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Items: 20

1.

Multiple roles for Piwi in silencing Drosophila transposons

(Submitter supplied) Silencing of transposons in the Drosophila ovary relies on three Piwi-family proteins, Piwi, Aubergine (Aub), and Ago3, acting in concert with their small RNA guides, the piRNAs. Aub and Ago3 are found in the germ cell cytoplasm, where they function in the ping-pong cycle to consume transposon mRNAs. The nuclear Piwi protein is required for transposon silencing in both germ and somatic follicle cells, yet the precise mechanisms by which Piwi acts remain largely unclear. more...
Organism:
Drosophila melanogaster
Type:
Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL13304 GPL16479
16 Samples
Download data:
GEO (TXT, XLS), SRA SRP017841
Series
Accession:
GSE43360
ID:
200043360
2.

Characterization of expression changes in qin by tiling array

(Submitter supplied) Qin, a novel protein comprising amino-terminal E3 ligase and five carboxy terminal Tudor domains, silences transposons and ensures genome stability in the Drosophila germline by promoting antisene piRNA amplification via Aubergine:Ago3 Ping-Pong and preventing futile Aubergine:Aubergine interactions.
Organism:
Drosophila melanogaster
Type:
Expression profiling by genome tiling array
Platform:
GPL6629
6 Samples
Download data:
GEO (CEL, TXT)
Series
Accession:
GSE30061
ID:
200030061
3.

Expression profile and RNA Polymerase II occupancy of transposable elements among knock down of the piRNA pathway components in OSCs

(Submitter supplied) The Piwi–piRNA complex (Piwi–piRISC) 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). more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL13304 GPL16479
10 Samples
Download data:
GEO (TXT), SRA SRP022848
Series
Accession:
GSE47006
ID:
200047006
4.

Characterization of expression changes in armi,rhino,aub,ago3 mutants by tiling array

(Submitter supplied) We characterized changes of transposon and mRNA expressions in armi, rhino ,aub, ago3 mutants with respect to wild type using Affy tiling array. In most of these mutants, mRNA expressions were mostly unchanged but increased expressions was observed for many transposons indicating the role of these proteins in silencing transposons in Drosophila ovaries Keywords: Tiling array transcriptome profiling
Organism:
Drosophila melanogaster
Type:
Expression profiling by genome tiling array
Platform:
GPL6629
15 Samples
Download data:
GEO (CEL, TXT)
Series
Accession:
GSE14370
ID:
200014370
5.

piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire

(Submitter supplied) PIWI-clade Argonaute proteins silence transposon expression in animal gonads. Their target specificity is defined by bound ~23-30nt piRNAs that are processed from single-stranded precursor transcripts via two distinct pathways. Primary piRNAs are defined by the endo-nuclease Zucchini, while biogenesis of secondary piRNAs depends on piRNA-guided transcript cleavage and results in piRNA amplification. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13304
46 Samples
Download data:
GEO (BW, TXT), SRA SRP062097
Series
Accession:
GSE71775
ID:
200071775
6.

FLX sequencing of Piwi-associated small RNAs extracted from Drosophila ovarian somatic cells (OSC)

(Submitter supplied) piRNAs function in silencing retrotransposons by associating with the PIWI proteins, AGO3, Aub, and Piwi, in Drosophila germlines. Bioinformatics analyses of piRNAs in Drosophila ovaries suggested that piRNAs are produced by two systems, the primary processing pathway and the amplification loop, from repetitive genes and piRNA clusters in the genome. The amplification loop occurs in a Dicer-independent, PIWI-Slicer-dependent manner. more...
Organism:
Drosophila melanogaster
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL9333
1 Sample
Download data:
GEO, SRA SRP001366
Series
Accession:
GSE15137
ID:
200015137
7.

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

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13304
41 Samples
Download data:
GEO (TXT)
Series
Accession:
GSE46101
ID:
200046101
8.

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

(Submitter supplied) 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. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13304
28 Samples
Download data:
GEO (TXT), SRA SRP021103
Series
Accession:
GSE46100
ID:
200046100
9.

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

(Submitter supplied) 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. more...
Organism:
Drosophila melanogaster
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13304
13 Samples
Download data:
GEO (TXT), SRA SRP021102
Series
Accession:
GSE46099
ID:
200046099
10.

Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state

(Submitter supplied) 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. more...
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL13304
19 Samples
Download data:
GEO (BEDGRAPH), SRA SRP018251
Series
Accession:
GSE43829
ID:
200043829
11.

Impact of nuclear Piwi elimination on chromatin state in Drosophila melanogaster ovaries

(Submitter supplied) The piRNA-interacting Piwi protein is involved in transcriptional silencing of transposable elements in ovaries of D. melanogaster. Here we characterized the genome-wide effect of nuclear Piwi elimination on the presence of the heterochromatic H3K9me3 mark and HP1a, as well as on the transcription-associated mark H3K4me2. Our results demonstrate that a significant increase in the H3K4me2 level upon nuclear Piwi loss is not accompanied by the alterations in H3K9me3 and HP1a levels for several germline-expressed transposons, suggesting that in this case Piwi prevents transcription by a mechanism distinct from H3K9 methylation. more...
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13304
16 Samples
Download data:
GEO (BEDGRAPH), SRA SRP040803
Series
Accession:
GSE56347
ID:
200056347
12.

