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Bombyx mori strain:BmN4

ABSTRACT: Two Gtsf paralogs orthogonally activate their partner PIWI proteins for target cleavage in silkworms

PROVIDER: PRJDB13728 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR380347.fastq.gz	Fastqsanger.gz
	DRR380348.fastq.gz	Fastqsanger.gz
	DRR380349.fastq.gz	Fastqsanger.gz
	DRR380350.fastq.gz	Fastqsanger.gz
	DRR380351.fastq.gz	Fastqsanger.gz

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Similar Datasets

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.

2014-12-31 | GSE58221 | GEO

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).

2020-09-02 | GSE150444 | GEO

Bombyx mori

Project description:Analysis of PIWI-bound piRNAs in silkworms

| PRJDB5142 | ENA

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

2021-02-01 | GSE161405 | GEO

Bombyx mori strain:BmN4

Project description:The dual role of Spn-E in supporting heterotypic ping-pong piRNA amplification in silkworms

| PRJDB17075 | ENA

Bombyx mori

Project description:The MID-PIWI module of Piwi proteins specifies nucleotide- and strand-biases of piRNAs

| PRJNA239665 | ENA

Bombyx mori

Project description:Hsp90 facilitates accurate loading of precursor piRNAs into PIWI proteins

| PRJDB2257 | ENA

RNA associating with PIWI proteins in Bombyx mori BmN4 cells

Project description:RNA associating with PIWI proteins in Bombyx mori BmN4 cells

| PRJNA632342 | ENA

Soaking RNAi in Bombyx mori BmN4-SID1 cells arrests cell cycle progression.

Project description:RNA interference (RNAi) is an evolutionarily conserved mechanism for sequence-specific gene silencing. Previously, the BmN4-SID1 cell expressing Caenorhabditis ele gans SID-1 was established, in which soaking RNAi could induce effective gene silencing. To establish its utility, 6 cell cycle progression related cDNAs, CDK1, MYC, MYB, RNRS, CDT1, and GEMININ, were isolated from the silkworm, Bombyx mori L. (Lepidoptera: Bombycidae), and their expressions were further silenced by soaking RNAi in the BmN4-SID1 cells. The cell cycle progression analysis using flow cytometer demonstrated that the small amount of double stranded RNA was enough to arrest cell cycle progression at the specific cell phases. These data suggest that RNAi in the BmN4-SID1 cells can be used as a powerful tool for loss-of-function analysis of B. mori genes.

| S-EPMC4015410 | biostudies-literature

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line.

Project description:BackgroundThe process of identifying all coding regions in a genome is crucial for any study at the level of molecular biology, ranging from single-gene cloning to genome-wide measurements using RNA-seq or mass spectrometry. While satisfactory annotation has been made feasible for well-studied model organisms through great efforts of big consortia, for most systems this kind of data is either absent or not adequately precise.ResultsCombining in-depth transcriptome sequencing and high resolution mass spectrometry, we here use proteotranscriptomics to improve gene annotation of protein-coding genes in the Bombyx mori cell line BmN4 which is an increasingly used tool for the analysis of piRNA biogenesis and function. Using this approach we provide the exact coding sequence and evidence for more than 6200 genes on the protein level. Furthermore using spatial proteomics, we establish the subcellular localization of thousands of these proteins. We show that our approach outperforms current Bombyx mori annotation attempts in terms of accuracy and coverage.ConclusionsWe show that proteotranscriptomics is an efficient, cost-effective and accurate approach to improve previous annotations or generate new gene models. As this technique is based on de-novo transcriptome assembly, it provides the possibility to study any species also in the absence of genome sequence information for which proteogenomics would be impossible.

| S-EPMC7541253 | biostudies-literature

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