ArticleGenome biology2019
Invasive DNA elements modify the nuclear architecture of their insertion site by KNOT-linked silencing in Arabidopsis thaliana.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 33 citations in OpenAlex.
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- Modeling the 3D genome of plants.Nucleus (Austin, Tex.) · 2021Article
- Altered chromatin architecture and gene expression during polyploidization and domestication of soybean.The Plant cell · 2021Article
- Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure.PLoS genetics · 2021Article
- ANCHOR: A Technical Approach to Monitor Single-Copy Locus LocalizationFrontiers in plant science · 2021Article
- Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective.Frontiers in cell and developmental biology · 2021Review
- Three-dimensional nuclear organization in Arabidopsis thaliana.Journal of plant research · 2020Review
- Toward an understanding of nuclear substructures beyond their classical functions.Journal of plant research · 2020Article
- Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis.Nature communications · 2020Article
- The Position and Complex Genomic Architecture of Plant T-DNA Insertions Revealed by 4SEE.International journal of molecular sciences · 2020Article
- Integrating transposable elements in the 3D genome.Mobile DNA · 2020Article
- Invasive DNA elements modify the nuclear architecture of their insertion site by KNOT-linked silencing in Arabidopsis thaliana.Genome biology · 2019Article
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2 authors at 1 institution in 1 country.
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Abstract
backgroundThe three-dimensional (3D) organization of chromosomes is linked to epigenetic regulation and transcriptional activity. However, only few functional features of 3D chromatin architecture have been described to date. The KNOT is a 3D chromatin structure in Arabidopsis, comprising 10 interacting genomic regions termed KNOT ENGAGED ELEMENTs (KEEs). KEEs are enriched in transposable elements and associated small RNAs, suggesting a function in transposon biology.
resultsHere, we report the KNOT's involvement in regulating invasive DNA elements. Transgenes can specifically interact with the KNOT, leading to perturbations of 3D nuclear organization, which correlates with the transgene's expression: high KNOT interaction frequencies are associated with transgene silencing. KNOT-linked silencing (KLS) cannot readily be connected to canonical silencing mechanisms, such as RNA-directed DNA methylation and post-transcriptional gene silencing, as both cytosine methylation and small RNA abundance do not correlate with KLS. Furthermore, KLS exhibits paramutation-like behavior, as silenced transgenes can lead to the silencing of active transgenes in trans.
conclusionTransgene silencing can be connected to a specific feature of Arabidopsis 3D nuclear organization, namely the KNOT. KLS likely acts either independent of or prior to canonical silencing mechanisms, such that its characterization not only contributes to our understanding of chromosome folding but also provides valuable insights into how genomes are defended against invasive DNA elements.
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