ArticleGenome research2015
Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
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Who cites it
90 citing papers in PubMed, 165 citations in OpenAlex.
- siRNA-guided DNA-methylation at a sucrose transporter gene potentially contributes to climatic plant adaptation.PLoS biology · 2026Article
- The nuclear cap-binding complex regulates subcellular RNA processing and surveillance of coding and noncoding RNAs.Nucleic acids research · 2026Article
- DNA methylation in plant heterosis: mechanisms and prospects.Functional & integrative genomics · 2025Review
- Factors determining chromosomal localization of transposable elements in plants.Plant biology (Stuttgart, Germany) · 2025Review
- DNA Methylation in Rice: Mechanisms, Regulatory Roles, and Beyond.International journal of molecular sciences · 2025Review
- Molecular Mechanisms Underlying the Establishment, Maintenance, and Removal of DNA Methylation in Plants.Annual review of plant biology · 2025Review
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- Ectopic enhancer-enhancer interactions as causal forces driving RNA-directed DNA methylation in gene regulatory regions.Plant biotechnology journal · 2024Article
- An RdDM-independent function of Pol V transcripts in gene regulation and plant defence.Nature plants · 2024Article
- Transcription elongation of the plant RNA polymerase IV is prone to backtracking.Science advances · 2024Article
- Paramutation at the maize pl1 locus is associated with RdDM activity at distal tandem repeats.PLoS genetics · 2024Article
- Barley AGO4 proteins show overlapping functionality with distinct small RNA-binding properties in heterologous complementation.Plant cell reports · 2024Article
- Article
- DNA-dependent RNA polymerases in plants.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
- DNA Methylation in Algae and Its Impact on Abiotic Stress Responses.Plants (Basel, Switzerland) · 2023Review
- Ovule siRNAs methylate protein-coding genes in trans.The Plant cell · 2022Article
- Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1.Nucleic acids research · 2022Article
- Transgenerationally Transmitted DNA Demethylation of a Spontaneous Epialleles Using CRISPR/dCas9-TET1cd Targeted Epigenetic Editing in Arabidopsis.International journal of molecular sciences · 2022Article
- Functional specialization of monocot DCL3 and DCL5 proteins through the evolution of the PAZ domain.Nucleic acids research · 2022Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
Twenty-four-nucleotide small interfering (si)RNAs are central players in RNA-directed DNA methylation (RdDM), a process that establishes and maintains DNA methylation at transposable elements to ensure genome stability in plants. The plant-specific RNA polymerase IV (Pol IV) is required for siRNA biogenesis and is believed to transcribe RdDM loci to produce primary transcripts that are converted to double-stranded RNAs (dsRNAs) by RDR2 to serve as siRNA precursors. Yet, no such siRNA precursor transcripts have ever been reported. Here, through genome-wide profiling of RNAs in genotypes that compromise the processing of siRNA precursors, we were able to identify Pol IV/RDR2-dependent transcripts from tens of thousands of loci. We show that Pol IV/RDR2-dependent transcripts correspond to both DNA strands, whereas the RNA polymerase II (Pol II)-dependent transcripts produced upon derepression of the loci are derived primarily from one strand. We also show that Pol IV/RDR2-dependent transcripts have a 5' monophosphate, lack a poly(A) tail at the 3' end, and contain no introns; these features distinguish them from Pol II-dependent transcripts. Like Pol II-transcribed genic regions, Pol IV-transcribed regions are flanked by A/T-rich sequences depleted in nucleosomes, which highlights similarities in Pol II- and Pol IV-mediated transcription. Computational analysis of siRNA abundance from various mutants reveals differences in the regulation of siRNA biogenesis at two types of loci that undergo CHH methylation via two different DNA methyltransferases. These findings begin to reveal features of Pol IV/RDR2-mediated transcription at the heart of genome stability in plants.
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