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Bombycidae strain:BmN4

ABSTRACT: Siwi and BmAgo3 IPed piRNA profile in BmN4 cells

PROVIDER: PRJDB17074 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR514992.fastq.gz	Fastqsanger.gz
	DRR514993.fastq.gz	Fastqsanger.gz

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Bombyx mori strain:BmN4

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Bombyx mori strain:BmN4

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High throughput sequencing of Siwi and BmAGO3 associated piRNAs from Bombyx mori BmN4 cells

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.

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Siwi cooperates with Par-1 kinase to regulate mitochondrial Papi scaffolding Siwi-piRISC biogenesis

Project description: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. Here, we show that Siwi targets Par-1 kinase to mitochondrial Papi to promote its phosphorylation at Ser547 in the auxiliary domain and that this modification enhances the ability of Papi to bind Siwi-bound piRNA precursors via the KH domains. Papi S547A mutant still bound to Siwi, like wild-type (WT) Papi, although it evaded phosphorylation by Par-1: Consequently, Papi lost the ability to bind RNAs, abrogating the generation of Siwi-piRISC. Papi mutant lacking the Tudor and auxiliary domains escaped coordinated regulation by Siwi and Par-1 and lost their bias to bind piRNA precursors. Pseudo-phosphorylation mutants of Papi restored Siwi-piRISC formation in Papi-lacking cells, but their ability to bind RNAs required Siwi, similar to WT Papi. Par-1-dependent, multilayered mechanism by which Siwi regulates the role of Papi in Siwi-piRISC biogenesis was revealed.

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RNA associating with PIWI proteins in Bombyx mori BmN4 cells

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).

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High throughput sequencing of Siwi associated piRNAs from Bombyx mori BmN4 cells

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A role for Fkbp6 and the chaperone machinery in piRNA amplification and transposon silencing

Project description:Epigenetic silencing of transposons by Piwi-interacting RNAs (piRNAs) constitutes an RNA-based genome defense mechanism. Piwi endonuclease action amplifies the piRNA pool by generating new piRNAs from target transcripts by a poorly understood mechanism. Here, we identified mouse Fkbp6 as a factor in this biogenesis pathway delivering piRNAs to the Piwi protein Miwi2. Mice lacking Fkbp6 derepress LINE1 (L1) retrotransposon and display reduced DNA methylation due to deficient nuclear accumulation of Miwi2. Like other co-chaperones, Fkbp6 associates with the molecular chaperone Hsp90 via its tetratricopeptide repeat (TPR) domain. Inhibition of the ATP-dependent Hsp90 activity in an insect cell culture model results in the accumulation of short antisense RNAs in Piwi complexes. We identify these to be by-products of piRNA amplification that accumulate only in nuage-localized Piwi proteins. We propose that the chaperone machinery normally ejects these inhibitory RNAs, allowing turnover of Piwi complexes for their continued participation in piRNA amplification. Small RNAs were purified for preparation of high-throughput sequencing libraries. All libraries except JX56, JX57, JX36 and JX37 were generated from isolated small RNAs obtained by immunoprecipitation of the indicated proteins (Mili, Miwi2, Siwi or Ago3). JX56 and JX57 were prepared from small RNAs extracted from mouse testis. JX36 and JX37 were prepared from polyA+ RNAs extracted from the Bombyx mori cell line BmN4. Libraries prepared from mouse were prepared from mice having the indicated genotype. BmN4 cells were treated with the Hsp90 inhibitor geldanamycin (GA) before performing the immunoprecipitation in the indicated libraries. This lead to accumulation to a short species of small RNAs (16nt long) in Ago3 complexes which we called ping-pong by-product. Details can be found in Xiol et al. 2012, Molecular Cell.

2012-09-04 | E-GEOD-39203 | biostudies-arrayexpress

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