Changes in gene expression in fruitfly ovaries in mutants affecting components of rasiRNA system

(Submitter supplied) rasiRNA (rasiRNAs, repeat-associated short interfering RNAs) system is a mechanism of silencing of mobile element transpositions in germline of a number of species including Drosophila melanogaster. rasiRNA itself is a short RNAs which participate in transposon transcription repression and mRNA degradation. Defects in rasiRNA system lead to increased transposition rate and developmental abnormalities due to accumulation of double-strand DNA breaks in fruitfly testes and ovaries. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by array
Platform:
GPL3603
6 Samples
Download data:
GEO (GPR)
Series
Accession:
GSE40768
ID:
200040768
13.

piRNA libraries from Drosophila melanogaster ovaries

(Submitter supplied) Drosophila Piwi-family proteins have been implicated in transposon control. Here, we examine piwi-interacting RNAs (piRNAs) associated with each Drosophila Piwi protein and find that Piwi and Aubergine bind RNAs that are predominantly antisense to transposons, whereas Ago3 complexes contain predominantly sense piRNAs. As in mammals, the majority of Drosophila piRNAs are derived from discrete genomic loci. more...
Organism:
Drosophila melanogaster
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL9058
4 Samples
Download data:
GEO
Series
Accession:
GSE6734
ID:
200006734
14.

The Function of Piwi is Independent of Its Slicer Activity

(Submitter supplied) In diverse organisms, the highly-conserved Piwi proteins bind to a complex class of small non-coding RNAs called piRNAs, and are essential for germline stem cell maintenance, transposon silencing, fertility, and offspring viability1. By homology with other Argonautes, Piwi proteins have been proposed and later reported to possess endonuclease activity in vitro, effected by its conserved aspartate catalytic triad2,3. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platform:
GPL9061
4 Samples
Download data:
GEO (TXT), SRA SRP009566
Series
Accession:
GSE34032
ID:
200034032
15.

PIWI slicing and EXD1 drive biogenesis of nuclear piRNAs from cytosolic targets of the mouse piRNA pathway

(Submitter supplied) PIWI-interacting RNAs (piRNAs) guide PIWI proteins to suppress transposable elements in animal gonads. Here we demonstrate that in the mouse embryonic male germline, endonucleolytic cleavage (slicing) of a transcript by cytosolic MILI acts as a trigger to initiate its further 5??3? processing into non-overlapping fragments. These fragments accumulate as new piRNAs within the nuclear PIWI protein MIWI2. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
13 Samples
Download data:
GEO (CSV, TXT), SRA SRP065396
Series
Accession:
GSE74423
ID:
200074423
16.

the analysis of piRNA shows the function of Slicer activity of AGO3 in piRNA biogenesis.

(Submitter supplied) Piwi-interacting RNAs (piRNAs) silence transposons in animal germ cells. In Drosophila, the reciprocal “Ping-Pong” cycle of piRNA-directed RNA cleavage, catalyzed by the PIWI proteins Aubergine (Aub) and Argonaute3 (AGO3) through their Slicer activity, is believed to expand the population of antisense piRNAs in response to transposon expression. Whether and how the Slicer activity of AGO3/Aub promotes the process of the secondary piRNA amplification remain unclear. more...
Organism:
Drosophila melanogaster
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL17520
3 Samples
Download data:
GEO (TXT), SRA SRP026223
Series
Accession:
GSE49436
ID:
200049436
17.

Panoramix enforces piRNA-dependent co-transcriptional silencing

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL13304 GPL16479
59 Samples
Download data:
GEO
Series
Accession:
GSE71374
ID:
200071374
18.

Panoramix enforces piRNA-dependent co-transcriptional silencing (small RNA-Seq)

(Submitter supplied) The Piwi-interacting RNA (piRNA) pathway is a small RNA-based innate immune system that defends germ cell genomes against transposons. In Drosophila ovaries, the nuclear Piwi protein is required for transcriptional silencing of transposons, though the precise mechanisms by which this occurs are unknown. Here we show that CG9754 is a component of Piwi complexes that functions downstream of Piwi and its binding partner, Asterix, in transcriptional silencing. more...
Organism:
Drosophila melanogaster
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL13304 GPL16479
8 Samples
Download data:
GEO (XLSX), SRA SRP061630
Series
Accession:
GSE71372
ID:
200071372
19.

Panoramix enforces piRNA-dependent co-transcriptional silencing (RNA-Seq)

(Submitter supplied) The Piwi-interacting RNA (piRNA) pathway is a small RNA-based innate immune system that defends germ cell genomes against transposons. In Drosophila ovaries, the nuclear Piwi protein is required for transcriptional silencing of transposons, though the precise mechanisms by which this occurs are unknown. Here we show that CG9754 is a component of Piwi complexes that functions downstream of Piwi and its binding partner, Asterix, in transcriptional silencing. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL13304 GPL16479
24 Samples
Download data:
GEO (XLSX), SRA SRP061629
Series
Accession:
GSE71371
ID:
200071371
20.

Panoramix enforces piRNA-dependent co-transcriptional silencing (GRO-Seq)

(Submitter supplied) The Piwi-interacting RNA (piRNA) pathway is a small RNA-based innate immune system that defends germ cell genomes against transposons. In Drosophila ovaries, the nuclear Piwi protein is required for transcriptional silencing of transposons, though the precise mechanisms by which this occurs are unknown. Here we show that CG9754 is a component of Piwi complexes that functions downstream of Piwi and its binding partner, Asterix, in transcriptional silencing. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL13304 GPL16479
10 Samples
Download data:
GEO (XLSX), SRA SRP061628
Series
Accession:
GSE71369
ID:
200071369
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