ArticleGenome biology2020
Chromatin regulates expression of small RNAs to help maintain transposon methylome homeostasis in Arabidopsis.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 98 citations in OpenAlex.
- Transposon expansion is associated with reorganization of small RNA and DNA methylation landscapes in the morphologically minimal angiosperm Wolffia brasiliensis.The Plant journal : for cell and molecular biology · 2026Article
- DNA methylation remodeling reveals epigenetic regulation of early embryogenesis in Arabidopsis hybrid.Communications biology · 2026Article
- New molecular players: siRNA expression and gene regulation in Hordeum vulgare L. ageing seeds after germination.BMC genomics · 2026Article
- TheProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Gaining insights into epigenetic memories through artificial intelligence and omics science in plants.Journal of integrative plant biology · 2025Review
- The Expansion and Diversification of Epigenetic Regulatory Networks Underpins Major Transitions in the Evolution of Land Plants.Molecular biology and evolution · 2025Article
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- Dancing with the enemy: symbiotic relationships between plant RNA viruses and their hosts.Frontiers in plant science · 2025Review
- DEMETER DNA demethylase reshapes the global DNA methylation landscape and controls cell identity transition during plant regeneration.BMC genomics · 2024Article
- CLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencing.Nature communications · 2024Article
- H1 restricts euchromatin-associated methylation pathways from heterochromatic encroachment.eLife · 2024Article
- Mind the gap: Epigenetic regulation of chromatin accessibility in plants.Plant physiology · 2024Review
- Two ARGONAUTE proteins loaded with transposon-derived small RNAs are associated with the reproductive cell lineage in Arabidopsis.The Plant cell · 2024Article
- Loops, crosstalk, and compartmentalization: it takes many layers to regulate DNA methylation.Current opinion in genetics & development · 2024Review
- Population-level annotation of lncRNAs in Arabidopsis reveals extensive expression variation associated with transposable element-like silencing.The Plant cell · 2023Article
- H2A.X promotes endosperm-specific DNA methylation in Arabidopsis thaliana.BMC plant biology · 2023Article
- Small RNA-mediated DNA methylation during plant reproduction.The Plant cell · 2023Review
- Epigenetic Regulation During Plant Development and the Capacity for Epigenetic Memory.Annual review of plant biology · 2023Review
- DDM1-Mediated TE Silencing in Plants.Plants (Basel, Switzerland) · 2023Review
- Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat.Genome biology · 2023Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
backgroundEukaryotic genomes are partitioned into euchromatic and heterochromatic domains to regulate gene expression and other fundamental cellular processes. However, chromatin is dynamic during growth and development and must be properly re-established after its decondensation. Small interfering RNAs (siRNAs) promote heterochromatin formation, but little is known about how chromatin regulates siRNA expression.
resultsWe demonstrate that thousands of transposable elements (TEs) produce exceptionally high levels of siRNAs in Arabidopsis thaliana embryos. TEs generate siRNAs throughout embryogenesis according to two distinct patterns depending on whether they are located in euchromatic or heterochromatic regions of the genome. siRNA precursors are transcribed in embryos, and siRNAs are required to direct the re-establishment of DNA methylation on TEs from which they are derived in the new generation. Decondensed chromatin also permits the production of 24-nt siRNAs from heterochromatic TEs during post-embryogenesis, and siRNA production from bipartite-classified TEs is controlled by their chromatin states.
conclusionsDecondensation of heterochromatin in response to developmental, and perhaps environmental, cues promotes the transcription and function of siRNAs in plants. Our results indicate that chromatin-mediated siRNA transcription provides a cell-autonomous homeostatic control mechanism to help reconstitute pre-existing chromatin states during growth and development including those that ensure silencing of TEs in the future germ line.
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