Conserved themes in small-RNA-mediated transposon control

Girard, Angélique; Hannon, Gregory J.

doi:10.1016/j.tcb.2008.01.004

Cited by 170 publications

(150 citation statements)

References 151 publications

(195 reference statements)

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“…In this study, we have generated mice carrying a foreign DNA insertion in a pachytene piRNA cluster and show that piRNAs generated from this fragment silence reporter genes in a sequence-specific manner at the post-transcriptional level. Our results show that the piRNA pathway can be used for targeted PTGS and support the idea that piRNA cluster regions serve as a trap for transposable elements (Girard and Hannon 2008), providing an opportunity for host cells to generate complementary piRNAs.…”

Section: [Supplemental Materials Is Available For This Article]supporting

confidence: 78%

“…et al 2011). It has been proposed that piRNA clusters may serve as a trap for new retrotransposon copies (Girard and Hannon 2008;Khurana et al 2011), thus providing an opportunity for the host cells to generate piRNAs with sequences identical to, or most similar to, the active copies. Our knock-in insertion of EGFP-neo into a piRNA cluster mimicked a retrotransposon insertion, and the resulting piRNA generation and silencing of the reporter genes support this hypothesis.…”

Section: Discussionmentioning

confidence: 99%

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Targeted gene silencing in mouse germ cells by insertion of a homologous DNA into a piRNA generating locus

et al. 2012

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In germ cells, early embryos, and stem cells of animals, PIWI-interacting RNAs (piRNAs) have an important role in silencing retrotransposons, which are vicious genomic parasites, through transcriptional and post-transcriptional mechanisms. To examine whether the piRNA pathway can be used to silence genes of interest in germ cells, we have generated knock-in mice in which a foreign DNA fragment was inserted into a region generating pachytene piRNAs. The knock-in sequence was transcribed, and the resulting RNA was processed to yield piRNAs in postnatal testes. When reporter genes possessing a sequence complementary to portions of the knock-in sequence were introduced, they were greatly repressed after the time of pachytene piRNA generation. This repression mainly occurred at the post-transcriptional level, as degradation of the reporter RNAs was accelerated. Our results show that the piRNA pathway can be used as a tool for sequence-specific gene silencing in germ cells and support the idea that the piRNA generating regions serve as traps for retrotransposons, enabling the host cell to generate piRNAs against active retrotransposons.

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Section: [Supplemental Materials Is Available For This Article]supporting

confidence: 78%

Section: Discussionmentioning

confidence: 99%

Targeted gene silencing in mouse germ cells by insertion of a homologous DNA into a piRNA generating locus

et al. 2012

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“…Since cellular defenses against the destabilizing effects of mobile elements involves capture of DNA fragments to direct CRISPR crRNAs in prokaryotes, piRNAs in animals and analogous siRNAs in plants, there is a well-established molecular path for mobile element origins of regulatory RNAs in all domains of life [236][237][238].…”

Section: Evolution Of Regulatory Circuits By Mobile Elementsmentioning

confidence: 99%

How life changes itself: The Read–Write (RW) genome

Shapiro

2013

Physics of Life Reviews

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The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read-Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.

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“…Moreover, like in higher eukaryotes, Ty1 expression and mobility are regulated by trans-acting antisense RNAs in S. cerevisiae (Berretta et al 2008). Related mechanisms may therefore control retrotransposon spreading in all these organisms, whether or not they harbor the RNAi machinery (Girard and Hannon 2008). This finding suggests the interesting possibility that, like in higher eukaryotes, trans-acting noncoding RNAs may mediate homology-dependent silencing of protein coding genes in budding yeast.…”

mentioning

confidence: 98%

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae

Camblong¹,

Beyrouthy²,

Guffanti³

et al. 2009

Genes Dev.

143

138

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Homology-dependent gene silencing, a phenomenon described as cosuppression in plants, depends on siRNAs. We provide evidence that in Saccharomyces cerevisiae, which is missing the RNAi machinery, protein coding gene cosuppression exists. Indeed, introduction of an additional copy of PHO84 on a plasmid or within the genome results in the cosilencing of both the transgene and the endogenous gene. This repression is transcriptional and position-independent and requires trans-acting antisense RNAs. Antisense RNAs induce transcriptional gene silencing both in cis and in trans, and the two pathways differ by the implication of the Hda1/2/3 complex. We also show that trans-silencing is influenced by the Set1 histone methyltransferase, which promotes antisense RNA production. Finally we show that although antisense-mediated cis-silencing occurs in other genes, transsilencing so far depends on features specific to PHO84. All together our data highlight the importance of noncoding RNAs in mediating RNAi-independent transcriptional gene silencing.[Keywords: Antisense RNA; cis and trans transcriptional gene silencing; PHO84; cosuppression; RNAi-independent TGS; noncoding RNA; S. cerevisiae] Supplemental material is available at http://www.genesdev.org.

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Conserved themes in small-RNA-mediated transposon control

Cited by 170 publications

References 151 publications

Targeted gene silencing in mouse germ cells by insertion of a homologous DNA into a piRNA generating locus

Targeted gene silencing in mouse germ cells by insertion of a homologous DNA into a piRNA generating locus

How life changes itself: The Read–Write (RW) genome

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae

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