The evolution of RNAi as a defence against viruses and transposable elements

Obbard, Darren J.; Gordon, Karl; Buck, Amy H.; Jiggins, Francis M.

doi:10.1098/rstb.2008.0168

Cited by 452 publications

(444 citation statements)

References 168 publications

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“…Given the striking evidence for rapid evolution of Nups, which is possibly driven by intragenomic conflict, we turned our attention to RNAi genes, which are also thought to evolve rapidly due to genomic conflict (Obbard et al 2006(Obbard et al , 2009a. Only 16 out of 23 RNAi genes studied by Obbard et al (2006Obbard et al ( , 2009a and Kolaczkowski et al (2011) were included in the initial D. mauritiana annotation.…”

Section: Signatures Of Positive Selection In D Mauritianamentioning

confidence: 99%

Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

Nolte¹,

Pandey²,

Kofler³

et al. 2012

Genome Res.

117

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Although it is well understood that selection shapes the polymorphism pattern in Drosophila, signatures of classic selective sweeps are scarce. Here, we focus on Drosophila mauritiana, an island endemic, which is closely related to Drosophila melanogaster. Based on a new, annotated genome sequence, we characterized the genome-wide polymorphism by sequencing pooled individuals (Pool-seq). We show that the interplay between selection and recombination results in a genome-wide polymorphism pattern characteristic for D. mauritiana. Two large genomic regions (>500 kb) showed the signature of almost complete selective sweeps. We propose that the absence of population structure and limited geographic distribution could explain why such pronounced sweep patterns are restricted to D. mauritiana. Further evidence for strong adaptive evolution was detected for several nucleoporin genes, some of which were not previously identified as genes involved in genomic conflict. Since this adaptive evolution is continuing after the split of D. mauritiana and Drosophila simulans, we conclude that genomic conflict is not restricted to short episodes, but rather an ongoing process in Drosophila.

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Section: Signatures Of Positive Selection In D Mauritianamentioning

confidence: 99%

Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

Nolte¹,

Pandey²,

Kofler³

et al. 2012

Genome Res.

117

View full text Add to dashboard Cite

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“…Degrading TE transcripts through RNA interference: RNA interference represents another post-transcriptional mechanism of TE suppression (Obbard et al, 2009). In this case, small RNAs operate through homology-based recognition to induce the degradation of complementary TE transcripts, through the recruitment of the RNAinduced silencing complex.…”

Section: Host Responses To Tes or How To Live With A Herd Of Squattersmentioning

confidence: 99%

Transposable elements in the mammalian germline: a comfortable niche or a deadly trap?

2010

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Retrotransposable elements comprise around 50% of the mammalian genome. Their activity represents a constant threat to the host and has prompted the development of adaptive control mechanisms to protect genome architecture and function. To ensure their propagation, retrotransposons have to mobilize in cells destined for the next generation. Accordingly, these elements are particularly well suited to transcriptional networks associated with pluripotent and germinal states in mammals. The relaxation of epigenetic control that occurs in the early developing germline constitutes a dangerous window in which retrotransposons can escape from host restraint and massively expand. What could be observed as risky behavior may turn out to be an insidious strategy developed by germ cells to sense retrotransposons and hold them back in check. Herein, we review recent insights that have provided a detailed picture of the defense mechanisms that concur toward retrotransposon silencing in mammalian genomes, and in particular in the germline. In this lineage, retrotransposons are hit at multiple stages of their life cycle, through transcriptional repression, RNA degradation and translational control. An organized cross-talk between PIWIinteracting small RNAs (piRNAs) and various nuclear and cytoplasmic accessories provides this potent and multilayered response to retrotransposon unleashing in early germ cells.

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“…We note that the TEs that are diverged from the dominant sequences in the piRNA pool are expected to enjoy less suppression and thus more replicative transposition. Also, several studies of the molecular evolution of genes in the piRNA pathway have reported evidence for adaptive evolution (Heger & Ponting 2007;Obbard et al 2009). The divergencebased escape to these two sequence-similarity-based mechanisms (piRNA pathway and ectopic exchange) has the potential to drive an additional TE-host coevolutionary arms race directly at the TE sequences.…”

Section: Piwi-interacting Rna As a Competing Model For Containmentmentioning

confidence: 99%

Transposable elements in natural populations ofDrosophila melanogaster

Lee

Langley

2010

Phil. Trans. R. Soc. B

105

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Transposable elements (TEs) are families of small DNA sequences found in the genomes of virtually all organisms. The sequences typically encode essential components for the replicative transposition sequences of that TE family. Thus, TEs are simply genomic parasites that inflict detrimental mutations on the fitness of their hosts. Several models have been proposed for the containment of TE copy number in outbreeding host populations such as Drosophila. Surveys of the TEs in genomes from natural populations of Drosophila have played a central role in the investigation of TE dynamics. The early surveys indicated that a typical TE insertion is rare in a population, which has been interpreted as evidence that each TE is selected against. The proposed mechanisms of this natural selection are reviewed here. Subsequent and more targeted surveys identify heterogeneity among types of TEs and also highlight the large role of homologous and possibly ectopic crossing over in the dynamics of the Drosophila TEs. The recent discovery of germline-specific RNA interference via the piwi-interacting RNA pathway opens yet another interesting mechanism that may be critical in containing the copy number of TEs in natural populations of Drosophila. The expected flood of Drosophila population genomics is expected to rapidly advance understanding of the dynamics of TEs.

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The evolution of RNAi as a defence against viruses and transposable elements

Cited by 452 publications

References 168 publications

Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

Transposable elements in the mammalian germline: a comfortable niche or a deadly trap?

Transposable elements in natural populations ofDrosophila melanogaster

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