A user-friendly chromatographic method to purify small regulatory RNAs

Recent Bioinformatic Progress to Identify Epigenetic Changes Associated to Transposable Elements

Transposable elements (TEs) are recognized for their great impact on the functioning and evolution of their host genomes. They are associated to various deleterious effects, which has led to the evolution of regulatory epigenetic mechanisms to control their activity. Despite these negative effects, TEs are also important actors in the evolution of genomes by promoting genetic diversity and new regulatory elements. Consequently, it is important to study the epigenetic modifications associated to TEs especially at a locus-specific level to determine their individual influence on gene functioning. To this aim, this short review presents the current bioinformatic tools to achieve this task.

Transposable Element Expression and Regulation Profile in Gonads of Interspecific Hybrids of Drosophila arizonae and Drosophila mojavensis wrigleyi

Interspecific hybridization may lead to sterility and/or inviability through differential expression of genes and transposable elements (TEs). In Drosophila, studies have reported massive TE mobilization in hybrids from interspecific crosses of species presenting high divergence times. However, few studies have examined the consequences of TE mobilization upon hybridization in recently diverged species, such as Drosophila arizonae and D. mojavensis. We have sequenced transcriptomes of D. arizonae and the subspecies D. m. wrigleyi and their reciprocal hybrids, as well as piRNAs, to analyze the impact of genomic stress on TE regulation. Our results revealed that the differential expression in both gonadal tissues of parental species was similar. Globally, ovaries and testes showed few deregulated TEs compared with both parental lines. Analyses of small RNA data showed that in ovaries, the TE upregulation is likely due to divergence of copies inherited from parental genomes and lack of piRNAs mapping to them. Nevertheless, in testes, the divergent expression of genes associated with chromatin state and piRNA pathway potentially indicates that TE differential expression is related to the divergence of regulatory genes that play a role in modulating transcriptional and post-transcriptional mechanisms.

Infections by Transovarially Transmitted DMelSV in Drosophila Have No Impact on Ovarian Transposable Element Transcripts but Increase Their Amounts in the Soma

Transposable elements (TEs) are genomic parasites, which activity is tightly controlled in germline cells. Using Sindbis virus, it was recently demonstrated that viral infections affect TE transcript amounts in somatic tissues. However, the strongest evolutionary impacts are expected in gonads, because that is where the genomes of the next generations lie. Here, we investigated this aspect using the Drosophila melanogaster Sigma virus. It is particularly relevant in the genome/TE interaction given its tropism to ovaries, which is the organ displaying the more sophisticated TE control pathways. Our results in Drosophila simulans flies allowed us to confirm the existence of a strong homeostasis of the TE transcriptome in ovaries upon infection, which, however, rely on TE-derived small RNA modulations. In addition, we performed a meta-analysis of RNA-seq data and propose that the immune pathway that is triggered upon viral infection determines the direction of TE transcript modulation in somatic tissues.

A universal method for the rapid isolation of all known classes of functional silencing small RNAs

Diverse classes of silencing small (s)RNAs operate via ARGONAUTE-family proteins within RNA-induced-silencing-complexes (RISCs). Here, we have streamlined various embodiments of a Q-sepharose-based RISC-purification method that relies on conserved biochemical properties of all ARGONAUTEs. We show, in multiple benchmarking assays, that the resulting 15-min benchtop extraction procedure allows simultaneous purification of all known classes of RISC-associated sRNAs without prior knowledge of the samples-intrinsic ARGONAUTE repertoires. Optimized under a user-friendly format, the method – coined ‘TraPR’ for Trans-kingdom, rapid, affordable Purification of RISCs – operates irrespectively of the organism, tissue, cell type or bio-fluid of interest, and scales to minute amounts of input material. The method is highly suited for direct profiling of silencing sRNAs, with TraPR-generated sequencing libraries outperforming those obtained via gold-standard procedures that require immunoprecipitations and/or lengthy polyacrylamide gel-selection. TraPR considerably improves the quality and consistency of silencing sRNA sample preparation including from notoriously difficult-to-handle tissues/bio-fluids such as starchy storage roots or mammalian plasma, and regardless of RNA contaminants or RNA degradation status of samples.

