Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA315501 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3233830.fastq.gz | Fastqsanger.gz | |||
| SRR3233821.fastq.gz | Fastqsanger.gz | |||
| SRR3233831.fastq.gz | Fastqsanger.gz | |||
| SRR3233822.fastq.gz | Fastqsanger.gz | |||
| SRR3233832.fastq.gz | Fastqsanger.gz |
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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.
2016-03-18 | GSE79325 | GEO
Project description:The piRNA pathway is a conserved small RNA-based immune system that protects animal germ cell genomes from the harmful effects of transposon mobilisation. In Drosophila ovaries, most piRNAs originate from dual-strand clusters, which generate piRNAs from both genomic strands. Dual-strand clusters use non-canonical transcription mechanisms. Although transcribed by RNA polymerase II, cluster transcripts lack splicing signatures and polyA tails. mRNA processing is important for general mRNA export mediated by Nuclear export factor 1. Although UAP56, a component of the transcription and export complex, has been implicated in piRNA precursor export, it remains unknown how dual-strand cluster transcripts are specifically targeted for piRNA biogenesis by export from the nucleus to cytoplasmic processing centers. Here we report that dual-strand cluster transcript export requires CG13741/Bootlegger and the Drosophila Nuclear export factor family protein, Nxf3. Bootlegger is specifically recruited to piRNA clusters and in turn brings Nxf3. We find that Nxf3 specifically binds to piRNA precursors and is essential for their export to piRNA biogenesis sites, a process that is critical for germline transposon silencing. Our data shed light on how dual-strand clusters bypass canonical mRNA features to be specifically exported via Nxf3, ensuring proper piRNA production
2019-07-29 | PXD014472 | Pride
Project description:Argonaute proteins of the PIWI clade are central to transposon silencing in animal gonads. Their target specificity is defined by 22-30nt PIWI interacting RNAs (piRNAs), which mostly originate from discrete genomic loci termed piRNA clusters. Here we show that the RDC complex composed of Rhino, Deadlock and Cutoff defines dual-strand piRNA clusters genome-wide in Drosophila ovaries. The RDC complex is anchored to H3K9me3-marked chromatin in part via RhinoM-bM-^@M-^Ys chromo-domain. Depletion of Piwi results in loss of the RDC and small RNAs at euchromatic piRNA source loci, demonstrating a feedback loop between Piwi and genomic piRNA sources. Intriguingly, profiles of RNA Polymerase II occupancy, nascent transcription and steady-state RNA levels reveal that the RDC licenses non-canonical transcription of dual-stranded piRNA clusters. Likely, this process involves 5M-bM-^@M-^Yend protection of nascent RNAs and subsequent suppression of transcription termination. Together, our data provide a comprehensive model for the regulation and evolution of piRNA clusters. This study aims at indentifying and characterizing genimc sources of piRNA percursour transcripts using genome-wide apporaches such as ChIP-seq, RNA-seq, smallRNA-seq and GRO-seq in adult Drosophila ovaries depleted for several factors implicated in piRNA cluster regulation
2014-06-08 | E-GEOD-55824 | biostudies-arrayexpress
Project description:Argonaute proteins of the PIWI clade are central to transposon silencing in animal gonads. Their target specificity is defined by 22-30nt PIWI interacting RNAs (piRNAs), which mostly originate from discrete genomic loci termed piRNA clusters. Here we show that the RDC complex composed of Rhino, Deadlock and Cutoff defines dual-strand piRNA clusters genome-wide in Drosophila ovaries. The RDC complex is anchored to H3K9me3-marked chromatin in part via Rhino’s chromo-domain. Depletion of Piwi results in loss of the RDC and small RNAs at euchromatic piRNA source loci, demonstrating a feedback loop between Piwi and genomic piRNA sources. Intriguingly, profiles of RNA Polymerase II occupancy, nascent transcription and steady-state RNA levels reveal that the RDC licenses non-canonical transcription of dual-stranded piRNA clusters. Likely, this process involves 5’end protection of nascent RNAs and subsequent suppression of transcription termination. Together, our data provide a comprehensive model for the regulation and evolution of piRNA clusters.
2014-06-08 | GSE55824 | GEO
Project description:Small non-coding RNAs called piRNAs serve as the sequence-specific guides for an adaptable immune system that represses transposable elements in germ cells of Metazoa. The adaptation of the piRNA pathway to novel transposons is believed to occur when active transposons integrate into piRNA clusters, special genomic regions, which encode piRNA precursors. In Drosophila the RDC complex, composed of Rhino, Deadlock and Cutoff (Cuff) binds chromatin of dual-strand piRNA clusters and is required for transcription of piRNA precursors, though the mechanism by which RDC license transcription remained unknown. Here we show that Cuff prevents premature termination of RNA polymerase II by two distinct mechanisms. First, Cuff prevents cleavage of nascent RNA at poly(A) sites by interfering with recruitment of the cleavage and polyadenylation specificity factor (CPSF) complex. Second, if processing does occur, Cuff protects processed transcripts from degradation by the exonuclease Rat1. Our work reveals a conceptually novel mechanism of transcriptional enhancement. In contrast to other factors that regulate termination by binding to specific signals on nascent RNA, the RDC complex inhibits termination in a chromatin-dependent and sequence-independent manner.
