Reassessment of Piwi binding to the genome and Piwi impact on RNA polymerase II distribution

Stonewall prevents expression of ectopic genes in the ovary and accumulates at insulator elements in D. melanogaster

Germline stem cells (GSCs) are the progenitor cells of the germline for the lifetime of an animal. In Drosophila, these cells reside in a cellular niche that is required for both their maintenance (self-renewal) and differentiation (asymmetric division resulting in a daughter cell that differs from the GSC). The stem cell—daughter cell transition is tightly regulated by a number of processes, including an array of proteins required for genome stability. The germline stem-cell maintenance factor Stonewall (Stwl) associates with heterochromatin, but its molecular function is poorly understood. We performed RNA-Seq on stwl mutant ovaries and found significant derepression of many transposon families but not heterochromatic genes. We also discovered inappropriate expression of multiple classes of genes. Most prominent are testis-enriched genes, including the male germline sex-determination switch Phf7, the differentiation factor bgcn, and a large testis-specific gene cluster on chromosome 2, all of which are upregulated or ectopically expressed in stwl mutant ovaries. Surprisingly, we also found that RNAi knockdown of stwl in somatic S2 cells results in ectopic expression of these testis genes. Using parallel ChIP-Seq and RNA-Seq experiments in S2 cells, we discovered that Stwl localizes upstream of transcription start sites and at heterochromatic sequences including repetitive sequences associated with telomeres. Stwl is also enriched at bgcn, suggesting that it directly regulates this essential differentiation factor. Finally, we identify Stwl binding motifs that are shared with known insulator binding proteins. We propose that Stwl affects gene regulation, including repression of male transcripts in the female germline, by binding insulators and establishing chromatin boundaries.

Stem cells are defined by their ability to divide asymmetrically, resulting in a differentiated cell and a stem cell daughter. In fruit flies, sperm and egg production begins with germline stem cells (GSCs). The ability of a GSC to differentiate or self-renew is tightly regulated by a myriad of factors. Some of these are transcription factors, which are responsible for activating or suppressing other genes to promote one state in favor of another. Stonewall is an ovarian nuclear protein required for GSC self-renewal, whose molecular function is poorly understood. Here we show that Stonewall is responsible for preventing the activation of “male” molecular programming in the fruit fly ovary. When Stonewall is absent from the ovary, egg production is terminated and testis-specific genes become highly expressed, including the male transcript of Phf7, which induces male sexual identity in female germ cells. We also show that Stonewall is likely localizing to genomic insulators, which are regions of the genome that shield genes from nearby regulators. Our findings suggest that Stonewall helps to organize the genome in ovarian germ cells and prevent expression of male genes.

piRNA- and siRNA-mediated transcriptional repression in Drosophila, mice, and yeast: new insights and biodiversity

The PIWI‐interacting RNA (piRNA) pathway acts as a self‐defense mechanism against transposons to maintain germline genome integrity. Failures in the piRNA pathway cause DNA damage in the germline genome, disturbing inheritance of “correct” genetic information by the next generations and leading to infertility. piRNAs execute transposon repression in two ways: degrading their RNA transcripts and compacting the genomic loci via heterochromatinization. The former event is mechanistically similar to siRNA‐mediated RNA cleavage that occurs in the cytoplasm and has been investigated in many species including nematodes, fruit flies, and mammals. The latter event seems to be mechanistically parallel to siRNA‐centered kinetochore assembly and subsequent chromosome segregation, which has so far been studied particularly in fission yeast. Despite the interspecies conservations, the overall schemes of the nuclear events show clear biodiversity across species. In this review, we summarize the recent progress regarding piRNA‐mediated transcriptional silencing in Drosophila and discuss the biodiversity by comparing it with the equivalent piRNA‐mediated system in mice and the siRNA‐mediated system in fission yeast.

Genome-wide mapping of Piwi association with specific loci in Drosophila ovaries

Small noncoding RNA pathways have been implicated in diverse mechanisms of gene regulation. In Drosophila ovaries, Piwi binds to Piwi-interacting RNAs (piRNAs) of mostly 24-28 nucleotides (nt) and plays an important role in germline stem cell maintenance, transposon repression, and epigenetic regulation. To understand the mechanism underlying these functions, we report the application of the DamID-seq method to identify genome-wide binding sites of Piwi in Drosophila ovaries. Piwi localizes to at least 4535 euchromatic regions that are enriched with piRNA target sites. Surprisingly, the density of Piwi binding to euchromatin is much higher than in heterochromatin. Disrupting the piRNA binding of Piwi results in an overall change of the genomic binding profile, which indicates the role of piRNAs in directing Piwi to specific genomic sites. Most Piwi binding sites were either within or in the vicinity of protein-coding genes, particularly enriched near the transcriptional start and termination sites. The methylation signal near the transcriptional termination sites is significantly reduced when Piwi was mutated to become defective in piRNA binding. These observations indicate that Piwi might directly regulate the expression of many protein-coding genes, especially through regulating the 3' ends of targeted transcripts.

