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RNA‐based regulation of transposon expression

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Throughout the domains of life, transposon activity represents a serious threat to genome integrity and evolution has realized different molecular mechanisms that aim to inhibit the transposition of mobile DNA. Small noncoding RNAs that function as guides for Argonaute effector proteins represent a key feature of so‐called RNA interference (RNAi) pathways and specialized RNAi pathways exist to repress transposon activity on the transcriptional and posttranscriptional level. Transposon transcription can be diminished by targeted DNA methylation or chromatin remodeling via repressive Histone modifications. Posttranscriptional transposon silencing bases on degradation of transposon transcripts to prevent either reverse transcription followed by genomic reintegration or translation into proteins that mediate the transposition process. In plants, Argonaute‐like proteins guided by short interfering RNAs (siRNAs) are essential for transposon repression on the epigenetic and posttranscriptional level. In the germline of animals, these tasks are often assumed by a second subclass of Argonaute proteins referred to as Piwi‐like proteins, which bind a distinct class of small noncoding RNAs named piwi‐interacting RNAs (piRNAs). Though the principals of RNAi pathways are essentially the same in all eukaryotic organisms, remarkable differences can be observed even in closely related species reflecting the astonishing plasticity and diversity of these pathways. WIREs RNA 2015, 6:687–708. doi: 10.1002/wrna.1310 This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
The short interfering RNA (siRNA) and piwi‐interacting RNA (piRNA) pathways at a glance. DNA is indicated in blue, RNA is displayed in red. Asterisks indicate different PIWI paralogs involved in canonical heterotypic ping‐pong cycle. Abbreviations: M, methylation; U, uracil; A, adenine; G, guanine, C, cytosine.
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DNA elimination in Tetrahymena. (a) Stages of sexual reproduction of Tetrahymena. (b) Twi1p and scnRNA‐mediated DNA elimination. Abbreviations: Mic, Micronucleus; Mac, Macronucleus; IES, internal eliminated sequences.
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Transposon silencing in the plant germline. Global DNA demethylation in companion cells and in the endosperm leads to reactivation of TEs and production of short interfering RNAs (siRNAs) that are transferred into gametes and embryo to reinforce TE silencing in germline and developing embryo. Abbreviations: VN, vegetative nucleus; SC, sperm cell; CC, central cell; Me, DNA methylation.
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Transition from PTGS to TGS in plants during a de novo genome invasion by an active TE.
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Canonical RNA‐directed DNA methylation (RdDM) in plants mediated by 24 nt short interfering RNAs (siRNAs).
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21U small RNA pathway in the germline of Caenorhabditis elegans.
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Piwi pathway in mammals. (a) Expression of Piwi paralogs and piwi‐interacting RNA (piRNA) pools during male gametogenesis. (b) Piwi‐mediated TE silencing in the male germline during pre‐pachytene stages.
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Piwi pathway in Drosophila. (a) Sketch of the Drosophila egg. (b) Piwi‐mediated transcriptional silencing in somatic follicle cells. (c) The piwi‐interacting RNA (piRNA) pathway in the fly's germline. Abbreviations: Rhi, Rhino; Me, methylation; PTS, piRNA trigger sequence.
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Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs
Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action
Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs

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