ArticleGenes & development2012
Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome.
Article in Genes & development, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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79 citing papers in PubMed.
- Gene Inactivation in Transgenic Plants-A Unique Model for Studying Epigenetic Regulation of Gene Expression.Plants (Basel, Switzerland) · 2026Review
- Small Interfering RNAs as Critical Regulators of Plant Life Process: New Perspectives on Regulating the Transcriptomic Machinery.International journal of molecular sciences · 2025Review
- From RdDM to plant defence.Nature plants · 2024Article
- Identification and Functional Analysis of Drought-Responsive Long Noncoding RNAs in Maize Roots.International journal of molecular sciences · 2023Article
- DNA-dependent RNA polymerases in plants.The Plant cell · 2023Article
- Beyond transcription: compelling open questions in plant RNA biology.The Plant cell · 2023Article
- 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
- BPM1 regulates RdDM-mediated DNA methylation via a cullin 3 independent mechanism.Plant cell reports · 2022Article
- Epigenetic Dynamics and Regulation of Plant Male Reproduction.International journal of molecular sciences · 2022Review
- MSI4/FVE is required for accumulation of 24-nt siRNAs and DNA methylation at a subset of target regions of RNA-directed DNA methylation.The Plant journal : for cell and molecular biology · 2021Article
- Reinforcement of transcriptional silencing by a positive feedback between DNA methylation and non-coding transcription.Nucleic acids research · 2021Article
- Non-perfectly matching small RNAs can induce stable and heritable epigenetic modifications and can be used as molecular markers to trace the origin and fate of silencing RNAs.Nucleic acids research · 2021Article
- Extreme Resistance to Viruses in Potato and Soybean.Frontiers in plant science · 2021Review
- Broad noncoding transcription suggests genome surveillance by RNA polymerase V.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- The expression of long non-coding RNAs is associated with H3Ac and H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex inNAR genomics and bioinformatics · 2020Article
- Epigenetic Modifications: An Unexplored Facet of Exogenous RNA Application in Plants.Plants (Basel, Switzerland) · 2020Article
- Epigenomic landscape and epigenetic regulation in maize.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Review
- Cytosine Methylation Affects the Mutability of Neighboring Nucleotides in Germline and Soma.Genetics · 2020Article
- Polymerase IV Plays a Crucial Role in Pollen Development inThe Plant cell · 2020Article
- High-Pressure-Sprayed Double Stranded RNA Does Not Induce RNA Interference of a Reporter Gene.Frontiers in plant science · 2020Article
19 more citing papers are in PubMed but not listed here.
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Abstract
Multisubunit RNA polymerases IV and V (Pols IV and V) mediate RNA-directed DNA methylation and transcriptional silencing of retrotransposons and heterochromatic repeats in plants. We identified genomic sites of Pol V occupancy in parallel with siRNA deep sequencing and methylcytosine mapping, comparing wild-type plants with mutants defective for Pol IV, Pol V, or both Pols IV and V. Approximately 60% of Pol V-associated regions encompass regions of 24-nucleotide (nt) siRNA complementarity and cytosine methylation, consistent with cytosine methylation being guided by base-pairing of Pol IV-dependent siRNAs with Pol V transcripts. However, 27% of Pol V peaks do not overlap sites of 24-nt siRNA biogenesis or cytosine methylation, indicating that Pol V alone does not specify sites of cytosine methylation. Surprisingly, the number of methylated CHH motifs, a hallmark of RNA-directed de novo methylation, is similar in wild-type plants and Pol IV or Pol V mutants. In the mutants, methylation is lost at 50%-60% of the CHH sites that are methylated in the wild type but is gained at new CHH positions, primarily in pericentromeric regions. These results indicate that Pol IV and Pol V are not required for cytosine methyltransferase activity but shape the epigenome by guiding CHH methylation to specific genomic sites.
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