|
| 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.
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| Overall design |
ATAC-seq of the whole intact ovaries across multiple fly species (Drosophilidae) to characterize the conserved chromatin accessibility landscape
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| 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 |
| E-mail(s) |
susanne.bornelov@cruk.cam.ac.uk
|
| 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 |
| |
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| Platforms (9)
|
| GPL22420 |
Illumina MiSeq (Drosophila pseudoobscura) |
| GPL25244 |
Illumina NovaSeq 6000 (Drosophila melanogaster) |
| GPL33164 |
Illumina NovaSeq 6000 (Drosophila erecta) |
| GPL33169 |
Illumina NovaSeq 6000 (Drosophila simulans) |
| GPL33170 |
Illumina NovaSeq 6000 (Drosophila yakuba) |
| GPL33685 |
Illumina MiSeq (Drosophila biarmipes) |
| GPL33686 |
Illumina MiSeq (Drosophila ficusphila) |
| GPL33687 |
Illumina MiSeq (Drosophila persimilis) |
| GPL33688 |
Illumina MiSeq (Drosophila suzukii) |
|
| Samples (18)
|
|
| This SubSeries is part of SuperSeries: |
| GSE225889 |
Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus |
|
| Relations |
| BioProject |
PRJNA1005682 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE240910_ATAC.dbia.GCF_018148935.biomerge.bw |
30.6 Mb |
(ftp)(http) |
BW |
| GSE240910_ATAC.dbia.GCF_018148935.biomerge.narrowPeak.gz |
465.4 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE240910_ATAC.dere.droEre1.biomerge.bw |
108.9 Mb |
(ftp)(http) |
BW |
| GSE240910_ATAC.dere.droEre1.biomerge.narrowPeak.gz |
688.2 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE240910_ATAC.dfic.GCF_018152265.biomerge.bw |
71.3 Mb |
(ftp)(http) |
BW |
| GSE240910_ATAC.dfic.GCF_018152265.biomerge.narrowPeak.gz |
601.7 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE240910_ATAC.dmel.dm6.biomerge.bw |
82.9 Mb |
(ftp)(http) |
BW |
| GSE240910_ATAC.dmel.dm6.biomerge.narrowPeak.gz |
724.8 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE240910_ATAC.dper.GCF_003286085.biomerge.bw |
67.3 Mb |
(ftp)(http) |
BW |
| GSE240910_ATAC.dper.GCF_003286085.biomerge.narrowPeak.gz |
586.6 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE240910_ATAC.dpse.GCF_009870125.biomerge.bw |
74.0 Mb |
(ftp)(http) |
BW |
| GSE240910_ATAC.dpse.GCF_009870125.biomerge.narrowPeak.gz |
637.9 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE240910_ATAC.dsuz.GCF_013340165.biomerge.bw |
81.7 Mb |
(ftp)(http) |
BW |
| GSE240910_ATAC.dsuz.GCF_013340165.biomerge.narrowPeak.gz |
544.9 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE240910_ATAC.dyak.droYak2.biomerge.bw |
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) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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