Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA107113 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR001337.fastq.gz | Fastqsanger.gz | |||
| SRR001338.fastq.gz | Fastqsanger.gz | |||
| SRR001339.fastq.gz | Fastqsanger.gz | |||
| SRR001340.fastq.gz | Fastqsanger.gz | |||
| SRR001341.fastq.gz | Fastqsanger.gz |
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Project description:Small interfering RNAs (siRNAs) direct RNA interference (RNAi) in eukaryotes. In flies, somatic cells produce siRNAs from exogenous double-stranded RNA as a defense against viral infection. Here, we identify 21-nt long, endogenous siRNAs (endo-siRNAs) corresponding to transposons and heterochromatic sequences in the somatic cells of Drosophila melanogaster. We also detected endo-siRNAs complementary to mRNAs: these siRNAs disproportionately mapped to the complementary regions of overlapping mRNAs predicted to form dsRNA in vivo. Normal accumulation of somatic endo-siRNAs requires the siRNA-generating ribonuclease, Dicer-2, and the RNAi effector protein, Ago2. We propose that endo-siRNAs generated by the fly RNAi pathway silence selfish genetic elements in the soma much as piRNAs do in the germ line. Keywords: Small RNA detection and quantification.
2008-04-11 | GSE11019 | GEO
Project description:Small interfering RNAs (siRNAs) direct RNA interference (RNAi) in eukaryotes. In flies, somatic cells produce siRNAs from exogenous double-stranded RNA as a defense against viral infection. Here, we identify 21-nt long, endogenous siRNAs (endo-siRNAs) corresponding to transposons and heterochromatic sequences in the somatic cells of Drosophila melanogaster. We also detected endo-siRNAs complementary to mRNAs: these siRNAs disproportionately mapped to the complementary regions of overlapping mRNAs predicted to form dsRNA in vivo. Normal accumulation of somatic endo-siRNAs requires the siRNA-generating ribonuclease, Dicer-2, and the RNAi effector protein, Ago2. We propose that endo-siRNAs generated by the fly RNAi pathway silence selfish genetic elements in the soma much as piRNAs do in the germ line. Keywords: Small RNA detection and quantification. Small RNAs (18-30 nt) from fly heads (WT, ago2 mutants, dcr-2 homozygous and heterozygous mutants, and WT expressing an inverted repeat directed against exon 3 of the gene "white") and S2 cells (transgenic for a construct expressing siRNAs against white and GFP) were sequenced using a Solexa Genome Analyzer instrument. Raw sequence data files for this study are available for download from the SRA FTP site at ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP000/SRP000181
2008-04-10 | E-GEOD-11019 | biostudies-arrayexpress
Project description:Unrestricted movement of mobile genetic elements could cause pre-mature lethality in Drosophila melanogaster. Specifically, retro transposons can disrupt genomic integrity through insertions, deletions and chromosomal rearrangements. Therefore, eukaryotes have developed defense mechanisms to silence these elements. In Drosophila, endogenous small interfering (endo-siRNAs) repress retro transposon mobility in somatic cells. The generation of endo-siRNAs requires Dicer-2 processing of double-stranded RNA precursors, yet the origins of this precursor are unknown. Here we show that retro transposons in Dmel-2 cells produce sense and antisense transcripts and identify bonafide transcription start sites for these RNAs. We determine that retro transposon antisense transcripts are less polyadenylated than sense transcripts. RNA-seq and small RNA-seq upon Dicer-2 depletion showed global decrease in endo-siRNAs mapping to retro transposons and increased expression of both S and AS retro transposon transcripts. These data support a model in which double-stranded RNA precursors are derived from convergent transcription and retained in the nucleus. Dicer-2 processes these precursors into endo-siRNAs that silence both sense and antisense retro transposon transcripts. Reduction of sense retro transposon transcripts potentially lowers element specific protein levels required for movement. This mechanism preserves genomic integrity and is especially important for Drosophila fitness because mobile genetic elements are highly active.
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Project description:Drosophila endogenous small RNAs bind to Argonaute2 in somatic cells
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Project description:Virus-derived siRNAs produced by Drosophila melanogaster
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Project description:Drosophila retrotransposon and inverted repeat-derived endogenous siRNAs are differentially processed in distinct cellular locations
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Project description: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. These loci comprise mainly defective transposon sequences, and some have previously been identified as master regulators of transposon activity. Our data suggest that heterochromatic piRNA loci interact with potentially active, euchromatic transposons to form an adaptive system for transposon control. Complementary relationships between sense and antisense piRNA populations suggest an amplification loop wherein each piRNA-directed cleavage event generates the 5’ end of a new piRNA. Thus, sense piRNAs, formed following cleavage of transposon mRNAs, may enhance production of antisense piRNAs, complementary to active elements, by directing cleavage of transcripts from master control loci. Keywords: small RNA libraries from Drosophila ovaries
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Project description:Colonization of genomes by a new selfish genetic element is detrimental to the host species and must lead to an efficient, repressive response. In vertebrates as well as in Drosophila, piRNAs repress transposons in the germ line while endogenous siRNAs take on this role in somatic cells. For endo-siRNAs as well as for piRNAs, it is unclear how an efficient response can be initiated de novo. Our experiments establish that the endo-siRNA pathway will target artificially introduced sequences without the need for a pre-existing template in the genome. This response is also triggered in transiently transfected cells, thus genomic integration is not essential. Deep sequencing revealed that corresponding endo-siRNAs are generated throughout the sequence, but preferentially from transcribed regions. Examination of 3 different cell lines.
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Project description:Colonization of genomes by a new selfish genetic element is detrimental to the host species and must lead to an efficient, repressive response. In vertebrates as well as in Drosophila, piRNAs repress transposons in the germ line while endogenous siRNAs take on this role in somatic cells. For endo-siRNAs as well as for piRNAs, it is unclear how an efficient response can be initiated de novo. Our experiments establish that the endo-siRNA pathway will target artificially introduced sequences without the need for a pre-existing template in the genome. This response is also triggered in transiently transfected cells, thus genomic integration is not essential. Deep sequencing revealed that corresponding endo-siRNAs are generated throughout the sequence, but preferentially from transcribed regions.
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