GEO DataSets

(Submitter supplied) PIWI-interacting RNAs (piRNAs) are germline-enriched small RNAs that control transposons to maintain genome integrity1,2,3. To achieve this, piRNAs bind PIWI proteins upon being processed from piRNA precursors1,2,3. Bioinformatic studies of piRNA biogenesis in Drosophila showed that the piRNA 5′ end is formed by PIWI-Slicer or Zucchini (Zuc) endonucleolytic cleavage, while the 3′ end is formed by Zuc or Nibbler (Nbr) 3′-to-5′ exonucleolytic activity4,5,6. more...

Organism:

Bombyx mori

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18754

8 Samples

Download data: TXT

(Submitter supplied) Bombyx Papi contains two K-homology (KH) domains and one Tudor domain, and acts as a scaffold for Siwi-piRISC biogenesis on the mitochondrial surface. To initiate this process, Papi binds first to Siwi via the Tudor domain and subsequently to piRNA precursors loaded onto Siwi via the KH domains. This second action depends on phosphorylation of Papi. However, its underlying mechanism remains unknown. more...

Organism:

Bombyx mori

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18754

6 Samples

Download data: TXT

(Submitter supplied) We show that heterologous RNA that lacks complementary piRNAs is processed into piRNAs upon recruitment of several piRNA pathway factors. Our approach utilizes tethering of components of the piRNA pathway to the transcript of a reporter and then small RNA cloning from total RNA from Drosophila ovaries. Our approach allows discrimination of proteins involved in transcription and export of piRNA precursors from components required for the cytoplasmic processing steps. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17275

70 Samples

Download data: BEDGRAPH, FA

(Submitter supplied) RNAs associating with PIWI proteins were Immunoisolated from BmN4 cells. Sequence libraries were generated with NEBNext Small RNA Library Prep Set for Illumina(NEB). Libraries were sequenced using Illumina MiSeq (single-end, 51 cycles).

Organism:

Bombyx mori

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18754

9 Samples

Download data: FA, TXT, XLSX

(Submitter supplied) Small regulatory RNAs guide Argonaute (Ago) proteins in a sequence-specific manner to their targets and therefore have important roles in eukaryotic gene silencing. Of the three small RNA classes, microRNAs and short interfering RNAs are processed from double-stranded precursors into defined 21- to 23-mers by Dicer, an endoribonuclease with intrinsic ruler function. PIWI- interacting RNAs (piRNAs)—the 22–30-nt-long guides for PIWI- clade Ago proteins that silence transposons in animal gonads— are generated independently of Dicer from single-stranded precursors. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17275

35 Samples

Download data: TXT

(Submitter supplied) PIWI-clade Argonaute proteins repress transposable elements in animal gonads. Their sequence specificity is conferred via bound ~23-30nt long piRNAs, which are processed from single stranded precursor RNAs. How transcripts are specified as precursors and processed into stereotypical piRNA populations are central unresolved questions. Here we show that piRNA-guided RNA cleavage in Drosophila results not only in generation of a ping-pong partner piRNA but further triggers efficient 3′ directed and phased primary piRNA biogenesis. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL13304

26 Samples

Download data: TXT

(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: BW, TXT

(Submitter supplied) In Drosophila, PIWI proteins and bound PIWI interacting RNAs (piRNAs) form the core of a small RNA mediated defense system against selfish genetic elements. Within germline cells piRNAs are processed from piRNA clusters and transposons to be loaded into Piwi/Aubergine/AGO3 and a subset of piRNAs undergoes target dependent amplification. In contrast, gonadal somatic support cells express only Piwi, lack signs of piRNA amplification and exhibit primary piRNA biogenesis from piRNA clusters. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9061

5 Samples

Download data: TXT

(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: CSV, TXT

(Submitter supplied) RNAs associating with PIWI proteins were Immunoisolated from BmN4 cells. Sequence libraries were generated with NEBNext Small RNA Library Prep Set for Illumina(NEB). Libraries were sequenced using Illumina MiSeq (single-end, 51 cycles).

Organism:

Bombyx mori

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18754

2 Samples

Download data: TXT

(Submitter supplied) In germ cells, piRNAs are amplified through the Ping-Pong cycle that depends on reciprocal Slicer-mediated target RNA cleavage by two PIWI members. A germ-specific DEAD-box protein Vasa is required for the process. However, Vasa’s function is poorly understood. Here, we show that target RNAs cleaved by a Bombyx mori (silkworm) PIWI, Siwi, remain to be bound with the protein upon cleavage, but are released in the presence of Vasa in B. more...

