Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA203266 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR851837.fastq.gz | Fastqsanger.gz | |||
| SRR851838.fastq.gz | Fastqsanger.gz | |||
| SRR851839.fastq.gz | Fastqsanger.gz | |||
| SRR851840.fastq.gz | Fastqsanger.gz | |||
| SRR851841.fastq.gz | Fastqsanger.gz |
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Project description:The PiwiM-bM-^@M-^SpiRNA complex (PiwiM-bM-^@M-^SpiRISC) in Drosophila ovarian somatic cells represses transposons transcriptionally to maintain genome integrity; however, the underlying mechanisms remain obscure. We performed mRNA-seq analysis from OSCs transfected with siRNAs against CG3893, the known piRNA pathway genes, Piwi, Maelstrom, HP1a and Armitage, and the control (EGFP), and PolII ChIP-seqanalysis from OSCs transfected with siRNAs against CG3893, Piwi, Mael and the control (EGFP). This result indicates that CG3893 is a novel factor for primary piRNA pathway in OSCs. RNA levels in wild-type (EGFP control knock-down) ovarian somatic cells (OSC) and RNAi knock-downs of Piwi, Armi, Mael, CG3893, and HP1a. RNA Polymerase II occupancy in wild-type (EGFP control knock-down) ovarian somatic cells (OSC) and RNAi knock-downs of Piwi, Mael, and CG3893.
2013-08-01 | E-GEOD-47006 | biostudies-arrayexpress
Project description:Eukaryotic genomes are colonized by transposable elements whose uncontrolled activity results in genomic instability. The piRNA pathway silences transposons in animal gonads, yet how this is achieved molecularly remains controversial. We assign an essential role to the HMG protein Maelstrom in the process of Piwi mediated silencing in Drosophila. Genome wide assays revealed highly correlated changes in RNA Polymerase II recruitment, nascent RNA output and steady state RNA levels of transposons upon loss of Piwi or Maelstrom. Our data demonstrate piRNA-mediated trans- silencing of hundreds of transposon copies at the transcriptional level. We show that Piwi is required for establishing heterochromatic H3K9me3 marks on transposons and their genomic surrounding. In contrast, loss of Maelstrom impacts transposon H3K9me3 patterns only marginally yet leads to increased heterochromatin spreading, suggesting that Maelstrom acts downstream of or in parallel to H3K9me3. Our work uncovers the widespread influence of transposons and the piRNA pathway on chromatin patterns and gene expression programs. RNA Polymerase II and H3K9me3 occupancy, and steady-state and nascent RNA levels in wild-type ovarian somatic cells (OSC) and RNAi knock-downs of the piRNA pathway components. RNA Polymerase II occupancy in tissue-specific knockdowns of tejas (control) and armi in somatic cells of Drosophila ovary.
2012-11-26 | E-GEOD-41729 | biostudies-arrayexpress
Project description:In the Metazoan germline, piwi proteins and associated piwi-interacting RNAs (piRNAs) provide a defense system against the expression of transposable elements. In the cytoplasm, piRNA sequences guide piwi complexes to destroy complementary transposon transcripts by endonucleolytic cleavage. However, some piwi family members are nuclear, raising the possibility of alternative pathways for piRNA-mediated regulation of gene expression. We found that Drosophila Piwi is recruited to chromatin, co-localizing with RNA polymerase II on polytene chromosomes. Knockdown of Piwi in the germline increases expression of transposable elements that are targeted by piRNAs, whereas protein-coding genes remain largely unaffected. De-repression of transposons upon Piwi depletion correlates with increased occupancy of RNA polymerase II on their promoters. Expression of piRNAs that target a reporter construct results in a decrease in Pol II occupancy and an increase in repressive H3K9me3 marks and HP1 on the reporter locus. Our results indicate that Piwi identifies targets complementary to the associated piRNA and induces transcriptional repression by establishing a repressive chromatin state when correct targets are found. Examination of mRNA levels, Pol II occupancy, and chromatin repressive state in D. melanogaster ovaries upon Piwi knockdown and Piwi mutation. This records present the sequencing data related to Piwi knockdown study portion.
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Project description:Natural variation of piRNA expression affects immunity to transposable elements
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Project description:PIWI-interacting RNAs (piRNAs) are genomically-encoded small RNAs that regulate germ cell development and guarantee germline integrity. Mature piRNAs engage Piwi Argonaute proteins to silence complementary transcripts, including transposable elements and endogenous genes. To date, piRNA biogenesis mechanisms are still unclear. Here, we show that the RNA Polymerase II subunit RPB-9 is required to promote transcription elongation at piRNA loci. Through genetic and biochemical experiments, we demonstrate that rpb-9-mediated piRNA production is needed to repress two DNA transposon families and a subset of somatic genes in the C. elegans germline.
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Project description:piRNAs are 26-30nt germ-line specific small non-coding RNAs that have evolutionarily conserved function in mobile genetic element silencing and maintenance of genome integrity. It has been shown that Drosophila Hsp70/90 Organizing Protein Homolog (Hop) – a co-chaperone interacts with piRNA binding protein Piwi and mediates silencing of phenotypic variations. However, it is not known if Hop has a direct role in piRNA biogenesis and transposon silencing. Here, we show that knock down of Hop in the germ-line nurse cells (GLKD) of Drosophila ovaries leads to activation of transposable elements. Females without germ-line Hop can lay eggs but the eggs do not hatch into larvae. GLKD of Hop leads to accumulation of γ-H2Av foci in the germline indicating increased DNA damage in the ovary. We also show that Hop is required for efficient piRNA biogenesis. Based on these results, we conclude that Hop is a critical component of piRNA pathway and it maintains genome integrity by silencing transposable elements.
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Project description:The conserved THO/TREX complex is critical for pre-mRNA processing and mRNA nuclear export. In Metazoa, TREX is loaded on nascent RNA transcribed by RNA polymerase II in a splicing-dependent fashion; however, how TREX functions is poorly understood. Here we show that Thoc5 and other TREX components are essential for the biogenesis of piRNA, a distinct class of small non-coding RNAs that control expression of transposable elements (TE) in the Drosophila germline. Mutations in TREX lead to defects in piRNA biogenesis resulting in derepression of multiple TE families, gametogenesis defects, and sterility. TREX components are enriched on piRNA precursors transcribed from dual-strand piRNA clusters and co-localize in distinct nuclear foci that overlap with sites of piRNA transcription. The localization of TREX in nuclear foci and its loading on piRNA precursor transcripts depends on Cutoff, a protein associated with chromatin of piRNA clusters. Finally, we show that TREX is required for accumulation of nascent piRNA precursors. Our study reveals a novel splicing-independent mechanism for TREX loading on nascent RNA and its importance in piRNA biogenesis.
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