ArticlePloS one2009
Heterochromatic siRNAs and DDM1 independently silence aberrant 5S rDNA transcripts in Arabidopsis.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
30 citing papers in PubMed, 1 synthesis or guideline pooled it, 51 citations in OpenAlex.
- Systematic Review of Plant Ribosome Heterogeneity and Specialization.Frontiers in plant science · 2020Pooled it
- Augmented CENH3 loading is accompanied by transcriptional and epigenetic reprogramming at rice centromeres during meiosis.Genome biology · 2026Article
- A comprehensive atlas of full-length Arabidopsis eccDNA populations identifies their genomic origins and epigenetic regulation.PLoS biology · 2025Article
- Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducingGenome research · 2025Article
- Functions of RNAi Pathways in Ribosomal RNA Regulation.Non-coding RNA · 2024Review
- Advances in the Study of the Transcriptional Regulation Mechanism of Plant miRNAs.Life (Basel, Switzerland) · 2023Review
- Enzymatic reactions of AGO4 in RNA-directed DNA methylation: siRNA duplex loading, passenger strand elimination, target RNA slicing, and sliced target retention.Genes & development · 2023Article
- DDM1-Mediated TE Silencing in Plants.Plants (Basel, Switzerland) · 2023Review
- Thousands of high-quality sequencing samples fail to show meaningful correlation between 5S and 45S ribosomal DNA arrays in humans.Scientific reports · 2021Article
- 3-Hydroxybutyrate Is Active Compound in Flax That Upregulates Genes Involved in DNA Methylation.International journal of molecular sciences · 2020Article
- The PEAT protein complexes are required for histone deacetylation and heterochromatin silencing.The EMBO journal · 2018Article
- Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana.Nucleic acids research · 2018Article
- Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding.Genome biology · 2017Article
- Review
- Article
- Cytosine hypomethylation at CHG and CHH sites in the pleiotropic mutants of Mendelian inheritance in Catharanthus roseus.Journal of genetics · 2013Article
- Poplars with a PtDDM1-RNAi transgene have reduced DNA methylation and show aberrant post-dormancy morphology.Planta · 2013Article
- Article
- Asymmetric purine-pyrimidine distribution in cellular small RNA population of papaya.BMC genomics · 2012Article
- Expression of 5 S rRNA genes linked to 35 S rDNA in plants, their epigenetic modification and regulatory element divergence.BMC plant biology · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
5S ribosomal RNA gene repeats are arranged in heterochromatic arrays (5S rDNA) situated near the centromeres of Arabidopsis chromosomes. The chromatin remodeling factor DDM1 is known to maintain 5S rDNA methylation patterns while silencing transcription through 5S rDNA intergenic spacers (IGS). We mapped small-interfering RNAs (siRNA) to a composite 5S rDNA repeat, revealing a high density of siRNAs matching silenced IGS transcripts. IGS transcript repression requires proteins of the heterochromatic siRNA pathway, including RNA polymerase IV (Pol IV), RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3). Using molecular and cytogenetic approaches, we show that the DDM1 and siRNA-dependent silencing effects are genetically independent. DDM1 suppresses production of the siRNAs, however, thereby limiting RNA-directed DNA methylation at 5S rDNA repeats. We conclude that DDM1 and siRNA-dependent silencing are overlapping processes that both repress aberrant 5S rDNA transcription and contribute to the heterochromatic state of 5S rDNA arrays.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.