Brodersen, P. & Voinnet, O. The diversity of RNA silencing pathways in plants. Trends Genet. 22, 268-280

French National Centre for Scientific Research, Lutetia Parisorum, Île-de-France, France
Trends in Genetics (Impact Factor: 9.92). 06/2006; 22(5):268-80. DOI: 10.1016/j.tig.2006.03.003
Source: PubMed


RNA silencing was discovered in plants as a mechanism whereby invading nucleic acids, such as transgenes and viruses, are silenced through the action of small (20-26 nt) homologous RNA molecules. Our understanding of small RNA biology has significantly improved in recent years, and it is now clear that there are several cellular silencing pathways in addition to those involved in defense. Endogenous silencing pathways have important roles in gene regulation at the transcriptional, RNA stability and translational levels. They share a common core of small RNA generator and effector proteins with multiple paralogs in plant genomes, some of which have acquired highly specialized functions. Here, we review recent developments in the plant RNA silencing field that have identified components of specific silencing pathways and have shed light on the mechanisms and biological roles of RNA silencing in plants.

Download full-text


Available from: Olivier Voinnet,
  • Source
    • "This may be the result from the target present at too low abundance to be detected (Zhou et al. 2012b). Furthermore, at least some of these miRNAs may silence their target activity via translational repression (Brodersen and Voinnet 2006). Based on the functional annotations of the target genes in the database, some of the targets for conserved miRNAs are highly conserved in Arabidopsis (Rhoades et al. 2002; Bartel 2004; Sunkar and Zhu 2004) and other plant species (Sunkar et al. 2005; Buhtz et al. 2008). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Paulownia witches' broom (PaWB) caused by the phytoplasma is a devastating disease of Paulownia trees. It has caused heavy yield losses to Paulownia production worldwide. However, knowledge of the transcriptional and post-transcriptional regulation of gene expression by microRNAs (miRNAs), especially miRNAs responsive to PaWB disease stress, is still rudimentary. In this study, to identify miRNAs and their transcript targets that are responsive to PaWB disease stress, six sequencing libraries were constructed from healthy (PF), PaWB-infected (PFI), and PaWB-infected, 20 mg L(-1) methyl methane sulfonate-treated (PFI20) P. fortunei seedlings. As a result, 95 conserved miRNAs belonging to 18 miRNA families, as well as 122 potential novel miRNAs, were identified. Most of them were found to be a response to PaWB disease-induced stress, and the expression levels of these miRNAs were validated by quantitative real-time PCR analysis. The study simultaneously identified 109 target genes from the P. fortunei for 14 conserved miRNA families and 24 novel miRNAs by degradome sequencing. Furthermore, the functions of the miRNA targets were annotated based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. The results presented here provide the groundwork for further analysis of miRNAs and target genes responsive to the PaWB disease stress, and could be also useful for addressing new questions to better understand the mechanisms of plant infection by phytoplasma in the future.
    MGG Molecular & General Genetics 08/2015; DOI:10.1007/s00438-015-1102-y · 2.73 Impact Factor
    • "The vector plasmid pSK(+)PICT1 (vector map in Appendices S1, IV, y) was constructed for the generation of double-stranded RNA transcripts from cloned genes effecting posttranscriptional gene silencing in Ulva transformants (Smith et al. 2000, Fuhrmann et al. 2001, Helliwell and Waterhouse 2003, Brodersen and Voinnet 2006). The singlestranded form of the pSK(+)PICT1 vector was prepared at first by infecting an E. coli strain carrying this plasmid with a f1-helper phage (Sambrook et al. 1989). "
    [Show abstract] [Hide abstract]
    ABSTRACT: A method for the stable transformation of the green marine macroalga Ulva mutabilis was developed based on vector plasmids integrating into the genome. By combination of the expression signals (promoter, enhancer and transcriptional termination sequences) of a chromosomal rbcS gene from Ulva mutabilis with the bleomycin resistance gene (ble) from Streptoalloteichus hindustanus, a dominant selectable marker gene was constructed for the preparation of a series of E. coli - Ulva mutabilis shuttle vector plasmids. Special vectors were prepared for the introduction and expression of foreign genes in Ulva, for insertional mutagenesis and gene tagging by plasmid integration into the genome, and for protein-tagging by the green fluorescent protein (GFP), as well as tools for post-transcriptional gene silencing and cosmid cloning to prepare genomic gene libraries for mutant gene complementation. The vectors were successfully tested in pilot experiments, where they were efficiently introduced into Ulva gametes, zoospores or protoplasts of somatic blade cells by treatment with Ca++-ions and polyethylene glycol under isotonic conditions at low ionic strength. The parthenogenetically propagated phleomycin resistant transformants of the mutant slender (sl) and the wildtype (wt) were demonstrated to be carrying the plasmids randomly, which were stably integrated into the chromosomes, often as tandem repeat clusters.This article is protected by copyright. All rights reserved.
    Journal of Phycology 08/2015; 51(5). DOI:10.1111/jpy.12336 · 2.84 Impact Factor
  • Source
    • "Long dsRNA molecules in plants are typically produced by several RNA-dependent RNA polymerases (Baulcombe 2004; Carthew and Sontheimer 2009), but can also be formed by intermolecular base-pairing from highly repetitive regions of plant genomes or due to convergent transcription (Borsani et al. 2005). Because dsRNA precursor-independent production of siRNAs has not been described in plants, it is assumed that most siRNAs in plants are derived from long dsRNA precursors through the activity of several Dicer-like, dsRNA RNAase III-type nucleases (Brodersen and Voinnet 2006). Based on this assumption, we exploited genome-wide small RNA sequencing to predict dsRNA-producing loci in corn and tomato (Jensen et al. 2013). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Environmental RNAi (eRNAi) is a sequence-specific regulation of endogenous gene expression in a receptive organism by exogenous double-stranded RNA (dsRNA). Although demonstrated under artificial dietary conditions and via transgenic plant presentations in several herbivorous insects, the magnitude and consequence of exogenous dsRNA uptake and the role of eRNAi remains unknown under natural insect living conditions. Our analysis of coleopteran insects sensitive to eRNAi fed on wild-type plants revealed uptake of plant endogenous long dsRNAs, but not small RNAs. Subsequently, the dsRNAs were processed into 21 nt siRNAs by insects and accumulated in high quantities in insect cells. No accumulation of host plant-derived siRNAs was observed in lepidopteran larvae that are recalcitrant to eRNAi. Stability of ingested dsRNA in coleopteran larval gut followed by uptake and transport from the gut to distal tissues appeared to be enabling factors for eRNAi. Although a relatively large number of distinct coleopteran insect-processed plant-derived siRNAs had sequence complementarity to insect transcripts, the vast majority of the siRNAs were present in relatively low abundance, and RNA-seq analysis did not detect a significant effect of plant-derived siRNAs on insect transcriptome. In summary, we observed a broad genome-wide uptake of plant endogenous dsRNA and subsequent processing of ingested dsRNA into 21 nt siRNAs in eRNAi-sensitive insects under natural feeding conditions. In addition to dsRNA stability in gut lumen and uptake, dosage of siRNAs targeting a given insect transcript is likely an important factor in order to achieve measurable eRNAi-based regulation in eRNAi-competent insects that lack an apparent silencing amplification mechanism. © 2015 Ivashuta et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
    RNA 03/2015; 21(5):840-850. DOI:10.1261/rna.048116.114 · 4.94 Impact Factor
Show more