A dual role of dLsd1 in oogenesis: regulating developmental genes and repressing transposons

The histone demethylase LSD1 is a key chromatin regulator that is often deregulated in cancer. Its ortholog, dLsd1 plays a crucial role in Drosophila oogenesis; however, our knowledge of dLsd1 function is insufficient to explain its role in the ovary. Here, we have performed genome-wide analysis of dLsd1 binding in the ovary, and we document that dLsd1 is preferentially associated to the transcription start site of developmental genes. We uncovered an unanticipated interplay between dLsd1 and the GATA transcription factor Serpent and we report an unexpected role for Serpent in oogenesis. Besides, our transcriptomic data show that reducing dLsd1 levels results in ectopic transposable elements (TE) expression correlated with changes in H3K4me2 and H3K9me2 at TE loci. In addition, our results suggest that dLsd1 is required for Piwi dependent TE silencing. Hence, we propose that dLsd1 plays crucial roles in establishing specific gene expression programs and in repressing transposons during oogenesis.

Ensemble learning method for the prediction of new bioactive molecules

Pharmacologically active molecules can provide remedies for a range of different illnesses and infections. Therefore, the search for such bioactive molecules has been an enduring mission. As such, there is a need to employ a more suitable, reliable, and robust classification method for enhancing the prediction of the existence of new bioactive molecules. In this paper, we adopt a recently developed combination of different boosting methods (Adaboost) for the prediction of new bioactive molecules. We conducted the research experiments utilizing the widely used MDL Drug Data Report (MDDR) database. The proposed boosting method generated better results than other machine learning methods. This finding suggests that the method is suitable for inclusion among the in silico tools for use in cheminformatics, computational chemistry and molecular biology.

Alternative Computational Analysis Shows No Evidence for Nucleosome Enrichment at Repetitive Sequences in Mammalian Spermatozoa

Samans et al. (2014) reported the enrichment of nucleosomes in human and bovine spermatozoa at centromere repeats and retrotransposon sequences such as LINE-1 and SINE. We demonstrate here that nucleosomal enrichments at repetitive sequences as reported result from bioinformatic analyses that make redundant use of sequencing reads that map to multiple locations in the genome. To illustrate that this computational approach is flawed, we observed comparable artificial enrichments at repetitive sequences when aligning control genomic DNA or simulated reads of uniform genome coverage. These results imply that the main conclusions of the article by Samans et al. (2014) are confounded by an inappropriate computational methodology used to analyze the primary data.

Piwi maintains germline stem cells and oogenesis in Drosophila through negative regulation of Polycomb group proteins

The Drosophila Piwi protein regulates both niche and intrinsic mechanisms to maintain germline stem cells, but its underlying mechanism remains unclear. Here we report that Piwi cooperates with Polycomb Group complexes PRC1 and PRC2 in niche and germline cells to regulate ovarian germline stem cells and oogenesis. Piwi physically interacts with PRC2 subunits Su(z)12 and Esc in the ovary and in vitro. Chromatin co-immunoprecipitation of Piwi, the PRC2 enzymatic subunit E(z), lysine-27-tri-methylated histone 3 (H3K27m3), and RNA polymerase II in wild-type and piwi mutant ovaries reveals that Piwi binds a conserved DNA motif at ~72 genomic sites, and inhibits PRC2 binding to many non-Piwi-binding genomic targets and H3K27 tri-methylation. Moreover, Piwi influences RNA Polymerase II activities in Drosophila ovaries likely via inhibiting PRC2. We hypothesize that Piwi negatively regulates PRC2 binding by sequestering PRC2 in the nucleoplasm, thus reducing PRC2 binding to many targets and influences transcription during oogenesis.

Unique transposon landscapes are pervasive across Drosophila melanogaster genomes

To understand how transposon landscapes (TLs) vary across animal genomes, we describe a new method called the Transposon Insertion and Depletion AnaLyzer (TIDAL) and a database of >300 TLs in Drosophila melanogaster (TIDAL-Fly). Our analysis reveals pervasive TL diversity across cell lines and fly strains, even for identically named sub-strains from different laboratories such as the ISO1 strain used for the reference genome sequence. On average, >500 novel insertions exist in every lab strain, inbred strains of the Drosophila Genetic Reference Panel (DGRP), and fly isolates in the Drosophila Genome Nexus (DGN). A minority (<25%) of transposon families comprise the majority (>70%) of TL diversity across fly strains. A sharp contrast between insertion and depletion patterns indicates that many transposons are unique to the ISO1 reference genome sequence. Although TL diversity from fly strains reaches asymptotic limits with increasing sequencing depth, rampant TL diversity causes unsaturated detection of TLs in pools of flies. Finally, we show novel transposon insertions negatively correlate with Piwi-interacting RNA (piRNA) levels for most transposon families, except for the highly-abundant roo retrotransposon. Our study provides a useful resource for Drosophila geneticists to understand how transposons create extensive genomic diversity in fly cell lines and strains.