Cytoplasmic Compartmentalization of the Fetal piRNA Pathway in Mice

Derepression of transposable elements (TEs) in the course of epigenetic reprogramming of the mouse embryonic germline necessitates the existence of a robust defense that is comprised of PIWI/piRNA pathway and de novo DNA methylation machinery. To gain further insight into biogenesis and function of piRNAs, we studied the intracellular localization of piRNA pathway components and used the combination of genetic, molecular, and cell biological approaches to examine the performance of the piRNA pathway in germ cells of mice lacking Maelstrom (MAEL), an evolutionarily conserved protein implicated in transposon silencing in fruit flies and mice. Here we show that principal components of the fetal piRNA pathway, MILI and MIWI2 proteins, localize to two distinct types of germinal cytoplasmic granules and exhibit differential association with components of the mRNA degradation/translational repression machinery. The first type of granules, pi-bodies, contains the MILI-TDRD1 module of the piRNA pathway and is likely equivalent to the enigmatic “cementing material” first described in electron micrographs of rat gonocytes over 35 years ago. The second type of granules, piP-bodies, harbors the MIWI2-TDRD9-MAEL module of the piRNA pathway and signature components of P-bodies, GW182, DCP1a, DDX6/p54, and XRN1 proteins. piP-bodies are found predominantly in the proximity of pi-bodies and the two frequently share mouse VASA homolog (MVH) protein, an RNA helicase. In Mael-mutant gonocytes, MIWI2, TDRD9, and MVH are lost from piP-bodies, whereas no effects on pi-body composition are observed. Further analysis revealed that MAEL appears to specifically facilitate MIWI2-dependent aspects of the piRNA pathway including biogenesis of secondary piRNAs, de novo DNA methylation, and efficient downregulation of TEs. Cumulatively, our data reveal elaborate cytoplasmic compartmentalization of the fetal piRNA pathway that relies on MAEL function

Normal microRNA Maturation and Germ-Line Stem Cell Maintenance Requires Loquacious, a Double-Stranded RNA-Binding Domain Protein

microRNAs (miRNAs) are single-stranded, 21- to 23-nucleotide cellular RNAs that control the expression of cognate target genes. Primary miRNA (pri-miRNA) transcripts are transformed to mature miRNA by the successive actions of two RNase III endonucleases. Drosha converts pri-miRNA transcripts to precursor miRNA (pre-miRNA); Dicer, in turn, converts pre-miRNA to mature miRNA. Here, we show that normal processing of Drosophila pre-miRNAs by Dicer-1 requires the double-stranded RNA-binding domain (dsRBD) protein Loquacious (Loqs), a homolog of human TRBP, a protein first identified as binding the HIV trans-activator RNA (TAR). Efficient miRNA-directed silencing of a reporter transgene, complete repression of white by a dsRNA trigger, and silencing of the endogenous Stellate locus by Suppressor of Stellate, all require Loqs. In loqs (f00791) mutant ovaries, germ-line stem cells are not appropriately maintained. Loqs associates with Dcr-1, the Drosophila RNase III enzyme that processes pre-miRNA into mature miRNA. Thus, every known Drosophila RNase-III endonuclease is paired with a dsRBD protein that facilitates its function in small RNA biogenesis

Measuring the rates of transcriptional elongation in the female Drosophila melanogaster germ line by nuclear run-on

We adapted the nuclear run-on method to measure changes in the rate of RNA polymerase II (pol II) transcription of repetitive elements and transposons in the female germ line of Drosophila melanogaster. Our data indicate that as little as an approximately 1.5-fold change in the rate of transcription can be detected by this method. Our nuclear run-on protocol likely measures changes in transcriptional elongation, because rates of transcription decline with time, consistent with a low rate of pol II re-initiation in the isolated nuclei. Surprisingly, we find that the retrotransposon gypsy and the repetitive sequence mst40 are silenced posttranscriptionally in fly ovaries

