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Series GSE88774 Query DataSets for GSE88774
Status Public on Jan 24, 2018
Title Transcriptional and chromatin changes accompanying de novo formation of transgenic piRNA clusters
Organism Drosophila melanogaster
Experiment type Other
Non-coding RNA profiling by high throughput sequencing
Summary Expression of transposable elements in the germline is controlled by Piwi-interacting (pi) RNAs produced by genomic loci termed piRNA clusters and associated with Rhino, a Heterochromatin Protein 1 (HP1) homolog. Previously, we have shown that transgenes containing a fragment of the I retrotransposon form de novo piRNA clusters in the Drosophila germline providing suppression of I-element activity. We noted that identical transgenes located in different genomic sites vary considerably in piRNA production and classified them as “strong” and “weak” piRNA clusters. Here, we investigated what chromatin and transcriptional changes occur at the transgene insertion sites after their conversion into piRNA clusters. We found that the formation of a transgenic piRNA cluster is accompanied by activation of transcription from both genomic strands that likely initiates at multiple random sites. The chromatin of all transgene-associated piRNA clusters contain high levels of trimethylated lysine 9 of histone H3 (H3K9me3) and HP1a, whereas Rhino binding is considerably higher at the strong clusters. None of these chromatin marks was revealed at the “empty” sites before transgene insertion. Finally, we have shown that in the nucleus of polyploid nurse cells, the formation of a piRNA cluster at a given transgenic genomic copy works according to an “all– or– nothing” model: either there is high Rhino enrichment or there is no association with Rhino at all. As a result, genomic copies of a weak piRNA transgenic cluster show a mosaic association with Rhino foci, while the majority of strong transgene copies associate with Rhino and are hence involved in piRNA production.
Overall design This study aims at characterizing the novel piRNA clusters formed at the site of transgene integration by using smallRNA-seq and GRO-seq in adult ovaries of transgenic Drosophila strains.
Contributor(s) Akulenko N, Ryazansky S, Kalmykova A
Citation(s) 29358235
Submission date Oct 14, 2016
Last update date May 15, 2019
Contact name Sergei Ryazansky
Phone +7-499-196-81-73
Organization name Institute of Molecular Genetics
Department Department of Molecular Genetics of Cell
Street address Kurchatov sq., 2
City Moscow
ZIP/Postal code 123182
Country Russia
Platforms (2)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
Samples (3)
GSM2345414 GRO-seq from ovaries of 1.9 transgenic strain
GSM2345415 GRO-seq from ovaries of 3.6 transgenic strain
GSM2345416 Small RNAs from ovaries of 2.4 transgenic strain
BioProject PRJNA348538
SRA SRP091575

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Supplementary file Size Download File type/resource
GSE88774_RAW.tar 109.7 Mb (http)(custom) TAR (of BW, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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