2016-05-05 | GSE81090 | GEO
Project description:The piRNA pathway is a conserved small RNA-based immune system that protects animal germ cell genomes from the harmful effects of transposon mobilisation. In Drosophila ovaries, most piRNAs originate from dual-strand clusters, which generate piRNAs from both genomic strands. Dual-strand clusters use non-canonical transcription mechanisms. Although transcribed by RNA polymerase II, cluster transcripts lack splicing signatures and polyA tails. mRNA processing is important for general mRNA export mediated by Nuclear export factor 1. Although UAP56, a component of the transcription and export complex, has been implicated in piRNA precursor export, it remains unknown how dual-strand cluster transcripts are specifically targeted for piRNA biogenesis by export from the nucleus to cytoplasmic processing centers. Here we report that dual-strand cluster transcript export requires CG13741/Bootlegger and the Drosophila Nuclear export factor family protein, Nxf3. Bootlegger is specifically recruited to piRNA clusters and in turn brings Nxf3. We find that Nxf3 specifically binds to piRNA precursors and is essential for their export to piRNA biogenesis sites, a process that is critical for germline transposon silencing. Our data shed light on how dual-strand clusters bypass canonical mRNA features to be specifically exported via Nxf3, ensuring proper piRNA production.
2019-07-27 | GSE133528 | GEO
Project description:Most piRNAs in the Drosophila female germline are transcribed from heterochromatic regions called dual-strand piRNA clusters. Histone 3 lysine 9 trimethylation (H3K9me3) is required for licensing piRNA production by these clusters. However, it is unclear when and how they acquire this permissive heterochromatic state. Although it has been suggested that piRNA cluster licensing is Piwi-independent, here we show that transient Piwi depletion in Drosophila embryos, using a refined knock-down system, results in H3K9me3 decrease at piRNA clusters. This is accompanied by aberrant maturation of piRNA precursor transcripts, accumulation of transposable element transcripts and female sterility. Conversely, Piwi knock-down at later developmental stages does not disturb piRNA cluster licensing, as previously reported. These results indicate that the identity of piRNA clusters is epigenetically acquired in a Piwi-dependent manner during a limited embryonic development window, which is reminiscent of the widespread genome reprogramming occurring during early mammalian zygotic development.
2017-04-27 | GSE83236 | GEO
Project description:Most piRNAs in the Drosophila female germline are transcribed from heterochromatic regions called dual-strand piRNA clusters. Histone 3 lysine 9 trimethylation (H3K9me3) is required for licensing piRNA production by these clusters. However, it is unclear when and how they acquire this permissive heterochromatic state. Although it has been suggested that piRNA cluster licensing is Piwi-independent, here we show that transient Piwi depletion in Drosophila embryos, using a refined knock-down system, results in H3K9me3 decrease at piRNA clusters. This is accompanied by aberrant maturation of piRNA precursor transcripts, accumulation of transposable element transcripts and female sterility. Conversely, Piwi knock-down at later developmental stages does not disturb piRNA cluster licensing, as previously reported. These results indicate that the identity of piRNA clusters is epigenetically acquired in a Piwi-dependent manner during a limited embryonic development window, which is reminiscent of the widespread genome reprogramming occurring during early mammalian zygotic development.
2017-04-27 | GSE83235 | GEO
Project description:Most piRNAs in the Drosophila female germline are transcribed from heterochromatic regions called dual-strand piRNA clusters. Histone 3 lysine 9 trimethylation (H3K9me3) is required for licensing piRNA production by these clusters. However, it is unclear when and how they acquire this permissive heterochromatic state. Although it has been suggested that piRNA cluster licensing is Piwi-independent, here we show that transient Piwi depletion in Drosophila embryos, using a refined knock-down system, results in H3K9me3 decrease at piRNA clusters. This is accompanied by aberrant maturation of piRNA precursor transcripts, accumulation of transposable element transcripts and female sterility. Conversely, Piwi knock-down at later developmental stages does not disturb piRNA cluster licensing, as previously reported. These results indicate that the identity of piRNA clusters is epigenetically acquired in a Piwi-dependent manner during a limited embryonic development window, which is reminiscent of the widespread genome reprogramming occurring during early mammalian zygotic development.
2017-04-27 | GSE83234 | GEO
Project description:PIWI-interacting (pi) RNAs provide silencing of transposable elements (TE) in the germline. Drosophila telomeres are maintained by transpositions of specialized telomeric retroelements. piRNAs generated from sense and antisense transcripts of telomeric elements provide telomere length control in the germline. Previously, we have found that antisense transcription of the major telomeric retroelement HeT-A is initiated upstream of the HeT-A sense transcription start site. Here, we performed a deletion analysis of the HeT-A promoter and show that common regulatory elements are shared by sense and antisense promoters of HeT-A. Therefore, the HeT-A promoter is a bidirectional promoter capable of processive sense and antisense transcription. Ovarian small RNA data shows that a solo HeT-A promoter within an euchromatic transgene initiates divergent transcription of transgenic reporter genes and subsequent processing of these transcripts into piRNAs. These events lead to the formation of a divergent uni-strand piRNA cluster at solo HeT-A promoters, in contrast to endogenous telomeres that represent strong dual-strand piRNA clusters. Solo HeT-A promoters are not immunoprecipitated with Heterochromatin Protein 1 (HP1) homolog Rhino, a marker of the dual-strand piRNA clusters, but are associated with HP1 itself, which provides piRNA-mediated transcriptional repression of the reporter genes. Unlike endogenous dual-strand piRNA clusters, the solo HeT-A promoter does not produce overlapping transcripts. In a telomeric context, however, bidirectional promoters of tandem HeT-A repeats provide read-through transcription of both genomic strands, followed by Rhi binding. These data indicate that Drosophila telomeres share properties of uni-strand and dual-strand piRNA clusters.
2016-12-07 | GSE78135 | GEO