species.
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