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Series GSE28617 Query DataSets for GSE28617
Status Public on Jun 18, 2012
Title Function, targets and evolution of Caenorhabditis elegans piRNAs (small RNA-Seq)
Organism Caenorhabditis elegans
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary piRNAs are required to maintain germline integrity and fertility but their mechanism of action is poorly understood. Here we demonstrate that C. elegans piRNAs silence transcripts in trans through imperfectly complementary sites. We find that target silencing is independent of Piwi endonuclease activity or “slicing”. Instead, we show that piRNAs initiate a localized secondary endogenous small interfering RNA (endo-siRNA) response. Endogenous protein-coding gene, pseudogene and transposon transcripts exhibit Piwi-dependent endo-siRNAs at sites complementary to piRNAs and are derepressed in Piwi mutants. Genomic loci of piRNA biogenesis are depleted of protein-coding genes but not pseudogenes or transposons. Our data suggest that nematode piRNA clusters are evolving to generate piRNAs against active mobile elements. Thus, piRNAs provide heritable, sequence-specific triggers for RNAi in C. elegans.
Overall design 7 small RNA libraries were sequenced as part of 25 flow cell lanes on the Illumina GA II platform. Samples were treated with tobacco acid pyrophosphatase to allow cloning of small RNAs with a 5'-triphosphate. Samples were labelled for multiplexing using 4-bp 5'-barcodes or barcodes included in Illumina TruSeq adapters. In most cases a single flow cell lane included several multiplexed libraries.
Contributor(s) Bagijn MP, Goldstein LD, Sapetschnig A, Weick E, Bouasker S, Lehrbach NJ, Simard MJ, Miska EA
Citation(s) 22700655, 22738725
Submission date Apr 14, 2011
Last update date Feb 15, 2024
Contact name Leonard Goldstein
Organization name Garvan Institute of Medical Research
Street address 384 Victoria St
City Darlinghurst
ZIP/Postal code 2010
Country Australia
Platforms (1)
GPL9269 Illumina Genome Analyzer II (Caenorhabditis elegans)
Samples (7)
GSM708660 wild-type (A)
GSM708661 prg-1 (A)
GSM708662 piRNA sensor in wild-type (B)
This SubSeries is part of SuperSeries:
GSE37433 Function, targets and evolution of Caenorhabditis elegans piRNAs
SRA SRP006390
BioProject PRJNA138745

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Supplementary file Size Download File type/resource
GSE28617_RAW.tar 128.1 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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