Bombyx mori
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA239665 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1179000.fastq.gz | Fastqsanger.gz | |||
| SRR1178997.fastq.gz | Fastqsanger.gz | |||
| SRR1178998.fastq.gz | Fastqsanger.gz | |||
| SRR1178999.fastq.gz | Fastqsanger.gz | |||
| SRR1333837.fastq.gz | Fastqsanger.gz |
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Project description:Piwi-interacting RNAs (piRNAs) guide Piwi Argonautes to suppress transposon activity in animal gonads. Known piRNA populations are extremely complex, with millions of individual sequences present in a single organism. Despite this complexity, specific Piwi proteins incorporate piRNAs with distinct nucleotide- and transposon strand-biases (antisense or sense) of unknown origin. Here we examined the contribution of structural domains in Piwi proteins towards defining these biases. We report the first crystal structure of the MID domain from a Piwi Argonaute and use docking experiments to show its ability to specify recognition of 5′ uridine (1U-bias) of piRNAs. Mutational analyses reveal the importance of 5’ end-recognition within the MID domain for piRNA biogenesis in vivo. Finally, domain-swapping experiments uncover an unexpected role for the MID-PIWI module of a Piwi protein in dictating the strand-orientation of its bound piRNAs. Our work identifies structural features that allow distinguishing individual Piwi members during piRNA biogenesis
2014-07-01 | GSE55451 | GEO
Project description:Piwi-interacting RNAs (piRNAs) guide Piwi Argonautes to suppress transposon activity in animal gonads. Known piRNA populations are extremely complex, with millions of individual sequences present in a single organism. Despite this complexity, specific Piwi proteins incorporate piRNAs with distinct nucleotide- and transposon strand-biases (antisense or sense) of unknown origin. Here we examined the contribution of structural domains in Piwi proteins towards defining these biases. We report the first crystal structure of the MID domain from a Piwi Argonaute and use docking experiments to show its ability to specify recognition of 5M-bM-^@M-2 uridine (1U-bias) of piRNAs. Mutational analyses reveal the importance of 5M-bM-^@M-^Y end-recognition within the MID domain for piRNA biogenesis in vivo. Finally, domain-swapping experiments uncover an unexpected role for the MID-PIWI module of a Piwi protein in dictating the strand-orientation of its bound piRNAs. Our work identifies structural features that allow distinguishing individual Piwi members during piRNA biogenesis Immunoprecipitated small RNA were purified from Bmn4 cells for preparation of high-throughput sequencing libraries.
2014-07-01 | E-GEOD-55451 | biostudies-arrayexpress
Project description:Hsp90 facilitates accurate loading of precursor piRNAs into PIWI proteins
| PRJDB2257 | ENA
Project description: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. mori (BmVasa) and ATP. Under normal conditions, BmVasa co-purifies with Siwi, but not with second B. mori PIWI BmAgo3. However, when BmVasa loses the ATP-binding and RNA-unwinding activities, BmVasa avidly associates with Siwi and BmAgo3, which contains transposon transcripts predominantly in sense orientation, the sources of BmAgo3-piRNAs. Without BmVasa, BmAgo3 is devoid of piRNAs. Thus, BmVasa actively releases target RNAs from Siwi, upon its cleavage, to urge BmAgo3-piRNA complex formation in the Ping-Pong cycle, enabling continuous supply of piRNAs in germ cells.
2014-12-31 | GSE58221 | GEO
Project description:Identification of the enzyme that trims the 3'-end of piRNAs in silkworms
| PRJDB4053 | ENA
Project description:High throughput sequencing of Siwi and BmAGO3 associated piRNAs from Bombyx mori BmN4 cells
| PRJNA251635 | ENA
Project description: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).
2020-09-02 | GSE150444 | GEO
Project description: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. piRNA 3′-end formation in Bombyx was shown to be mediated by PNLDC1/Trimmer (Trim) 3′-to-5′ exonuclease7, while piRNA intermediates are bound with PIWI anchored onto mitochondrial protein PAPI8. However, the requirement for Zuc and Nbr in piRNA biogenesis in Bombyx has not been elucidated. Here, we applied biochemical approaches to understand their involvement in piRNA biogenesis and revealed that Zuc endonuclease, but not Trim and Nbr exonucleases, plays a crucial role in Bombyx piRNA 3′-end formation. Loss of Zuc had little effect on the levels of Trim and Nbr, but led to the aberrant accumulation of piRNA intermediates within the PAPI complex, which were processed to mature piRNAs by recombinant Zuc. Zuc copurified with PAPI, and PAPI exerted RNA-binding activity only when Siwi coexisted with it and PAPI was phosphorylated, suggesting that complex assembly proceeds via a hierarchical process. Bioinformatic analyses of piRNA intermediates within the PAPI complex revealed that both the 5′ and the 3′ ends showed the hallmark of PIWI-Slicer, yet no phasing pattern was observed in mature piRNAs. These findings strongly support the notion that, in Bombyx piRNA, the 5′ end is formed by PIWI-Slicer, but independently of Zuc, while the 3′ end is formed by Zuc endonuclease. The Bombyx piRNA biogenesis is simpler than that of Drosophila, which is reasonable considering that Bombyx has no transcriptional silencing machinery relying on phased piRNAs.
2018-03-01 | GSE107371 | GEO
Project description:PIWI-interacting RNAs (piRNAs) bind to PIWI proteins to assemble the piRISC, which represses germline transposons. Maelstrom (Mael) is necessary for piRISC biogenesis in germ cells, but its function remains unclear. Here, we show that Mael interconnects Spindle-E (Spn-E), a key piRISC biogenesis factor, with unloaded Siwi, one of two silkworm PIWI members. Mael also assembles a subset of nuage, a non-membranous organelle involved in piRISC biogenesis. Loss of Mael abrogated the Spn-E–Siwi interaction and Ago3-piRISC biogenesis, but Siwi-piRISC was produced. Bioinformatic analysis showed that Siwi-bound piRNAs in Mael-lacking cells were rich in transposon-targeting piRNAs as in normal cells but were biased toward transposons that are marginally controlled by Siwi-piRISC. This explains the impairment in Ago3-piRISC production because transposon mRNAs cleaved by Siwi are the origin of Ago3-loaded piRNAs. We argue that Mael plays a role in the production of primary Siwi-piRISC capable of regulating transposon expression in germ cells.
2022-03-02 | GSE180191 | GEO