ArticleRNA biology2013
Genome-wide identification of genes regulated in trans by transposable element small interfering RNAs.
Article in RNA biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 102 citations in OpenAlex.
- TheProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Factors determining chromosomal localization of transposable elements in plants.Plant biology (Stuttgart, Germany) · 2025Review
- The role of mobile DNA elements in the dynamics of plant genome plasticity.Journal of experimental botany · 2025Review
- Retrotransposon addiction promotes centromere function via epigenetically activated small RNAs.Nature plants · 2024Article
- Chromosome-level genome assemblies ofHorticulture research · 2024Article
- The evolution of transposable elements ineLife · 2024Article
- Phased secondary small interfering RNAs inNAR genomics and bioinformatics · 2023Article
- Homoeologous evolution of the allotetraploid genome of Poa annua L.BMC genomics · 2023Article
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- Reprogramming of RNA silencing triggered by cucumber mosaic virus infection in Arabidopsis.Genome biology · 2021Article
- Enrichment of Cytoplasmic RNA Granules fromBio-protocol · 2021Article
- Review
- Which factors contribute most to genome size variation within angiosperms?Ecology and evolution · 2021Article
- Genomic and Transcriptomic Survey Provides New Insight into the Organization and Transposition Activity of Highly Expressed LTR Retrotransposons of Sunflower (International journal of molecular sciences · 2020Article
- Telomeric TART elements target the piRNA machinery in Drosophila.PLoS biology · 2020Article
- UNBRANCHED3 Expression and Inflorescence Development is Mediated by UNBRANCHED2 and the Distal Enhancer, KRN4, in Maize.PLoS genetics · 2020Article
- Article
- Post-transcriptional gene silencing triggers dispensable DNA methylation in gene body in Arabidopsis.Nucleic acids research · 2019Article
- Host-transposon interactions: conflict, cooperation, and cooption.Genes & development · 2019Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TEs) are known to influence the regulation of neighboring genes through a variety of mechanisms. Additionally, it was recently discovered that TEs can regulate non-neighboring genes through the trans-acting nature of small interfering RNAs (siRNAs). When the epigenetic repression of TEs is lost, TEs become transcriptionally active, and the host cell acts to repress mutagenic transposition by degrading TE mRNAs into siRNAs. In this study, we have performed a genome-wide analysis in the model plant Arabidopsis thaliana and found that TE siRNA-based regulation of genic mRNAs is more pervasive than the two formerly characterized proof-of-principle examples. We identified 27 candidate genic mRNAs that do not contain a TE fragment but are regulated through partial complementarity by the accumulation of TE siRNAs and are therefore influenced by TE epigenetic activation. We have experimentally confirmed several gene targets and demonstrated that they respond to the accumulation of specific 21 nucleotide TE siRNAs that are incorporated into the Arabidopsis Argonaute1 protein. Additionally, we found that one TE siRNA specifically targets and inhibits the formation of a host protein that acts to repress TE activity, suggesting that TEs harbor and potentially evolutionarily select short sequences to act as suppressors of host TE repression.
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