Short Silencing RNA: The Dark Matter of Genetics?

Baulcombe, David C.

doi:10.1101/sqb.2006.71.052

Cited by 39 publications

(27 citation statements)

References 62 publications

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“…The biogenesis of these small RNAs in plants shares similarities with their biogenesis in other eukaryotes, suggesting that RNA-based silencing mechanisms, involving mi-and siRNA, have a common ancient origin (Chapman and Carrington 2007;Shabalina and Koonin 2008). However, duplication and subfunctionalization of genes involved in miRNA-or siRNA-mediated processes in plants has led to the evolution of multiple pathways that are specialized to accomplish specific tasks (Herr 2005;Baulcombe 2006;Xie and Qi 2008;Chen 2009;Vazquez et al 2010). These include (1) a pathway for the biogenesis of miRNAs that are complementary to target sequences, resulting in the downregulation of individual transcribed mRNAs (Sec.…”

Section: Molecular Components Of Rna-mediated Gene Silencing Pathwaysmentioning

confidence: 99%

“…Epigenetic mechanisms involving RNA molecules were shown to naturally protect plants from uncontrolled replication of viruses, which can be both inducers and targets of PTGS. It was soon realized that these mechanisms could be exploited to experimentally down-regulate plant genes by constructing viral vectors containing plant gene sequences, thus harnessing the virus-induced gene silencing pathway (VIGS, a topic discussed in more detail in Baulcombe andDean 2014 andreviewed in Senthil-Kumar andMysore 2011). Another mechanism discovered in viroid-infected plants is the RNA-guided specification of DNA methylation (RNA-directed DNA methylation, RdDM) and other heterochromatic marks at homologous DNA regions (Wassenegger et al 1994).…”

Section: Overviewmentioning

confidence: 99%

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Epigenetic Regulation in Plants

Pikaard

Scheid

2014

Cold Spring Harbor Perspectives in Biology

327

289

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SUMMARYThe study of epigenetics in plants has a long and rich history, from initial descriptions of non-Mendelian gene behaviors to seminal discoveries of chromatin-modifying proteins and RNAs that mediate gene silencing in most eukaryotes, including humans. Genetic screens in the model plant Arabidopsis have been particularly rewarding, identifying more than 130 epigenetic regulators thus far. The diversity of epigenetic pathways in plants is remarkable, presumably contributing to the phenotypic plasticity of plant postembryonic development and the ability to survive and reproduce in unpredictable environments.

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Section: Molecular Components Of Rna-mediated Gene Silencing Pathwaysmentioning

confidence: 99%

Section: Overviewmentioning

confidence: 99%

Epigenetic Regulation in Plants

Pikaard

Scheid

2014

Cold Spring Harbor Perspectives in Biology

327

289

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“…These small RNAs are processed from RNA precursors by type III RNase enzymes, referred to as DICER or DICER-LIKE proteins (DCL), and incorporated into RNA induced silencing complexes (RISC) to mediate post-transcriptional gene silencing (PTGS) by translational arrest or mRNA cleavage, or into RNA-induced transcriptional silencing complexes (RITS) to mediate transcriptional gene silencing (TGS) by repressive DNA and histone modifications (Baulcombe 2006;Li and Ding 2006;Ding and Voinnet 2007;Henderson and Jacobsen 2007;Slotkin and Martienssen 2007). In Arabidopsis, small RNA biogenesis enzymes are encoded by gene families in which the individual members have specialized functions in parallel pathways.…”

mentioning

confidence: 99%

Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs

Kuang

Padmanabhan²,

Li³

et al. 2008

Genome Res.

156

150

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Small RNAs regulate the genome by guiding transcriptional and post-transcriptional silencing machinery to specific target sequences, including genes and transposable elements (TEs). Although miniature inverted-repeat transposable elements (MITEs) are closely associated with euchromatic genes, the broader functional impact of these short TE insertions in genes is largely unknown. We identified 22 families of MITEs in the Solanaceae (MiS1-MiS22) and found abundant MiS insertions in Solanaceae genomic DNA and expressed sequence tags (EST). Several Solanaceae MITEs generate genome changes that potentially affect gene function and regulation, most notably, a MiS insertion that provides a functionally indispensable alternative exon in the tobacco mosaic virus N resistance gene. We show that MITEs generate small RNAs that are primarily 24 nt in length, as detected by Northern blot hybridization and by sequencing small RNAs of Solanum demissum, Nicotiana glutinosa, and Nicotiana benthamiana. Additionally, we show that stable RNAi lines silencing DICER-LIKE3 (DCL3) in tobacco and RNA-dependent RNA polymerase 2 (RDR2) in potato cause a reduction in 24-nt MITE siRNAs, suggesting that, as in Arabidopsis, TE-derived siRNA biogenesis is DCL3 and RDR2 dependent. We provide evidence that DICER-LIKE4 (DCL4) may also play a role in MITE siRNA generation in the Solanaceae.

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“…Cycles that include production of secondary small RNAs are not restricted to the piRNA pathway (Baulcombe 2006). Indeed, situations in which production of secondary siRNAs depends on primary siRNAs or miRNAs have been described in fission yeast (Sugiyama et al 2005), C. elegans (Pak and Fire 2007;Sijen et al 2007), and plants (Allen et al 2005;Axtell et al 2006;Daxinger et al 2009).…”

Section: The Piwi/pirna Pathway As An Epigenetic Sensor and Memory Inmentioning

confidence: 99%

Small RNA Silencing Pathways in Germ and Stem Cells

Aravin¹,

Hannon²

2008

Cold Spring Harbor Symposia on Quantitative Biology

106

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During the past several years, it has become clear that small RNAs guard germ cell genomes from the activity of mobile genetic elements. Indeed, in mammals, a class of small RNAs, known as Piwi-interacting RNAs (piRNAs), forms an innate immune system that discriminates transposons from endogenous genes and selectively silences the former. piRNAs enforce silencing by directing transposon DNA methylation during male germ cell development. As such, piRNAs represent perhaps the only currently known sequence-specific factor for deposition of methylcytosine in mammals. The three mammalian Piwi proteins Miwi2, Mili, and Miwi are required at different stages of germ cell development. Moreover, distinct classes of piRNAs are expressed in developmental waves, with particular generative loci and different sequence content distinguishing piRNAs populations in embryonic germ cells from those that appear during meiosis. Although our understanding of Piwi proteins and piRNA biology have deepened substantially during the last several years, major gaps still exist in our understanding of these enigmatic RNA species.

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Short Silencing RNA: The Dark Matter of Genetics?

Cited by 39 publications

References 62 publications

Epigenetic Regulation in Plants

Epigenetic Regulation in Plants

Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs

Small RNA Silencing Pathways in Germ and Stem Cells

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