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| Status |
Public on Jul 01, 2021 |
| Title |
Piwi–piRNA complexes induce stepwise changes in nuclear architecture at target loci |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
|
| Summary |
PIWI-interacting RNAs (piRNAs) are germline-specific small RNAs that form effector complexes with PIWI proteins (Piwi–piRNA complexes), and plays a critical role for preserving genomic integrity by repressing transposable elements (TEs). Drosophila Piwi transcriptionally silences specific targets through heterochromatin formation, and increases H3K9me3 and histone H1. Additionally, Nxf2, a nuclear RNA export factor variant, has been identified as a co-factor. Using ChEP and DamID-seq, we uncover Piwi/Nxf2-dependent target association with nuclear lamins. Hi-C analysis of Piwi or Nxf2 depleted cells reveals decreased intra-TAD and increased inter-TAD interaction in regions harboring Piwi–piRNA target TEs. Using a forced tethering system, we analyze the functional effects of Piwi–piRNA/Nxf2-mediated recruitment of piRNA target regions to the nuclear periphery. Removal of active histone marks is followed by transcriptional silencing, chromatin conformational changes, and H3K9me3 and H1 association. Our data show that the Piwi–piRNA pathway can induce stepwise changes in nuclear architecture and chromatin state at target loci for transcriptional silencing.
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| |
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| Overall design |
Lamin-DamID-seq, Hi-C, and ChIP-seq upon knockdown of Piwi-piRNApathway factors using OSCs.
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| Contributor(s) |
Iwasaki YW, Siomi H |
| Citation(s) |
34337769 |
| |
| Submission date |
Sep 16, 2020 |
| Last update date |
Aug 04, 2021 |
| Contact name |
Yuka W. Iwasaki |
| E-mail(s) |
iwasaki@keio.jp
|
| Organization name |
Keio University School of Medicine
|
| Department |
Department of Molecular Biology
|
| Lab |
Siomi Lab
|
| Street address |
35 Shinanomachi, Shinjuku-ku,
|
| City |
Tokyo |
| ZIP/Postal code |
160-8582 |
| Country |
Japan |
| |
|
| Platforms (3) |
| GPL16479 |
Illumina MiSeq (Drosophila melanogaster) |
| GPL21306 |
Illumina HiSeq 4000 (Drosophila melanogaster) |
| GPL23702 |
HiSeq X Ten (Drosophila melanogaster) |
|
| Samples (36)
|
|
| Relations |
| BioProject |
PRJNA663907 |
| SRA |
SRP282626 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE158082_EGFP_forEGGH1merge_40kb.ICEcor.Norm.ginteractions.tsv.gz |
41.6 Mb |
(ftp)(http) |
TSV |
| GSE158082_EGFP_forHP1merge_40kb.ICEcor.Norm.ginteractions.tsv.gz |
42.7 Mb |
(ftp)(http) |
TSV |
| GSE158082_EGFP_forNXF2merge_40kb.ICEcor.Norm.ginteractions.tsv.gz |
54.0 Mb |
(ftp)(http) |
TSV |
| GSE158082_EGFPmerge_40kb.ICEcor.Norm.ginteractions.tsv.gz |
53.6 Mb |
(ftp)(http) |
TSV |
| GSE158082_EGGmerge_40kb.ICEcor.Norm.ginteractions.tsv.gz |
41.5 Mb |
(ftp)(http) |
TSV |
| GSE158082_H1merge_40kb.ICEcor.Norm.ginteractions.tsv.gz |
40.6 Mb |
(ftp)(http) |
TSV |
| GSE158082_HP1merge_40kb.ICEcor.Norm.ginteractions.tsv.gz |
38.2 Mb |
(ftp)(http) |
TSV |
| GSE158082_NXF2merge_40kb.ICEcor.Norm.ginteractions.tsv.gz |
53.7 Mb |
(ftp)(http) |
TSV |
| GSE158082_PIWImerge_40kb.ICEcor.Norm.ginteractions.tsv.gz |
54.0 Mb |
(ftp)(http) |
TSV |
| GSE158082_RAW.tar |
185.6 Mb |
(http)(custom) |
TAR (of WIG) |
| GSE158082_siEGFP_rep1.LamDam-vs-Dam.gatc.bedgraph.gz |
4.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE158082_siEGFP_rep2.LamDam-vs-Dam.gatc.bedgraph.gz |
4.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE158082_siNxf2_rep1.LamDam-vs-Dam.gatc.bedgraph.gz |
5.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE158082_siNxf2_rep2.LamDam-vs-Dam.gatc.bedgraph.gz |
4.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE158082_siPiwi_rep1.LamDam-vs-Dam.gatc.bedgraph.gz |
5.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE158082_siPiwi_rep2.LamDam-vs-Dam.gatc.bedgraph.gz |
4.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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