Viral infection impacts transposable element transcript amounts in Drosophila

Transposable elements (TEs) are genomic parasites that are found in all genomes, some of which display sequence similarity to certain viruses. In insects, TEs are controlled by the Piwi-interacting small interfering RNA (piRNA) pathway in gonads, while the small interfering RNA (siRNA) pathway is dedicated to TE somatic control and defense against viruses. So far, these two small interfering RNA pathways are considered to involve distinct molecular effectors and are described as independent. Using Sindbis virus (SINV) in Drosophila, here we show that viral infections affect TE transcript amounts via modulations of the piRNA and siRNA repertoires, with the clearest effects in somatic tissues. These results suggest that viral acute or chronic infections may impact TE activity and, thus, the tempo of genetic diversification. In addition, these results deserve further evolutionary considerations regarding potential benefits to the host, the virus, or the TEs.

The somatic piRNA pathway controls germline transposition over generations

Transposable elements (TEs) are parasitic DNA sequences that threaten genome integrity by replicative transposition in host gonads. The Piwi-interacting RNAs (piRNAs) pathway is assumed to maintain Drosophila genome homeostasis by downregulating transcriptional and post-transcriptional TE expression in the ovary. However, the bursts of transposition that are expected to follow transposome derepression after piRNA pathway impairment have not yet been reported. Here, we show, at a genome-wide level, that piRNA loss in the ovarian somatic cells boosts several families of the endogenous retroviral subclass of TEs, at various steps of their replication cycle, from somatic transcription to germinal genome invasion. For some of these TEs, the derepression caused by the loss of piRNAs is backed up by another small RNA pathway (siRNAs) operating in somatic tissues at the post transcriptional level. Derepressed transposition during 70 successive generations of piRNA loss exponentially increases the genomic copy number by up to 10-fold.

Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids

Interspecific hybridization is a genomic stress condition that leads to the activation of transposable elements (TEs) in both animals and plants. In hybrids between Drosophila buzzatii and Drosophila koepferae, mobilization of at least 28 TEs has been described. However, the molecular mechanisms underlying this TE release remain poorly understood. To give insight on the causes of this TE activation, we performed a TE transcriptomic analysis in ovaries (notorious for playing a major role in TE silencing) of parental species and their F1 and backcrossed (BC) hybrids. We find that 15.2% and 10.6% of the expressed TEs are deregulated in F1 and BC1 ovaries, respectively, with a bias toward overexpression in both cases. Although differences between parental piRNA (Piwi-interacting RNA) populations explain only partially these results, we demonstrate that piRNA pathway proteins have divergent sequences and are differentially expressed between parental species. Thus, a functional divergence of the piRNA pathway between parental species, together with some differences between their piRNA pools, might be at the origin of hybrid instabilities and ultimately cause TE misregulation in ovaries. These analyses were complemented with the study of F1 testes, where TEs tend to be less expressed than in D. buzzatii. This can be explained by an increase in piRNA production, which probably acts as a defence mechanism against TE instability in the male germline. Hence, we describe a differential impact of interspecific hybridization in testes and ovaries, which reveals that TE expression and regulation are sex-biased.

Expression of the Retrotransposon Helena Reveals a Complex Pattern of TE Deregulation in Drosophila Hybrids

Transposable elements (TEs), repeated mobile sequences, are ubiquitous in the eukaryotic kingdom. Their mobilizing capacity confers on them a high mutagenic potential, which must be strongly regulated to guarantee genome stability. In the Drosophila germline, a small RNA-mediated silencing system, the piRNA (Piwi-interacting RNA) pathway, is the main responsible TE regulating mechanism, but some stressful conditions can destabilize it. For instance, during interspecific hybridization, genomic stress caused by the shock of two different genomes can lead, in both animals and plants, to higher transposition rates. A recent study in D. buzatii-D. koepferae hybrids detected mobilization of 28 TEs, yet little is known about the molecular mechanisms explaining this transposition release. We have characterized one of the mobilized TEs, the retrotransposon Helena, and used quantitative expression to assess whether its high transposition rates in hybrids are preceded by increased expression. We have also localized Helena expression in the gonads to see if cellular expression patterns have changed in the hybrids. To give more insight into changes in TE regulation in hybrids, we analysed Helena-specific piRNA populations of hybrids and parental species. Helena expression is not globally altered in somatic tissues, but male and female gonads have different patterns of deregulation. In testes, Helena is repressed in F1, increasing then its expression up to parental values. This is linked with a mislocation of Helena transcripts along with an increase of their specific piRNA levels. Ovaries have additive levels of Helena expression, but the ping-pong cycle efficiency seems to be reduced in F1 hybrids. This could be at the origin of new Helena insertions in hybrids, which would be transmitted to F1 hybrid female progeny.