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.

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    • "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). "
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    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.
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    • "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). "
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    • "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). "
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