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Series GSE240910 Query DataSets for GSE240910
Status Public on Sep 26, 2023
Title Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus [ATAC-Seq]
Organisms Drosophila erecta; Drosophila melanogaster; Drosophila persimilis; Drosophila pseudoobscura; Drosophila simulans; Drosophila yakuba; Drosophila suzukii; Drosophila ficusphila; Drosophila biarmipes
Experiment type Genome binding/occupancy 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 ATAC-seq of the whole intact ovaries across multiple fly species (Drosophilidae) to characterize the conserved chromatin accessibility landscape
Contributor(s) van Lopik J, Alizada A, Trapotsi M, Hannon GJ, Bornelöv S, Czech Nicholson B
Citation(s) 37957172
Submission date Aug 15, 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 (9)
GPL22420 Illumina MiSeq (Drosophila pseudoobscura)
GPL25244 Illumina NovaSeq 6000 (Drosophila melanogaster)
GPL33164 Illumina NovaSeq 6000 (Drosophila erecta)
Samples (18)
GSM7711957 ATAC_dbia_ovary_rep1
GSM7711958 ATAC_dbia_ovary_rep2
GSM7711959 ATAC_dere_ovary_rep1
This SubSeries is part of SuperSeries:
GSE225889 Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus
BioProject PRJNA1005682

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 30.6 Mb (ftp)(http) BW
GSE240910_ATAC.dbia.GCF_018148935.biomerge.narrowPeak.gz 465.4 Kb (ftp)(http) NARROWPEAK 108.9 Mb (ftp)(http) BW
GSE240910_ATAC.dere.droEre1.biomerge.narrowPeak.gz 688.2 Kb (ftp)(http) NARROWPEAK 71.3 Mb (ftp)(http) BW
GSE240910_ATAC.dfic.GCF_018152265.biomerge.narrowPeak.gz 601.7 Kb (ftp)(http) NARROWPEAK 82.9 Mb (ftp)(http) BW
GSE240910_ATAC.dmel.dm6.biomerge.narrowPeak.gz 724.8 Kb (ftp)(http) NARROWPEAK 67.3 Mb (ftp)(http) BW
GSE240910_ATAC.dper.GCF_003286085.biomerge.narrowPeak.gz 586.6 Kb (ftp)(http) NARROWPEAK 74.0 Mb (ftp)(http) BW
GSE240910_ATAC.dpse.GCF_009870125.biomerge.narrowPeak.gz 637.9 Kb (ftp)(http) NARROWPEAK 81.7 Mb (ftp)(http) BW
GSE240910_ATAC.dsuz.GCF_013340165.biomerge.narrowPeak.gz 544.9 Kb (ftp)(http) NARROWPEAK 121.4 Mb (ftp)(http) BW
GSE240910_ATAC.dyak.droYak2.biomerge.narrowPeak.gz 707.1 Kb (ftp)(http) NARROWPEAK
GSE240910_RAW.tar 868.5 Mb (http)(custom) TAR (of BW, NARROWPEAK)
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Raw data are available in SRA
Processed data provided as supplementary file

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