piRNA-Guided Transposon Silencing and Response to Stress in Drosophila Germline

Transposons are integral genome constituents that can be domesticated for host functions, but they also represent a significant threat to genome stability. Transposon silencing is especially critical in the germline, which is dedicated to transmitting inherited genetic material. The small Piwi-interacting RNAs (piRNAs) have a deeply conserved function in transposon silencing in the germline. piRNA biogenesis and function are particularly well understood in Drosophila melanogaster, but some fundamental mechanisms remain elusive and there is growing evidence that the pathway is regulated in response to genotoxic and environmental stress. Here, we review transposon regulation by piRNAs and the piRNA pathway regulation in response to stress, focusing on the Drosophila female germline.

The Landscape of the DNA Transposons in the Genome of the Horezu_LaPeri Strain of Drosophila melanogaster

Natural transposons (NTs) represent mobile DNA sequences found in both prokaryotic and eukaryotic genomes. Drosophila melanogaster (the fruit fly) is a eukaryotic model organism with NTs standing for about 20% of its genome and has contributed significantly to the understanding of various aspects of transposon biology. Our study describes an accurate approach designed to map class II transposons (DNA transposons) in the genome of the Horezu_LaPeri fruit fly strain, consecutive to Oxford Nanopore Technology sequencing. A whole genome bioinformatics analysis was conducted using Genome ARTIST_v2, LoRTE and RepeatMasker tools to identify DNA transposons insertions. Then, a gene ontology enrichment analysis was performed in order to evaluate the potential adaptive role of some DNA transposons insertions. Herein, we describe DNA transposon insertions specific for the Horezu_LaPeri genome and a predictive functional analysis of some insertional alleles. The PCR validation of P-element insertions specific for this fruit fly strain, along with a putative consensus sequence for the KP element, is also reported. Overall, the genome of the Horezu_LaPeri strain contains several insertions of DNA transposons associated with genes known to be involved in adaptive processes. For some of these genes, insertional alleles obtained via mobilization of the artificial transposons were previously reported. This is a very alluring aspect, as it suggests that insertional mutagenesis experiments conducting adaptive predictions for laboratory strains may be confirmed by mirroring insertions which are expected to be found at least in some natural fruit fly strains.

[The P-Element Has Not Significant Effect on the Drosophila simulans Viability]

Cases of horizontal transfer of transposable elements (TEs) between species are known for the Drosophilidae family. In the middle of the last century, the case of horizontal transfer of the P-element from the Drosophila willistoni to the D. melanogaster was described. A novel P-element invasion into the D. simulans genome from D. melanogaster occurred approximately 10 years ago. Currently, the P-element has spread across all D. melanogaster population and 30% of D. simulans populations in Europe, Africa and America. In this paper, we investigated the presence of the P-element in D. simulans lines caught in different years in three Asian populations (Tashkent, Nalchik and Sakhalin Island). We also examined the physiological characteristics (cytotype, lifespan, fecundity and locomotor activity) of D. simulans lines with and without the P-element to determine the significance of this new mobile element in the genome. The P-element was found in lines isolated from nature after 2012. The number of P-element copies per genome (two-to-three dozen according to fluorescence in situ hybridization data) was greater than in the American and comparable to the African populations. There were signs of intraspecific hybrid dysgenesis for some pairs of lines. However, in general the presence of the P-element did not adversely affect the physiological characteristics. Either adaptation to the new TE occurs very quickly, or the rate of movement of the P-element is so insignificant that its appearance in the genome remains unnoticed.

Optogenetics in Drosophila

The fruit fly Drosophila melanogaster, an insect 4 mm long, has served as the experimental subject in a wide range of biological research, including neuroscience. In this chapter, we briefly introduce optogenetic applications in Drosophila neuroscience research. First, we describe the development of Drosophila from egg to adult. In fly neuroscience, temperature-controlled perturbation of neural activity, sometimes called "thermogenetics," has been an invaluable tool that predates the advent of optogenetics. After briefly introducing this perturbation technique, we describe the process of generating transgenic flies that express optogenetic probes in a specific group of cells. Transgenic techniques are crucial in the application of optogenetics in Drosophila neuroscience; here we introduce the transposon P-elements, ϕC31 integrase, and CRISPR-Cas9 methods. As for cell-specific gene expression techniques, the binary expression systems utilizing Gal4-UAS, LexA-lexAop, and Q-system are described. We also present a short and basic optogenetic experiment with Drosophila larvae as a practical example. Finally, we review a few recent studies in Drosophila neuroscience that made use of optogenetics. In this overview of fly development, transgenic methods, and applications of optogenetics, we present an introductory background to optogenetics in Drosophila.

