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A transcriptome-wide RNAi screen in the Drosophila ovary reveals factors of the germline piRNA pathway

ABSTRACT: A transcriptome-wide RNAi screen in the Drosophila ovary reveals factors of the germline piRNA pathway

PROVIDER: PRJNA197265 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR827714.fastq.gz	Fastqsanger.gz
	SRR827715.fastq.gz	Fastqsanger.gz
	SRR827716.fastq.gz	Fastqsanger.gz
	SRR827717.fastq.gz	Fastqsanger.gz
	SRR827718.fastq.gz	Fastqsanger.gz

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A transcriptome-wide RNAi screen in the Drosophila ovary reveals factors of the germline piRNA pathway [smallRNA-Seq]

Project description:The Drosophila piRNA pathway provides an RNA-based immune system that defends the germline genome against selfish genetic elements. Two inter-related branches of the piRNA system exist: somatic cells that support oogenesis only employ Piwi, whereas germ cells utilize a more elaborated pathway centered on the three gonad-specific Argonaute proteins Piwi, Aubergine, and Argonaute3. While several key factors of each branch have been identified, our current knowledge is insufficient to explain the complex workings of the piRNA machinery. Here, we report a reverse genetic screen spanning the ovarian transcriptome in an attempt to uncover the full repertoire of genes required for piRNA-mediated transposon silencing in the female germline. Our screen reveals new key factors of piRNA-mediated transposon silencing, including the novel piRNA biogenesis factors, CG2183 (GASZ) and Deadlock. Last, our data uncovers a previously unanticipated set of factors preferentially required for repression of different transposons types. Examination of small RNA levels from nos-GAL4 or tj-GAL4 driven UAS-dsRNA knockdowns of control genes and piRNA pathway components in ovaries of Drosophila melanogaster by deep sequencing (using Illumina HiSeq2000).

2013-05-10 | E-GEOD-46099 | biostudies-arrayexpress

A transcriptome-wide RNAi screen in the Drosophila ovary reveals factors of the germline piRNA pathway [RNA-Seq]

Project description:The Drosophila piRNA pathway provides an RNA-based immune system that defends the germline genome against selfish genetic elements. Two inter-related branches of the piRNA system exist: somatic cells that support oogenesis only employ Piwi, whereas germ cells utilize a more elaborated pathway centered on the three gonad-specific Argonaute proteins Piwi, Aubergine, and Argonaute3. While several key factors of each branch have been identified, our current knowledge is insufficient to explain the complex workings of the piRNA machinery. Here, we report a reverse genetic screen spanning the ovarian transcriptome in an attempt to uncover the full repertoire of genes required for piRNA-mediated transposon silencing in the female germline. Our screen reveals new key factors of piRNA-mediated transposon silencing, including the novel piRNA biogenesis factors, CG2183 (GASZ) and Deadlock. Last, our data uncovers a previously unanticipated set of factors preferentially required for repression of different transposons types. Examination of total RNA levels from nos-GAL4 or tj-GAL4 driven UAS-dsRNA knockdowns of control genes and piRNA pathway components in ovaries of Drosophila melanogaster by deep sequencing (using Illumina HiSeq2000).

2013-05-10 | E-GEOD-46100 | biostudies-arrayexpress

A transcriptome-wide RNAi screen in the Drosophila ovary reveals factors of the germline piRNA pathway [RNA-Seq]

2013-05-10 | GSE46100 | GEO

A transcriptome-wide RNAi screen in the Drosophila ovary reveals factors of the germline piRNA pathway [smallRNA-Seq]

2013-05-10 | GSE46099 | GEO

Analysis of redundancy between RNAi and piRNA pathways in the mouse oocytes

Project description:Suppression of retrotransposons is an integral part of germline genome defense. The PIWI-associated RNA (piRNA) pathway mediates post-transcriptional and transcriptional silencing of retrotransposons in vertebrates. The loss of the piRNA pathway in mice results in male sterility while females remain fertile. Unlike spermatogenic cells, mouse oocytes utilize also RNA interference (RNAi) pathway, another small RNA pathway capable of retrotransposon suppression. To examine redundancy of piRNA and RNAi pathway in the mouse female germline, we produced an RNAi pathway mutant DicerSOM and crossed it with a catalytically-dead mutant of Mili, an essential piRNA factor. Ovaries and follicular development in mice lacking both pathways appear normal suggesting that RNAi in oocytes does not rescue a piRNA pathway knock-out phenotype. We observed that one of the pathways dominates in suppression of different retrotransposons. Intracisternal A Particle retrotransposon is mainly targeted by the piRNA pathway, MT and RLTR10 retrotransposons were targeted mainly by RNAi. Importantly, both pathways redundantly suppress LINE-1 retrotransposons where the loss of both RNA silencing pathways yielded ~6-fold upregulation of negligible levels of LINE-1 transcripts. This implies that another transcriptional silencing mechanism must contribute to LINE-1 repression and could explain why both, RNAi and piRNA pathways, are non-essential defense pathway in the mouse female germline.

2019-11-22 | GSE132121 | GEO

Transcriptional regulation of the germline piRNA pathway in the Drosophila ovary

Project description:Transcriptional regulation of the germline piRNA pathway in the Drosophila ovary

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A genetic toolkit for studying transposon control in the Drosophila melanogaster ovary

Project description:Argonaute proteins of the PIWI-clade, complexed with PIWI-interacting RNAs (piRNAs), protect the animal germline genome by silencing transposable elements. One of the leading experimental systems for studying piRNA biology is the Drosophila melanogaster ovary. In addition to classical mutagenesis, transgenic RNA interference (RNAi), which enables tissue-specific silencing of gene expression, plays a central role in piRNA research. Here, we establish a versatile toolkit focused on piRNA biology that integrates transgenic RNAi in the germline, GFP-marker lines for key proteins of the piRNA pathway, and reporter transgenes to establish genetic hierarchies. We compare constitutive, pan-germline RNAi with an equally potent transgenic RNAi system that is activated only upon germ cell cyst formation. Stage specific RNAi allows investigating the role of genes essential for cell survival (e.g. nuclear RNA export or the SUMOylation pathways) in piRNA-dependent and independent transposon silencing. Our work forms the basis for an expandable genetic toolkit available from the Vienna Drosophila Resource Center.

2021-05-19 | GSE174611 | GEO

Transcriptional regulation of the germline piRNA pathway in the Drosophila ovary [RNA-seq]

Project description:The gene-regulatory mechanisms behind the female germline piRNA pathway in ovaries of metazoan species remain largely unexplored. Here, using the Drosophila model and combinations of RNA-seq, ATAC-seq, and single-cell approaches, we reveal the transcription factors that regulate the female germline piRNA pathway in animal ovaries.

2024-12-23 | GSE233245 | GEO

Transcriptional regulation of the germline piRNA pathway in the Drosophila ovary [ATAC-seq]

2024-12-23 | GSE233241 | GEO

Transcriptional regulation of the germline piRNA pathway in the Drosophila ovary [ChIP-Seq]

Project description:The gene-regulatory mechanisms behind the female germline piRNA pathway in ovaries of metazoan species remain largely unexplored. Here, using the Drosophila model and combinations of ChIP-seq, RNA-seq, ATAC-seq, and single-cell approaches, we reveal the transcription factors that regulate the female germline piRNA pathway in animal ovaries.

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