Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA237930 | ENA |
REPOSITORIES: ENA
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Project description:piRNAs direct Piwi to repress transposons to maintain genome integrity in Drosophila ovarian somatic cells. piRNA maturation and association with Piwi occur at perinuclear Yb bodies, the centers of piRNA biogenesis. Here, we show that piRNA intermediates arising from the piRNA cluster flamenco (flam) concentrate into perinuclear foci adjacent to Yb bodies, termed Flam bodies. Although flam expression is not required for Yb body formation, Yb, the core component of Yb bodies, is required for Flam body formation. Abolishment of the RNA-binding activity of Yb disrupts both Yb bodies and Flam bodies. Loss of Zucchini, an endoribonuclease necessary for piRNA maturation, enlarges Flam bodies, which now superimpose with Yb bodies. Yb directly binds flam, but not neighboring protein-coding gene, transcripts. Thus, Yb integrates piRNA processing factors and piRNA intermediates into Yb bodies and Flam bodies, respectively, through direct binding to enhance piRNA biogenesis and formation of piRNA-inducing silencing complexes. HITS-CLIP was performed using OSC (Ovarian Somatic Cells). The antibody for Drosophila Yb, which was generated in this study, was used. Obtained CLIP tags were analyzed using illumina HiSeq200.
2014-06-24 | E-GEOD-54875 | biostudies-arrayexpress
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2013-10-30 | E-MTAB-1706 | biostudies-arrayexpress
Project description:Primary piRNAs in Drosophila ovarian somatic cells arise from piRNA cluster transcripts and the 3′ UTRs of a subset of mRNAs, including Traffic jam (Tj) mRNA. However, it is unclear how these RNAs are determined as primary piRNA sources. Here, we identify a cis-acting 100-nt fragment in the Tj 3′ UTR that is sufficient for producing artificial piRNAs from unintegrated DNA. These artificial piRNAs were effective in endogenous gene transcriptional silencing. Yb, a core component of primary piRNA biogenesis center Yb bodies, directly bound the Tj-cis-element. Disruption of this interaction markedly reduced piRNA production. Thus, Yb is the trans-acting partner of the Tj-cis-element. Yb-CLIP revealed that Yb-binding correlated with somatic piRNA production but Tj-cis-element downstream sequences produced few artificial piRNAs. Thus, Yb determines primary piRNA sources by two modes of action; primary binding to cis-elements to specify substrates, and secondary binding to downstream regions to increase diversity in piRNA populations. HITS-CLIP of Yb in OSCs (Ovarian Somatic Cells) depleted for tj cis-element, and small RNA sequencing of Piwi-piRNAs in OSCs depleted for tj cis-element.
2015-06-05 | E-GEOD-69625 | biostudies-arrayexpress
Project description:In order to identify TARBP2 binding sites on endogenous RNA, we performed HITS-CLIP on a myc-tagged TARBP2 expressing cell-line (transient transfection) Cells were transfected with tagged TARBP2 vector (Origene) and 48-hr post-transfection, they were subjected to the HITS-CLIP procedure (Licatalosi D, et al. 2008, Nature 456:464-U22)
2014-07-24 | E-GEOD-49648 | biostudies-arrayexpress
Project description:Genome-wide analyses of Su(Hw) binding in Drosophila ovary
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Project description:In order to identify TARBP2 binding sites on endogenous RNA, we performed HITS-CLIP on a myc-tagged TARBP2 expressing cell-line (transient transfection)
2014-07-24 | GSE49648 | GEO
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