A distinct small RNA pathway silences selfish genetic elements in the germline

In the Drosophila germline, repeat-associated small interfering RNAs (rasiRNAs) ensure genomic stability by silencing endogenous selfish genetic elements such as retrotransposons and repetitive sequences. Whereas small interfering RNAs (siRNAs) derive from both the sense and antisense strands of their double-stranded RNA precursors, rasiRNAs arise mainly from the antisense strand. rasiRNA production appears not to require Dicer-1, which makes microRNAs (miRNAs), or Dicer-2, which makes siRNAs, and rasiRNAs lack the 2\u27,3\u27 hydroxy termini characteristic of animal siRNA and miRNA. Unlike siRNAs and miRNAs, rasiRNAs function through the Piwi, rather than the Ago, Argonaute protein subfamily. Our data suggest that rasiRNAs protect the fly germline through a silencing mechanism distinct from both the miRNA and RNA interference pathways

Transcription of the 1.688 Satellite DNA Family Is Under the Control of RNA Interference Machinery in Drosophila melanogaster Ovaries

Here we show that RNA interference (RNAi) machinery operates in Drosophila melanogaster 1.688 satellite transcription. Mutation in the spn-E gene, known to be involved in RNAi in the oocytes, causes an increase of satellite transcript abundance. Transcripts of both strands of 1.688 satellite repeats in germinal tissues were detected. The strength of the effects of the spn-E mutation differs for 1.688 satellite DNA subfamilies and is more pronounced for autosomal pericentromeric satellites compared to the X-linked centromeric ones. The spn-E1 mutation causes an increase of the H3-AcK9 mark and TAF1 (a component of the polymerase II transcriptional complex) occupancy in the chromatin of autosomal pericentromeric repeats. Thus, we revealed that RNAi operates in ovaries to maintain the silenced state of centromeric and pericentromeric 1.688 repeats

The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC

Small silencing RNAs repress gene expression by a set of related mechanisms collectively called RNA-silencing pathways [1, 2]. In the RNA interference (RNAi) pathway [3], small interfering mRNA (siRNAs) defend cells from invasion by foreign nucleic acids, such as those produced by viruses. In contrast, microRNAs (miRNAs) sculpt endogenous mRNA expression [4]. A third class of small RNAs, Piwi-interacting RNAs (piRNAs), defends the genome from transposons [5-9]. Here, we report that Drosophila piRNAs contain a 2\u27-O-methyl group on their 3\u27 termini; this is a modification previously reported for plant miRNAs and siRNAs [10] and mouse and rat piRNAs [11, 12, 13]. Plant small-RNA methylation is catalyzed by the protein HEN1 [10, 14, 15]. We find that DmHen1, the Drosophila homolog of HEN1, methylates the termini of siRNAs and piRNAs. Without DmHen1, the length and abundance of piRNAs are decreased, and piRNA function is perturbed. Unlike plant HEN1, DmHen1 acts on single strands, not duplexes, explaining how it can use as substrates both siRNAs-which derive from double-stranded precursors-and piRNAs-which do not [8, 13]. 2\u27-O-methylation of siRNAs may be the final step in assembly of the RNAi-enzyme complex, RISC, occurring after an Argonaute-bound siRNA duplex is converted to single-stranded RNA

Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members

In germ cells, Piwi proteins interact with a specific class of small noncoding RNAs, piwi-interacting RNAs (piRNAs). Together, these form a pathway that represses transposable elements, thus safeguarding germ cell genomes. Basic models describe the overall operation of piRNA pathways. However, the protein compositions of Piwi complexes, the critical protein–protein interactions that drive small RNA production and target recognition, and the precise molecular consequences of conserved localization to germline structures, call nuage, remains poorly understood. We purified the three murine Piwi family proteins, MILI, MIWI, and MIWI2, from mouse germ cells and characterized their interacting protein partners. Piwi proteins were found in complex with PRMT5/WDR77, an enzyme that dimethylates arginine residues. By immunoprecipitation with specific antibodies and by mass spectrometry, we found that Piwi proteins are arginine methylated at conserved positions in their N termini. These modifications are essential to direct complex formation with specific members of the Tudor protein family. Recognition of methylarginine marks by Tudor proteins can drive the localization of Piwi proteins to cytoplasmic foci in an artificial setting, supporting a role for this interaction in Piwi localization to nuage, a characteristic that correlates with proper operation of the piRNA pathway and transposon silencing in multiple organisms