Organism:

Bombyx mori

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18754

5 Samples

Download data: TXT

(Submitter supplied) piRNAs are 26-30nt germ-line specific small non-coding RNAs that have evolutionarily conserved function in mobile genetic element silencing and maintenance of genome integrity. It has been shown that Drosophila Hsp70/90 Organizing Protein Homolog (Hop) – a co-chaperone interacts with piRNA binding protein Piwi and mediates silencing of phenotypic variations. However, it is not known if Hop has a direct role in piRNA biogenesis and transposon silencing. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17275

6 Samples

Download data: TXT

(Submitter supplied) Piwi-interacting RNAs are 25-32 nt small RNAs bound to Piwi proteins. To know the steps where factors involved in the piRNA biogenesis (MILI, MIWI2, ZUC (MitoPLD), MVH) work, we sequenced small RNAs from mutant mouse testes and analyzed piRNAs.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9250

6 Samples

Download data: TXT

(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

(Submitter supplied) Armitage (Armi) is a component of Yb bodies and functions in the primary piRNA processing pathway. Armi interaction with Piwi does not require Yb expression; however, without Yb, the Armi-Piwi complex does not localize at Yb bodies and contains few piR-ILs (small RNAs associated with Armitage complex). These results suggest that only upon its localization at Yb bodies does the Armi-Piwi-Yb complex gain an opportunity to interact with piR-ILs. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10876

1 Sample

Download data: FNA

(Submitter supplied) In Drosophila, Piwi proteins associate with Piwi-interacting RNAs (piRNAs) and protect the germline genome by silencing mobile genetic elements. This defense system acts in germline and gonadal somatic tissue to preserve germline development. Genetic control for these silencing pathways varies greatly between tissues of the gonad. Here, we identified Vreteno (Vret), a novel gonad-specific protein essential for germline development. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

12 Samples

Download data: CEL

(Submitter supplied) Here, we analyzed small RNA libraries derived from ovarian tissues heterozygous or mutant for the Tudor gene, Vreteno. In the absence of vret, Piwi-bound piRNAs are lost without changes in piRNA precursor transcript production, supporting a role for Vret in primary piRNA biogenesis. In the germline, piRNAs can engage in an Aub/Argonaute 3 (AGO3)-dependent amplification in the absence of Vret, suggesting that Vret function can distinguish between primary piRNAs loaded into Piwi/Aub complexes and piRNAs engaged in the amplification cycle. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9061

2 Samples

Download data: CSV

(Submitter supplied) PIWI proteins and their associated small RNAs called PIWI-interacting RNAs (piRNAs) restrict transposon activity in animal gonads to ensure fertility. Distinct biogenesis pathways load piRNAs into the PIWI proteins MILI and MIWI2 in the mouse male embryonic germline. While most of MILI piRNAs derive via a slicer-independent pathway, a MILI slicer endonuclease-initiated pathway loads nuclear MIWI2 with a series of phased piRNAs. more...

Organism:

Mus musculus

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

32 Samples

Download data: CSV

(Submitter supplied) Heterochromatin, representing the silenced state of transcription, largely consists of transposon-enriched and highly repetitive sequences. Implicated in heterochromatin formation and transcriptional silencing in Drosophila are PIWI and repeat-associated small interfering RNAs (rasiRNAs). Despite this, the role of PIWI in rasiRNA expression and heterochromatic silencing remains unknown. Here we report the identification and characterization of 12,903 PIWI-interacting RNAs (piRNAs) in Drosophila, demonstrating that rasiRNAs represent a subset of piRNAs. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL5922

1 Sample

Download data: TXT

(Submitter supplied) Small RNAs called PIWI -interacting RNAs (piRNAs) are essential for transposon control and fertility in animals. Primary processing is the small RNA biogenesis pathway that uses long single-stranded RNA precursors to generate millions of individual piRNAs, but the molecular mechanisms that identify a transcript as a precursor are poorly understood. Here we demonstrate that artificial tethering of the piRNA biogenesis factor, Armi, to a transcript is sufficient to direct it into primary processing in Drosophila ovaries and in an ovarian cell culture model. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13304

108 Samples

Download data: TXT