Environmentally-induced epigenetic conversion of a piRNA cluster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA477333 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7406440.fastq.gz | Fastqsanger.gz | |||
| SRR7406441.fastq.gz | Fastqsanger.gz | |||
| SRR7406442.fastq.gz | Fastqsanger.gz | |||
| SRR7406443.fastq.gz | Fastqsanger.gz | |||
| SRR7406444.fastq.gz | Fastqsanger.gz |
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Project description:Transposable element (TE) activity is repressed in animal gonads by PIWI-interacting RNAs (piRNAs) produced by piRNA clusters. Current models propose that piRNA clusters are functionally defined by the maternal inheritance of piRNAs produced during the previous generation. Taking advantage of an inactive cluster of P-element derived transgene insertions in Drosophila melanogaster, we show here that raising flies at high temperature (29°C) instead of 25°C results in stable conversion of this locus into an active piRNAs producing one reporting thus the first case of the establishment of an active piRNA cluster by environmental changes and without maternal inheritance of homologous piRNAs.
2019-03-14 | GSE116122 | GEO
Project description:Environmentally-induced epigenetic conversion of a piRNA cluster.
| PRJEB25286 | ENA
Project description:Transposable element (TE) activity is repressed in animal gonads by PIWI-interacting RNAs (piRNAs) produced by piRNA clusters. Current models in flies propose that germinal piRNA clusters are functionally defined by the maternal inheritance of piRNAs produced during the previous generation. Taking advantage of an inactive, but ready to go, cluster of P-element derived transgene insertions in Drosophila melanogaster, we show here that raising flies at high temperature (29°C) instead of 25°C triggers the stable conversion of this locus from inactive into actively producing functional piRNAs. The increase of antisense transcripts from the cluster at 29°C combined with the requirement of transcription of euchromatic homologous sequences, suggests a role of double stranded RNA in the production of de novo piRNAs. This report describes the first case of the establishment of an active piRNA cluster by environmental changes in the absence of maternal inheritance of homologous piRNAs. This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
| S-EPMC6420265 | biostudies-literature
Project description:In order to control transposable element (TE) activity, PIWI-interacting RNAs (piRNAs) have been evolved to silence TE transcriptionally and post-transcriptionally, and produced from heterochromatic genomic loci, called piRNA cluster. Maternal inherited piRNAs transmission is considered as the key step of piRNA cluster maintenance and induction of de nove piRNA cluster formation, however, how the original piRNAs were produced without maternal piRNAs deposition remains unclear. In this paper, we created a repetitive GFP reporter and found a Rhino-dependent piRNA cluster conversion spontaneously occurs to the reporter over generations. Importantly, this conversion is reversible by removal of maternal piRNAs of GFP reporter. Taking advantage of this reversible GFP reporter piRNA cluster, we found that siRNA is able to initiate piRNA cluster formation epigenetically, even when only maternal siRNA presence is capable to do so. Our results suggest the importance of siRNA on initiation of piRNA biogenesis and describe a whole picture of initiation and maintenance of piRNA cluster.
2024-01-05 | GSE193091 | GEO
Project description:This study examines the conservation of Piwi-interacting RNA (piRNA) clusters that come from protein coding gene transcripts. By sequencing small RNA libraries from gonad tissues of Drosophilids and Glires we discover a diverse set of genic piRNA clusters conserved across animals. This dataset reveals new expression patterns for genic piRNA clusters and examines whether changing piRNA expression patterns correlates with sequence changes in piRNA cluster genomic sequence across a variety of animal species.
2015-11-01 | GSE62556 | GEO
Project description:Maternal inherited siRNA initiate piRNA cluster formation
| PRJNA794746 | ENA
Project description:This study examines the conservation of Piwi-interacting RNA (piRNA) clusters that come from protein coding gene transcripts. By sequencing small RNA libraries from gonad tissues of Drosophilids and Glires we discover a diverse set of genic piRNA clusters conserved across animals. This dataset reveals new expression patterns for genic piRNA clusters and examines whether changing piRNA expression patterns correlates with sequence changes in piRNA cluster genomic sequence across a variety of animal species. We dissected gonad tissues consisting of ovaries from wildtype adult Drosophilids (D.melanogaster, D.erecta, D.yakuba, D.virilis) and testes from wildtype pre-pubsecent and adult mouse and rats. Adult testes from rabbits were purchased from Pel-Freez Biologicals. Total or immunopreciptated RNAs were extracted from the pulvirized gonad tissues of Drosophilids and Glires. Small RNAs were purified from these samples, converted into cDNA libraries, and sequenced on an Illumina HiSeq2000.
2015-11-01 | E-GEOD-62556 | biostudies-arrayexpress
Project description:The evolution of genic piRNA cluster loci expression patterns
| PRJNA264407 | ENA
Project description:Expression of transposable elements in the germline is controlled by Piwi-interacting (pi) RNAs produced by genomic loci termed piRNA clusters and associated with Rhino, a Heterochromatin Protein 1 (HP1) homolog. Previously, we have shown that transgenes containing a fragment of the I retrotransposon form de novo piRNA clusters in the Drosophila germline providing suppression of I-element activity. We noted that identical transgenes located in different genomic sites vary considerably in piRNA production and classified them as “strong” and “weak” piRNA clusters. Here, we investigated what chromatin and transcriptional changes occur at the transgene insertion sites after their conversion into piRNA clusters. We found that the formation of a transgenic piRNA cluster is accompanied by activation of transcription from both genomic strands that likely initiates at multiple random sites. The chromatin of all transgene-associated piRNA clusters contain high levels of trimethylated lysine 9 of histone H3 (H3K9me3) and HP1a, whereas Rhino binding is considerably higher at the strong clusters. None of these chromatin marks was revealed at the “empty” sites before transgene insertion. Finally, we have shown that in the nucleus of polyploid nurse cells, the formation of a piRNA cluster at a given transgenic genomic copy works according to an “all– or– nothing” model: either there is high Rhino enrichment or there is no association with Rhino at all. As a result, genomic copies of a weak piRNA transgenic cluster show a mosaic association with Rhino foci, while the majority of strong transgene copies associate with Rhino and are hence involved in piRNA production.
2018-01-24 | GSE88774 | GEO
Project description:In a broad range of organisms, Piwi-interacting RNAs (piRNAs) have emerged as core components of a surveillance system that protects the genome by silencing transposable and repetitive elements. A vast proportion of piRNAs is produced from discrete genomic loci, termed piRNA clusters. The molecular mechanisms and the factors that govern the expression of these loci are largely unknown. We have preciously shown the Cutoff (Cuff), a protein with similarity to yeast Rai1, is a component of the piRNA pathway. In order to understand the function of the Cuff protein in piRNA production, we produced small RNA libraries from cn, bw (wt) and cuffwm25 mutant ovaties. The analysis of these libraries revealed that approximately 80% of the total piRNA population is depleted in the absence of a functional Cuff protein. We also determined that Cuff is mostly a nuclear protein and is enriched at the level of certain piRNA clusters. Our results point to a role for Cuff in the transcriptional regulation of piRNA generating loci and in the production of the proper piRNA complement during Drosophila oogenesis. piRNA profiling in ovaries from cn, bw and cuffwm25 mutant ovaries
2013-06-07 | E-GEOD-47738 | biostudies-arrayexpress