loqs^f00791 Fail to Maintain Germ-Line Stem Cells

<div><p>(A) Wild-type ovarioles contain a germarium and a developmentally ordered array of six to eight egg chambers, whereas <i>loqs</i>^f00791 mutant ovarioles contain a smaller than normal germarium, two or three pre-vitellogenic egg chambers, and a late-stage egg chamber. Wild-type and <i>loqs</i> ovarioles are shown at the same magnification.</p> <p>(B) In wild-type ovarioles, the germarium contains several newly formed germ-line cysts surrounded by somatic follicle cells. In contrast, <i>loqs</i>^f00791 mutant germaria contain few germ-line cells, which are not organized into distinct cysts. The follicle cell layer is also significantly reduced in<i>loqs</i>^f00791 germaria.</p> <p>(C) Wild-type and <i>loqs</i> mutant germaria labeled for α-Spectrin (green) and filamentous Actin (red). In wild type, anti-α-Spectrin labels the spectrosome (ss), a structure characteristic of germ-line stem cells, which are normally found at the anterior of the germarium, apposed to the somatic terminal cells (tc). The cystoblasts, the daughters of the stem cells, also contain a spectrosome, but are located posterior to the stem cells. In <i>loqs</i> mutant ovaries, spectrosome-containing cells were not detected, indicating that normal germ-line stem cells are not present. These observations indicate that stem cells are not maintained.</p> <p>In (A) and (B), ovaries were labeled for filamentous actin (red) using rhodamine phalloidin, DNA (blue) using TOTO3 (Molecular Probes), and the germ-line marker Vasa (green) using rabbit anti-Vasa antibody detected with fluorescein-conjugated anti-rabbit secondary antibody. In (B) and (C), wild-type and <i>loqs</i> germaria are shown at the same magnification.</p></div

Silencing of a miRNA-Responsive YFP Reporter Requires <i>loqs</i> but Not <i>r2d2</i>

<div><p>(A) A YFP transgene expressed from the Pax6-promoter showed strong fluorescence in the eye and weaker fluorescence in the antennae. Due to the underlying normal red eye pigment, the YFP fluorescence was observed in only those ommatidia that are aligned with the optical axis of the stereomicroscope. In heterozygous <i>loqs</i>^f00791/CyO flies bearing a miR-277-responsive, Pax6-promotor-driven, YFP transgene, YFP fluorescence was visible in the antennae but was repressed in the eye. In contrast, in homozygous mutant <i>loqs</i>^f00791 flies, YFP fluorescence was readily detected in the eye. A strong mutation in <i>r2d2</i> did not comparably alter repression of the miR-277-regulated YFP reporter. The exposure time for the unregulated YFP reporter strain was one-fourth that used for the miR-277-responsive YFP strain. The exposure times were identical for the heterozygous and homozygous <i>loqs</i> and <i>r2d2</i> flies.</p> <p>(B) Additional images of eyes from <i>loqs</i>^f00791 heterozygous and homozygous flies bearing the miR-277-responsive YFP reporter transgene diagrammed in (A).</p> <p>(C) Quantification of fluorescence of the miR-277-responsive YFP transgene in eyes heterozygous or homozygous for <i>loqs</i> or <i>r2d2</i>. The maximum pixel intensity was measured for each eye (excluding antennae and other tissues where miR-277 does not appear to function). The graph displays the average (<i>n</i> = 13) maximum pixel intensity ± standard deviation for each homozygous genotype, normalized to the average value for the corresponding heterozygotes. Statistical significance was estimated using a two-sample Student's <i>t</i>-test assuming unequal variance.</p> <p>The images in (A) were acquired using a sensitive, GFP long-pass filter set that transmits yellow and red autofluorescence. Images in (B) and for quantitative analysis were acquired using a YFP-specific band-pass filter set that reduced the autofluorescence recorded.</p></div