Drosophila virilis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA257192 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1533730.fastq.gz | Fastqsanger.gz | |||
| SRR1533740.fastq.gz | Fastqsanger.gz | |||
| SRR1533731.fastq.gz | Fastqsanger.gz | |||
| SRR1533741.fastq.gz | Fastqsanger.gz | |||
| SRR1533732.fastq.gz | Fastqsanger.gz |
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Project description:Piwi interacting (pi)RNAs repress diverse transposable elements in the germ cells of metazoans and are essential for fertility in both invertebrates and vertebrates. The precursors of piRNAs are transcribed from distinct genomic regions, the so-called piRNA clusters; however, how piRNA clusters are differentiated from the rest of the genome is not known. To address this question, we studied piRNA biogenesis in two Drosophila virilis strains that show differential ability to generate piRNAs from several genomic regions. We found that active piRNA biogenesis correlates with high levels of histone 3 lysine 9 trimethylation (H3K9me3) over genomic regions that give rise to piRNAs. Furthermore, piRNA biogenesis in the progeny requires the trans-generational inheritance of an epigenetic signal, presumably in form of homologous piRNAs that are generated in the maternal germline and deposited into the oocyte. The inherited piRNAs enhance piRNA biogenesis by installment of H3K9me3 mark on piRNA clusters and by promoting ping-pong processing of homologous transcripts into mature piRNAs. We submitted the resequencing data together with the functional genomic datasets because it was generated with the sole purpose of supporting those. The SRA accession numbers are SRR1536176 and SRR1536175. ChIP-seq against H3K9me3 and Pol2, Total RNA-seq, in Drosophila virilis Strain9 and Strain160 as well as crosses between them
2014-09-01 | E-GEOD-59965 | biostudies-arrayexpress
Project description:Piwi interacting (pi)RNAs repress diverse transposable elements in the germ cells of metazoans and are essential for fertility in both invertebrates and vertebrates. The precursors of piRNAs are transcribed from distinct genomic regions, the so-called piRNA clusters; however, how piRNA clusters are differentiated from the rest of the genome is not known. To address this question, we studied piRNA biogenesis in two Drosophila virilis strains that show differential ability to generate piRNAs from several genomic regions. We found that active piRNA biogenesis correlates with high levels of histone 3 lysine 9 trimethylation (H3K9me3) over genomic regions that give rise to piRNAs. Furthermore, piRNA biogenesis in the progeny requires the trans-generational inheritance of an epigenetic signal, presumably in form of homologous piRNAs that are generated in the maternal germline and deposited into the oocyte. The inherited piRNAs enhance piRNA biogenesis by installment of H3K9me3 mark on piRNA clusters and by promoting ping-pong processing of homologous transcripts into mature piRNAs. We submitted the resequencing data together with the functional genomic datasets because it was generated with the sole purpose of supporting those. The SRA accession numbers are SRR1536176 and SRR1536175.
2014-09-01 | GSE59965 | GEO
Project description:Piwi-interacting RNAs (piRNAs) play a crucial role in silencing transposable elements (TEs) in the germ cells of Metazoa by acting as sequence-specific guides. Originating from distinct genomic loci, called piRNA clusters, piRNA can trigger an epigenetic conversion of TE insertions into piRNA clusters by means of paramutation-like process. However, the variability in piRNA clusters' capacity to induce such conversion remains poorly understood. Here, we investigated two Drosophila virilis strains with differing capacities to produce piRNAs from the RhoGEF3 and Adar gene loci. We found that active piRNA generation correlates with high levels of the heterochromatic mark H3K9me3 over genomic regions that give rise to piRNAs. Importantly, maternal transmission of piRNAs drives their production in the progeny, even from homologous loci previously inactive in piRNA biogenesis. The subtelomeric RhoGEF3 locus, once epigenetically converted, maintained enhanced piRNA production in subsequent generations lacking the original allele carrying the active piRNA cluster. In contrast, piRNA expression from the converted Adar locus was lost in offspring lacking the inducer allele. Our findings highlight that the paramutation-like behavior of piRNA clusters is influenced not only by piRNAs but also by structural features of chromosomal regions, providing new insights into epigenetic regulation in Drosophila.
2025-03-20 | GSE292339 | GEO
Project description:Gene annoation and determination of gene expression levels in Drosophila virilis and Drosophila yakuba by deep sequencing.
2015-01-29 | GSE61222 | GEO
Project description:Drosophila virilis Transcriptome or Gene expression
| PRJNA168950 | ENA
Project description:Examination of temporal small RNA expression during the embryonic development, larval and adult stages of Drosophila virilis
2014-01-13 | GSE54009 | GEO
Project description:Although small RNAs efficiently control transposition activity of most transposons in the host genome, such immune system is not always applicable against new transposon's invasions. Here we explored a possibility to introduce potentially mobile copy of the Penelope retroelement previously implicated in hybrid dysgenesis syndrome in Drosophila virilis into the genomes of two distant Drosophila species. The consequences of such introduction were monitored at different phases after experimental colonization as well as in D. virilis species which is apparently in the process of ongoing Penelope invasion. We investigated the expression of Penelope and biogenesis of Penelope-derived small RNAs in D. virilis and D. melanogaster strains originally lacking active copies of this element after experimental Penelope invasion. These strains were transformed by constructs containing intact Penelope copies. We show that immediately after transformation, which imitates the first stage of retroelement invasion, Penelope undergoes transposition predominantly in somatic tissues, and may produce siRNAs that are apparently unable to completely silence its activity. However, at the later stages of colonization Penelope copies may jump into one of the piRNA-clusters, which results in production of homologous piRNAs that are maternally deposited and can silence euchromatic transcriptionally active copies of Penelope in trans and, hence, prevent further amplification of the invader in the host genome. Intact Penelope copies and different classes of Penelope-derived small RNAs were found in most geographical strains of D. virilis collected throughout the world. Importantly, all strains of this species containing full-length Penelope tested do not produce gonadal sterility in dysgenic crosses and, hence, exhibit neutral cytotype. In order to understand whether RNA interference mechanism able to target Penelope operates in related species of the virilis group we correlated the presence of full-length and potentially active Penelope with the occurrence of piRNAs homologous to this TE in the ovaries of species comprising the group. It was demonstrated, that Penelope-derived piRNAs are present in all virilis group species containing full-length but transcriptionally silent copies of this element that probably represent the remnants of its previous invasions taking place in the course of the virilis species divergent evolution. piRNA size profile (23-29nt) was examined in D. melanogaster strains, where Penelope-piRNAs are detected by Northern blot
2012-10-31 | E-GEOD-41953 | biostudies-arrayexpress
Project description:The fruit fly Drosophila virilis is a member of the virilis group of the subgenus Drosophila
| PRJNA12687 | ENA