ArticleNature plants2018
RNA-directed DNA methylation involves co-transcriptional small-RNA-guided slicing of polymerase V transcripts in Arabidopsis.
Article in Nature plants, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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Who cites it
89 citing papers in PubMed, 170 citations in OpenAlex.
- Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline.Nature communications · 2026Article
- siRNA-guided DNA-methylation at a sucrose transporter gene potentially contributes to climatic plant adaptation.PLoS biology · 2026Article
- Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq).Nature protocols · 2026Review
- A spontaneous termination mechanism of RNA polymerase V shapes the DNA methylation landscape in plants.The EMBO journal · 2026Article
- The landscape of cotton DNA methylation and its epigenetic regulation in Verticillium wilt resistance.Plant cell reports · 2026Article
- Photorespiration is linked to DNA methylation by formate as a one-carbon source.Nature plants · 2026Article
- DNA Methylation Dynamics in Plant Abiotic Stress Response: Mechanisms, Memory, and Breeding Applications.Genes · 2026Review
- Integrative multi-omics analysis widens annotation and functional insights into long non-coding RNAs of Arabidopsis thaliana.Biology direct · 2026Article
- Epigenomics and Non-Coding RNAs in Soybean Adaptation to Abiotic Stresses.International journal of molecular sciences · 2025Review
- An antagonistic epigenetic mechanism regulating gene expression in pollen revealed through single-nucleus multiomics.Nature communications · 2025Article
- An antagonistic epigenetic mechanism regulating gene expression in pollen revealed through single-nucleus multiomics.bioRxiv : the preprint server for biology · 2025Article
- Epigenetically poised chromatin states regulateaBIOTECH · 2025Article
- Epigenetics in Plant Response to Climate Change.Biology · 2025Review
- A Brief Overview of the Epigenetic Regulatory Mechanisms in Plants.International journal of molecular sciences · 2025Review
- LEC2 induces somatic cell reprogramming through epigenetic activation of plant cell totipotency regulators.Nature communications · 2025Article
- Molecular Mechanisms Underlying the Establishment, Maintenance, and Removal of DNA Methylation in Plants.Annual review of plant biology · 2025Review
- Advances in Small RNA Regulation of Female Gametophyte Development in Flowering Plants.Plants (Basel, Switzerland) · 2025Review
- Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducingGenome research · 2025Article
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.Nature communications · 2024Article
29 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
Abstract
Small RNAs regulate chromatin modifications such as DNA methylation and gene silencing across eukaryotic genomes. In plants, RNA-directed DNA methylation (RdDM) requires 24-nucleotide small interfering RNAs (siRNAs) that bind to ARGONAUTE 4 (AGO4) and target genomic regions for silencing. RdDM also requires non-coding RNAs transcribed by RNA polymerase V (Pol V) that probably serve as scaffolds for binding of AGO4-siRNA complexes. Here, we used a modified global nuclear run-on protocol followed by deep sequencing to capture Pol V nascent transcripts genome-wide. We uncovered unique characteristics of Pol V RNAs, including a uracil (U) common at position 10. This uracil was complementary to the 5' adenine found in many AGO4-bound 24-nucleotide siRNAs and was eliminated in a siRNA-deficient mutant as well as in the ago4/6/9 triple mutant, suggesting that the +10 U signature is due to siRNA-mediated co-transcriptional slicing of Pol V transcripts. Expression of wild-type AGO4 in ago4/6/9 mutants was able to restore slicing of Pol V transcripts, but a catalytically inactive AGO4 mutant did not correct the slicing defect. We also found that Pol V transcript slicing required SUPPRESSOR OF TY INSERTION 5-LIKE (SPT5L), an elongation factor whose function is not well understood. These results highlight the importance of Pol V transcript slicing in RNA-mediated transcriptional gene silencing, which is a conserved process in many eukaryotes.
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