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Series GSE225888 Query DataSets for GSE225888
Status Public on Sep 26, 2023
Title Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus [small RNA-Seq]
Organisms Drosophila ananassae; Drosophila bifasciata; Drosophila erecta; Drosophila melanogaster; Drosophila mojavensis; Drosophila persimilis; Drosophila pseudoobscura; Drosophila simulans; Drosophila subobscura; Drosophila virilis; Drosophila yakuba; Drosophila azteca; Drosophila suzukii; Drosophila takahashii; Drosophila ficusphila; Drosophila biarmipes
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary The PIWI-interacting RNA (piRNA) pathway plays a crucial role in preventing endogenous genomic parasites, transposable elements (TEs), from damaging the genetic material of animal gonadal cells. Specific regions in the genome, called piRNA clusters, define each species’ piRNA repertoire and therefore its capacity to recognize and silence transposons. In the somatic cells of the Drosophila melanogaster ovary, the flamenco (flam) unistrand cluster is the main source of piRNAs and primarily regulates Gypsy family TEs that are able to form virus-like particles and infect neighbouring germ cells. Disruption of the flam locus or failure to process flam precursor transcripts into piRNAs results in sterility, yet it remains unknown whether this silencing mechanism is employed widely across Drosophilidae. Here, using both synteny-based analyses and de novo TE annotation, we identify candidate loci sharing both their organisation and TE targeting repertoire with flam in widely divergent Drosophila species groups. Small RNA-sequencing validated these loci as bona-fide unistrand piRNA clusters and revealed their predominant expression in somatic cells of the ovary, likely to counter TE mobilisation in this tissue. This study provides compelling evidence of co-evolution between virus-like Gypsy family transposons and a host defence mechanism in form of soma-expressed, unistrand piRNA clusters.
Overall design Small RNA-seq from dissected ovaries (total or enriched for somatic follicle cells) from 15 Drosophila species, 1-3 replicates per species and library type.
Contributor(s) van Lopik J, Alizada A, Trapotsi M, Hannon GJ, Bornelöv S, Czech Nicholson B
Citation(s) 37957172
Submission date Feb 22, 2023
Last update date Dec 06, 2023
Contact name Susanne Bornelöv
Organization name University of Cambridge
Department Cancer Research UK - Cambridge Institute
Lab Hannon
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
Platforms (15)
GPL25244 Illumina NovaSeq 6000 (Drosophila melanogaster)
GPL32718 Illumina NovaSeq 6000 (Drosophila virilis)
GPL33163 Illumina NovaSeq 6000 (Drosophila ananassae)
Samples (65)
GSM7059843 Dana.ovary_FC.2 small-RNA-Seq
GSM7059844 Dana.ovary_FC.1 small-RNA-Seq
GSM7059845 Dana.ovary.1 small-RNA-Seq
This SubSeries is part of SuperSeries:
GSE225889 Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus
BioProject PRJNA937774

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

Supplementary file Size Download File type/resource
GSE225888_RAW.tar 1.1 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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