Genetic and Epigenetic Changes Involving (Retro)transposons in Animal Hybrids and Polyploids

Arkhipova, Irina R.; Rodríguez, Fernando

doi:10.1159/000352069

Cited by 26 publications

(22 citation statements)

References 190 publications

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“…It will be interesting to determine what may be the upper limit for animal cell genomes to accommodate additional de novo TE insertions while under PIWI regulation and during changes in cell ploidy (Supplemental Fig. S1; Ng et al 2012;Arkhipova and Rodriguez 2013). The natural dynamism of TE landscapes in Drosophila follicle cell cultures will be integral for further studies on how the Piwi pathway and TEs influence gene and genome regulation.…”

Section: Discussionmentioning

confidence: 99%

Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures

et al. 2014

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Piwi proteins and Piwi-interacting RNAs (piRNAs) repress transposable elements (TEs) from mobilizing in gonadal cells. To determine the spectrum of piRNA-regulated targets that may extend beyond TEs, we conducted a genome-wide survey for transcripts associated with PIWI and for transcripts affected by PIWI knockdown in Drosophila ovarian somatic sheet (OSS) cells, a follicle cell line expressing the Piwi pathway. Despite the immense sequence diversity among OSS cell piRNAs, our analysis indicates that TE transcripts are the major transcripts associated with and directly regulated by PIWI. However, several coding genes were indirectly regulated by PIWI via an adjacent de novo TE insertion that generated a nascent TE transcript. Interestingly, we noticed that PIWI-regulated genes in OSS cells greatly differed from genes affected in a related follicle cell culture, ovarian somatic cells (OSCs). Therefore, we characterized the distinct genomic TE insertions across four OSS and OSC lines and discovered dynamic TE landscapes in gonadal cultures that were defined by a subset of active TEs. Particular de novo TEs appeared to stimulate the expression of novel candidate long noncoding RNAs (lncRNAs) in a cell lineage-specific manner, and some of these TE-associated lncRNAs were associated with PIWI and overlapped PIWI-regulated genes. Our analyses of OSCs and OSS cells demonstrate that despite having a Piwi pathway to suppress endogenous mobile elements, gonadal cell TE landscapes can still dramatically change and create transcriptome diversity.

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Section: Discussionmentioning

confidence: 99%

Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures

et al. 2014

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“…It may cause chromosomal rearrangements, inversions, deletions, changes in gene expression, changes in DNA methylation, among other effects12. Global activation of transposable elements (TEs), which induces profound changes in the hybrid genome, has also been described.…”

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confidence: 99%

Identification of misexpressed genetic elements in hybrids between Drosophila-related species

Lopez-Maestre

Carnelossi

Lacroix

et al. 2017

Sci Rep

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Crosses between close species can lead to genomic disorders, often considered to be the cause of hybrid incompatibility, one of the initial steps in the speciation process. How these incompatibilities are established and what are their causes remain unclear. To understand the initiation of hybrid incompatibility, we performed reciprocal crosses between two species of Drosophila (D. mojavensis and D. arizonae) that diverged less than 1 Mya. We performed a genome-wide transcriptomic analysis on ovaries from parental lines and on hybrids from reciprocal crosses. Using an innovative procedure of co-assembling transcriptomes, we show that parental lines differ in the expression of their genes and transposable elements. Reciprocal hybrids presented specific gene categories and few transposable element families misexpressed relative to the parental lines. Because TEs are mainly silenced by piwi-interacting RNAs (piRNAs), we hypothesize that in hybrids the deregulation of specific TE families is due to the absence of such small RNAs. Small RNA sequencing confirmed our hypothesis and we therefore propose that TEs can indeed be major players of genome differentiation and be implicated in the first steps of genomic incompatibilities through small RNA regulation.

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“…Bursts of TE activity in hybrids have been highlighted in numerous homoploid hybrid plants [22,29], fruit flies [19,21,36] and wallabies [20]. In Drosophila melanogaster and D. virilis , hybrid dysgenic crosses may lead to bursts in activity of various TEs [21,97] due to release from cytoplasmic repression [37,95,96,103]. Interestingly, there is a slight trend of decreasing Pokey site heterozygosity (Table 3; Additional file 10) and a trend of increasing Pokey insertions sites (Figure 2) as host average heterozygosity increases.…”

Section: Discussionmentioning

confidence: 99%

“…Bursts of TE activity are thought to have a substantial impact on genome rearrangement [27] and may lead to phenotypic diversification in hybrids and polyploids [24,28]. Many studies have explored the effects of hybridization and polyploidization on TE dynamics in plants [22,23,26,28-34], but few studies have focused on these effects in animals, with the exception of studies in carp [35], Drosophila [36] and wallaby [20], all of which have been reviewed [37]. Studying the dynamics of TEs in hybrids and polyploids may provide insight on the evolution of their genomes and their propensity to adapt to various environments.…”

Section: Introductionmentioning

confidence: 99%

Impact of ploidy level on the distribution of Pokey element insertions in the Daphnia pulex complex

2014

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BackgroundTransposable elements (TEs) play a major role in genome evolution. Their capacity to move and/or multiply in the genome of their host may have profound impacts on phenotypes and dramatic consequences on genome structure. The population dynamics and distribution of TEs are influenced by their mode of transposition, the availability of niches in host genomes, and host population dynamics. Theories predict an increase in the number of TE insertions following hybridization or polyploidization. Evolution of TEs in hybrids and polyploids has mostly been studied in plants; few studies have examined the impacts of hybridization and/or polyploidization on TEs in animals. Hybrids and polyploids have arisen multiple times in the Daphnia pulex complex and are thought to reproduce by obligate parthenogenesis. Our study examines the effects of ploidy level on polymorphism and number of Pokey element insertions in diploid and polyploid hybrid isolates from the Daphnia pulex complex.ResultsThe polymorphism of Pokey insertion sites did not depend solely on either the ploidy level or the genetic background of their host; therefore, it may be the result of interactions between these parameters and other parameters such as Pokey activity, selection and/or drift. No significant effect of ploidy level was found on the number of Pokey insertions using TE display and qPCR. However, the load of Pokey insertion sites and the number of unique insertion sites were slightly (but not significantly) higher in polyploids than in diploids.ConclusionsThese results suggest a lack of increase in the number of Pokey insertions following polyploidization but higher availability of Pokey insertion sites in polyploids than in diploids. Compared to previous TE display and qPCR results, the load of Pokey insertions in hybrid diploids was higher than in non-hybrid sexual and asexual diploids, which suggests an increase in the density of Pokey insertions following hybridization.

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Genetic and Epigenetic Changes Involving (Retro)transposons in Animal Hybrids and Polyploids

Cited by 26 publications

References 190 publications

Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures

Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures

Identification of misexpressed genetic elements in hybrids between Drosophila-related species

Impact of ploidy level on the distribution of Pokey element insertions in the Daphnia pulex complex

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