Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA117295 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform
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Project description:Virus-derived siRNAs produced by Drosophila melanogaster
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Project description:High throughput seqeuncing of small RNAs (PAGE isolated from total RNA or Argonaute immunoprecipitates) from Drosophila melanogaster using the Illumina platform. Adapter ligation requires 5' monophosphate and 3' OH. Full analysis of all libraries in this set is published (Czech B. et al. 2008), leading to the description of endogenous siRNAs in flies. Keywords: Solexa sequences
2008-04-30 | GSE11086 | 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:In Drosophila, siRNAs are classified as endo- or exo-siRNAs based on their origin. Both are processed from double-stranded RNA precursors by Dcr-2, then loaded into the Argonaute protein Ago2. While exo-siRNAs serve to defend the cell against viruses, endo-siRNAs restrict the spread of selfish DNA in somatic cells, analogous to piRNAs in the germ line. Endo- and exo-siRNAs display a differential requirement for double-stranded RNA binding domain proteins (dsRBPs): R2D2 is needed to load exo-siRNAs into Ago2 while the PD isoform of Loquacious (Loqs-PD) stimulates Dcr-2 during the nucleolytic processing of hairpin-derived endo-siRNAs. In cell culture assays, R2D2 antagonizes Loqs-PD in endo-siRNA silencing and Loqs-PD is an inhibitor of RNA interference. Loqs-PD can interact via the C-terminus unique to this isoform with the DExH/D-helicase domain of Drosophila Dcr-2, where binding of R2D2 has also been localized. Separation of the two pathways is not complete; rather, the dicing and Ago2-loading steps appear uncoupled, analogous to the corresponding steps in miRNA biogenesis. Analysis of deep sequencing data further demonstrates that in r2d2 mutant flies, siRNAs can be loaded into Ago2 but not all siRNA classes are equally proficient for this. Thus, the canonical Ago2-RISC loading complex can be bypassed under certain circumstances.
2011-02-10 | GSE26230 | GEO
Project description:Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells
| PRJNA107113 | ENA
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:Euchromatic transposon insertions trigger production of novel pi- and endo-siRNAs at the target sites in the Drosophila germline
| PRJNA197272 | ENA
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.
2016-01-26 | GSE67725 | GEO