Reconstructing the Invasion Route of the P-Element in Drosophila melanogaster Using Extant Population Samples

The P-element, one of the best understood eukaryotic transposable elements, spread in natural Drosophila melanogaster populations in the last century. It invaded American populations first and later spread to the Old World. Inferring this invasion route was made possible by a unique resource available in D. melanogaster: Many strains sampled from different locations over the course of the last century. Here, we test the hypothesis that the invasion route of the P-element may be reconstructed from extant population samples using internal deletions (IDs) as markers. These IDs arise at a high rate when DNA transposons, such as the P-element, are active. We suggest that inferring invasion routes is possible as: 1) the fraction of IDs increases in successively invaded populations, which also explains the striking differences in the ID content between American and European populations, and 2) successively invaded populations end up with similar sets of IDs. This approach allowed us to reconstruct the invasion route of the P-element with reasonable accuracy. Our approach also sheds light on the unknown timing of the invasion in African populations: We suggest that African populations were invaded after American but before European populations. Simulations of TE invasions in spatially distributed populations confirm that IDs may allow us to infer invasion routes. Our approach might be applicable to other DNA transposons in different host species.

Har-P, a short P-element variant, weaponizes P-transposase to severely impair Drosophila development

Without transposon-silencing Piwi-interacting RNAs (piRNAs), transposition causes an ovarian atrophy syndrome in Drosophila called gonadal dysgenesis (GD). Harwich (Har) strains with P-elements cause severe GD in F1 daughters when Har fathers mate with mothers lacking P-element-piRNAs (i.e. ISO1 strain). To address the mystery of why Har induces severe GD, we bred hybrid Drosophila with Har genomic fragments into the ISO1 background to create HISR-D or HISR-N lines that still cause Dysgenesis or are Non-dysgenic, respectively. In these lines, we discovered a highly truncated P-element variant we named ‘Har-P’ as the most frequent de novo insertion. Although HISR-D lines still contain full-length P-elements, HISR-N lines lost functional P-transposase but retained Har-P’s that when crossed back to P-transposase restores GD induction. Finally, we uncovered P-element-piRNA-directed repression on Har-P’s transmitted paternally to suppress somatic transposition. The Drosophila short Har-P’s and full-length P-elements relationship parallels the MITEs/DNA-transposase in plants and SINEs/LINEs in mammals.

DNA provides the instructions needed for life, a role that relies on it being a very stable and organized molecule. However, some sections of DNA are able to move from one place in the genome to another. When these “mobile genetic elements” move they may disrupt other genes and cause disease. For example, a mobile section of DNA known as the P-element causes a condition called gonadal dysgenesis in female fruit flies, leading to infertility.

Only certain strains of fruit flies carry P-elements and the severity of gonadal dysgenesis in their daughters varies. For example, when male fruit flies of a strain known as Harwich (or Har for short) is crossed with female fruit flies that do not contain P-elements, all of their daughters develop severe gonadal dysgenesis and are infertile. However, if the cross is done the other way around, and female Har flies mate with males that do not contain P-elements, the daughters are fertile because the Har mothers provide their daughters with protective molecules that silence the P-elements. But it was a mystery as to why the P-elements from the Har fathers always caused such severe gonadal dysgenesis in all the daughters.

Here, Srivastav et al. bred fruit flies to create offspring that had different pieces of Har DNA in a genetic background that was normally free from P-elements; they then analyzed the ‘hybrid’ offspring to identify which pieces of the Har genome caused gonadal dysgenesis in the daughter flies. These experiments showed that Har flies possess a very short variant of the P-element (named “Har-P”) that is more mobile than other variants. However, the Har-P variants still depended on an enzyme known as P-transposase encoded by the full-length P-elements to move around the genome. Further experiments showed that other strains of fruit flies that cause severe gonadal dysgenesis also had very short P-element variants that were almost identical to Har-P.

These findings may explain why Har and some other strains of fruit flies drive severe gonadal dysgenesis. In the future, it may be possible to transfer P-transposase and Har-P into mosquitoes, ticks and other biting insects to make them infertile and help reduce the spread of certain diseases in humans.

A rapid change in P-element-induced hybrid dysgenesis status in Ukrainian populations of Drosophila melanogaster

The Drosophila melanogaster P-transposable element is an example of mobile DNA transferred horizontally and known to have spread globally over the last 50-60 years. In Drosophila, the P-element causes a syndrome known as 'P-M hybrid dysgenesis' that obstructs normal ovary development in the female progeny of susceptible populations. Despite extensive research, the stability and global population dynamics of P-M dysgenic phenotypes remain poorly understood. Here, we report a recent and rapid transition in the P-M status of D. melanogaster populations from Ukraine. We demonstrate that these populations are currently dominated by the P'-cytotype characterized by active genomic P-elements and unknown from Ukraine just two decades ago. Our results suggest a recent invasion of the P-element in Ukraine, a pattern that matches recent discoveries from Turkey.

The recent invasion of natural Drosophila simulans populations by the P-element

The P-element is one of the best understood eukaryotic transposable elements. It invaded Drosophila melanogaster populations within a few decades but was thought to be absent from close relatives, including Drosophila simulans. Five decades after the spread in D. melanogaster, we provide evidence that the P-element has also invaded D. simulans. P-elements in D. simulans appear to have been acquired recently from D. melanogaster probably via a single horizontal transfer event. Expression data indicate that the P-element is processed in the germ line of D. simulans, and genomic data show an enrichment of P-element insertions in putative origins of replication, similar to that seen in D. melanogaster. This ongoing spread of the P-element in natural populations provides a unique opportunity to understand the dynamics of transposable element spread and the associated piwi-interacting RNAs defense mechanisms.