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Series GSE213379 Query DataSets for GSE213379
Status Public on Sep 19, 2022
Title Mechanistic divergence of piRNA biogenesis in Drosophila [ChIP-seq]
Organisms Drosophila bifasciata; Drosophila pseudoobscura
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Organisms require mechanisms to distinguish self and non-self RNA. This distinction is crucial to initiate the biogenesis of piRNAs. In Drosophila ovaries, PIWI-guided slicing and the recognition of piRNA precursor transcripts by the DEAD-box RNA helicase Yb are the two known mechanisms to initiate biogenesis in the germline and the soma, respectively. Both, the PIWI proteins and Yb are highly conserved across most Drosophila species and are thought to be essential to the piRNA pathway and for silencing TEs. However, we find that species closely related to D. melanogaster have lost the yb gene, as well as the PIWI gene Ago3. We show that neither mechanism is required to efficiently produce TE antisense piRNAs in Drosophila. Thus, there are more possible routes through which the piRNA pathway can achieve specificity than previously suggested.
 
Overall design The study aims at understanding the mechanism of Piwi-interacting RNA (piRNA) in a variety of Drosophila species. We generated small RNA sequencing libraries from freshly collected ovaries and embryos as well as immuno-precipitated samples using antibodies against PIWI proteins. We also generated RNA sequencing libraries from poly-A plus RNA and ChIP sequencing libraries using antibodies against RNA polymerase II to determine the genomic origin of the piRNA precursor RNA.
 
Contributor(s) Hayashi R, Chary S
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Submission date Sep 14, 2022
Last update date Sep 21, 2022
Contact name Rippei Hayashi
E-mail(s) rippei.hayashi@anu.edu.au
Phone +61-261259396
Organization name The Australian National University
Department John Curtin School of Medical Research
Street address 131 Garran Road
City Acton
State/province Australian Capital Territory
ZIP/Postal code 2601
Country Australia
 
Platforms (2)
GPL32664 Illumina HiSeq 2500 (Drosophila pseudoobscura)
GPL32666 Illumina HiSeq 2500 (Drosophila bifasciata)
Samples (6)
GSM6585294 Dpse_ChIP_input_rep1
GSM6585295 Dpse_ChIP_polII-CTD_rep1
GSM6585296 Dpse_ChIP_input_rep2
This SubSeries is part of SuperSeries:
GSE213383 Mechanistic divergence of piRNA biogenesis in Drosophila
Relations
BioProject PRJNA881003

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE213379_RAW.tar 1.4 Gb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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