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| Status |
Public on Nov 04, 2024 |
| Title |
Transposon and mRNA are distinguished by piRNA’s pairing and piRNA’s expression levels in Ovarian Somatic Cell. |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
Other
Non-coding RNA profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Piwi-interacting RNAs (piRNAs) are the main repressors of transposable elements (TEs) in animal germlines. In Drosophila, Piwi-piRNA complexes associate with nascent TE transcripts to drive heterochromatin formation and TE repression. However, previous studies have shown that Piwi also associates with large amounts of mRNAs, raising the question of how Piwi discriminates between mRNAs and TEs. To answer this question, we performed a comprehensive analysis of Piwi-associated RNAs, compositionally and functionally, to decipher the targeting rules of Piwi-piRNA complexes. While Piwi initially identifies its targets through the seed sequence, it requires pairing well beyond the seed, nearly a perfect match, to elicit a repressive response. In addition to the complementarity of piRNAs to their targets, their abundance must reach a certain threshold to be functional. Together, these findings explain large differences in target repression of Piwi-associated RNAs and reveals how Piwi efficiently distinguishes TEs from mRNAs despite associating with both.
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| Overall design |
ChIP-seq for H3K9me3 and H3K4me3 in pMT- Ovarian Somatic Cell (OSC), Piwi CLASH in WT OSC, CAGE in EGFP KD and Piwi KD OSC, Iso-seq in EGFP KD and Piwi KD OSC, Pacbio Genome sequensing in OSC, scRNA-seq in OSC
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| Contributor(s) |
Ariura M, Siomi H, Iwasaki YW, Ishizu H |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
May 28, 2024 |
| Last update date |
Nov 04, 2024 |
| Contact name |
Masaru Ariura |
| E-mail(s) |
ariura.masaru2@keio.jp
|
| Organization name |
Keio university
|
| Street address |
Shinanomachi, Shinjuku-ku
|
| City |
Tokyo |
| ZIP/Postal code |
1608582 JAPAN |
| Country |
Japan |
| |
|
| Platforms (4)
|
| GPL16479 |
Illumina MiSeq (Drosophila melanogaster) |
| GPL17275 |
Illumina HiSeq 2500 (Drosophila melanogaster) |
| GPL28353 |
Sequel II (Drosophila melanogaster) |
| GPL28354 |
Sequel (Drosophila melanogaster) |
|
| Samples (33)
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|
| Relations |
| BioProject |
PRJNA1117485 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE268512_20A_hap1_TE.bed.gz |
688 b |
(ftp)(http) |
BED |
| GSE268512_20A_hap1_region.fasta.gz |
11.0 Kb |
(ftp)(http) |
FASTA |
| GSE268512_20A_hap2_TE.bed.gz |
690 b |
(ftp)(http) |
BED |
| GSE268512_20A_hap2_region.fasta.gz |
11.1 Kb |
(ftp)(http) |
FASTA |
| GSE268512_CAGE_matrix.tsv.gz |
446.7 Kb |
(ftp)(http) |
TSV |
| GSE268512_OSC_hifiasm.asm.hic.hap1.p_ctg.fa.gz |
38.1 Mb |
(ftp)(http) |
FA |
| GSE268512_OSC_hifiasm.asm.hic.hap2.p_ctg.fa.gz |
42.6 Mb |
(ftp)(http) |
FA |
| GSE268512_TE.collapsed.filtered_classification.txt.gz |
56.0 Kb |
(ftp)(http) |
TXT |
| GSE268512_TE.collapsed.filtered_corrected.fasta.gz |
185.6 Kb |
(ftp)(http) |
FASTA |
| GSE268512_TE.collapsed.filtered_corrected.gtf.gz |
13.5 Kb |
(ftp)(http) |
GTF |
| GSE268512_anti_H3K4me3_10.bw |
11.0 Mb |
(ftp)(http) |
BW |
| GSE268512_anti_H3K4me3_luc_1.bedgraph.gz |
10.4 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE268512_anti_H3K9me3_10.bw |
7.7 Mb |
(ftp)(http) |
BW |
| GSE268512_anti_H3K9me3_luc_1.bedgraph.gz |
9.8 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE268512_anti_input_10.bw |
20.4 Mb |
(ftp)(http) |
BW |
| GSE268512_anti_input_luc_1.bedgraph.gz |
20.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE268512_anti_ni_10.bw |
382.2 Kb |
(ftp)(http) |
BW |
| GSE268512_anti_ni_luc_1.bedgraph.gz |
1.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE268512_clash_colapse.csv.gz |
960.0 Kb |
(ftp)(http) |
CSV |
| GSE268512_clash_selection.csv.gz |
31.4 Mb |
(ftp)(http) |
CSV |
| GSE268512_flam_hap1_TE.bed.gz |
7.3 Kb |
(ftp)(http) |
BED |
| GSE268512_flam_hap1_region.fasta.gz |
88.9 Kb |
(ftp)(http) |
FASTA |
| GSE268512_flam_hap2_TE.bed.gz |
12.5 Kb |
(ftp)(http) |
BED |
| GSE268512_flam_hap2_region.fasta.gz |
184.5 Kb |
(ftp)(http) |
FASTA |
| GSE268512_gene.collapsed.filtered_classification.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
| GSE268512_gene.collapsed.filtered_corrected.fasta.gz |
10.5 Mb |
(ftp)(http) |
FASTA |
| GSE268512_gene.collapsed.filtered_corrected.gtf.gz |
1.0 Mb |
(ftp)(http) |
GTF |
| GSE268512_piRNA_CPM_GEO.tsv.gz |
7.3 Mb |
(ftp)(http) |
TSV |
| GSE268512_polish_isoforms_fusion_classification.txt.gz |
66.5 Kb |
(ftp)(http) |
TXT |
| GSE268512_polish_isoforms_fusion_corrected.fasta.gz |
664.2 Kb |
(ftp)(http) |
FASTA |
| GSE268512_polish_isoforms_fusion_corrected.gtf.gz |
73.4 Kb |
(ftp)(http) |
GTF |
| GSE268512_sense_H3K4me3_10.bw |
9.4 Mb |
(ftp)(http) |
BW |
| GSE268512_sense_H3K4me3_luc_1.bedgraph.gz |
9.8 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE268512_sense_H3K9me3_10.bw |
5.7 Mb |
(ftp)(http) |
BW |
| GSE268512_sense_H3K9me3_luc_1.bedgraph.gz |
5.1 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE268512_sense_input_10.bw |
23.0 Mb |
(ftp)(http) |
BW |
| GSE268512_sense_input_luc_1.bedgraph.gz |
20.2 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE268512_sense_ni_10.bw |
1.0 Mb |
(ftp)(http) |
BW |
| GSE268512_sense_ni_luc_1.bedgraph.gz |
2.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE268512_siEGFP.CTSS.normalized.minus.bw |
2.1 Mb |
(ftp)(http) |
BW |
| GSE268512_siEGFP.CTSS.normalized.plus.bw |
2.1 Mb |
(ftp)(http) |
BW |
| GSE268512_siEGFP.tagClusters.bed.gz |
85.5 Kb |
(ftp)(http) |
BED |
| GSE268512_siPiwi.CTSS.normalized.minus.bw |
2.1 Mb |
(ftp)(http) |
BW |
| GSE268512_siPiwi.CTSS.normalized.plus.bw |
2.1 Mb |
(ftp)(http) |
BW |
| GSE268512_siPiwi.tagClusters.bed.gz |
85.7 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
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