ArticleThe EMBO journal2009
A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation.
Article in The EMBO journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
82 citing papers in PubMed, 171 citations in OpenAlex.
- Exogenous 24nt siRNAs induce AGO4A-dependent silencing via promoter DNA methylation and H3K9me2 deposition.Frontiers in plant science · 2026Article
- Article
- SPT6L, a newly discovered ancestral component of the plant RNA-directed DNA methylation pathway.Frontiers in plant science · 2024Article
- A GFP splicing reporter in a coilin mutant background reveals links between alternative splicing, siRNAs, and coilin function in Arabidopsis thaliana.G3 (Bethesda, Md.) · 2023Article
- Plant gene silencing signals move from the phloem to influence gene expression in shoot apical meristems.BMC plant biology · 2022Article
- Long Non-Coding RNAs: New Players in Plants.International journal of molecular sciences · 2022Review
- The evolutionary history of small RNAs in Solanaceae.Plant physiology · 2022Article
- RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm.PLoS biology · 2022Article
- Article
- Big Role of Small RNAs in Female Gametophyte Development.International journal of molecular sciences · 2022Review
- Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus.BMC genomics · 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
- Targets and Mechanisms of Geminivirus Silencing Suppressor Protein AC2.Frontiers in microbiology · 2021Review
- Secondary siRNAs in Plants: Biosynthesis, Various Functions, and Applications in Virology.Frontiers in plant science · 2021Review
- Genome-Wide Analysis Reveals Dynamic Epigenomic Differences in Soybean Response to Low-Phosphorus Stress.International journal of molecular sciences · 2020Article
- Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize.Nature communications · 2020Article
- Article
- Mechanisms and Functions of Long Non-Coding RNAs at Multiple Regulatory Levels.International journal of molecular sciences · 2019Review
- Molecular basis of transitivity in plant RNA silencing.Molecular biology reports · 2019Review
- Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita.BMC genomics · 2018Article
22 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We used a transgene system to study spreading of RNA-directed DNA methylation (RdDM) during transcriptional gene silencing in Arabidopsis thaliana. Forward and reverse genetics approaches using this system delineated a stepwise pathway for the biogenesis of secondary siRNAs and unidirectional spreading of methylation from an upstream enhancer element into downstream sequences. Trans-acting, hairpin-derived primary siRNAs induce primary RdDM, independently of an enhancer-associated 'nascent' RNA, at the target enhancer region. Primary RdDM is a key step in the pathway because it attracts the secondary siRNA-generating machinery, including RNA polymerase IV, RNA-dependent RNA polymerase2 and Dicer-like3 (DCL3). These factors act in a turnover pathway involving a nascent RNA, which normally accumulates stably in non-silenced plants, to produce cis-acting secondary siRNAs that induce methylation in the downstream region. The identification of DCL3 in a forward genetic screen for silencing-defective mutants demonstrated a strict requirement for 24-nt siRNAs to direct methylation. A similar stepwise process for spreading of DNA methylation may occur in mammalian genomes, which are extensively transcribed in upstream regulatory regions.
Indexed as
Identifiers
What OpenQuestion holds
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.