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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila

ABSTRACT: Combining RNAi in cultured cells and analysis of mutant animals, we probed roles of known piRNA pathway components in the initiation and effector phases of transposon silencing. total RNA and RNA associated with Piwi was isolated and size-fractionated by PAGE into 19-29nt. These were processed and sequenced on Illumina Genome Analyzer II.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Astrid Haase

PROVIDER: E-GEOD-24108 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila.

Haase Astrid D AD Fenoglio Silvia S Muerdter Felix F Guzzardo Paloma M PM Czech Benjamin B Pappin Darryl J DJ Chen Caifu C Gordon Assaf A Hannon Gregory J GJ

Genes & development 20101021 22

Combining RNAi in cultured cells and analysis of mutant animals, we probed the roles of known Piwi-interacting RNA (piRNA) pathway components in the initiation and effector phases of transposon silencing. Squash associated physically with Piwi, and reductions in its expression led to modest transposon derepression without effects on piRNAs, consistent with an effector role. Alterations in Zucchini or Armitage reduced both Piwi protein and piRNAs, indicating functions in the formation of a stable ...[more]

PMID: 20966049

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Production of artificial piRNAs in flies and mice

Project description:In animals, a discrete class of small RNAs, the piwi-interacting RNAs (piRNAs), guard germ cell genomes against the activity of mobile genetic elements. piRNAs are generated, via an unknown mechanism, from apparently single-stranded precursors that arise from discrete genomic loci, termed piRNA clusters. The content of piRNA clusters, determines the capacity of the system to respond to a given element, in essence comprising an organism's evolving molecular definition of transposons. Presently, little is known about the signals that distinguish a locus as a source of piRNAs and about how abundant piRNAs are selected. To address these questions, we inserted new sequence information into piRNA clusters in mice and flies. In all cases, this information was incorporated into the piRNA repertoire and in one instance was shown to confer the ability to recognize and silence a corresponding element. Notably, patterns of piRNA abundance suggested that both intrinsic sequence and context with the cluster inform piRNA generation. Though piRNAs themselves are not conserved between species, the genomic location of clusters is often retained. We were able to create artificial piRNA clusters in non-native contexts in both mice and flies, indicating that the signals that define these as generative loci must lie within the clusters themselves rather than being implicit in their genomic position. Total RNA and RNA associated with Piwi proteins were isolated and size-fractionated by PAGE into 19-33nt. These were processed and sequenced on the Illumina GA2 platform.

2012-01-01 | E-GEOD-32435 | biostudies-arrayexpress

FLX sequencing of Piwi-associated small RNAs extracted from Drosophila ovarian somatic cells (OSC)

Project description:piRNAs function in silencing retrotransposons by associating with the PIWI proteins, AGO3, Aub, and Piwi, in Drosophila germlines. Bioinformatics analyses of piRNAs in Drosophila ovaries suggested that piRNAs are produced by two systems, the primary processing pathway and the amplification loop, from repetitive genes and piRNA clusters in the genome. The amplification loop occurs in a Dicer-independent, PIWI-Slicer-dependent manner. However, the primary processing pathway remains largely conceptual. Here we show that in ovarian somatic cells, which lack Aub and AGO3 but express Piwi, the primary processing pathway for piRNAs indeed exists. Keywords: Small RNA profiling by high throughput sequencing Piwi-associated small RNAs were extracted from Drosophila ovarian somatic cells and their deep sequencing was carried out.

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2014-09-15 | E-GEOD-45112 | biostudies-arrayexpress

RNA elements in precursors instruct directional and processive primary piRNA biogenesis

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2015-07-09 | E-GEOD-69102 | biostudies-arrayexpress

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2016-08-01 | E-GEOD-83871 | biostudies-arrayexpress

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