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Series GSE158082 Query DataSets for GSE158082
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
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.
Overall design Lamin-DamID-seq, Hi-C, and ChIP-seq upon knockdown of Piwi-piRNApathway factors using OSCs.
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
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)
GSM4790413 OSC - EGFP-KD - HiC_rep1
GSM4790414 OSC - EGFP-KD - HiC_rep2
GSM4790415 OSC - Piwi-KD - HiC_rep1
BioProject PRJNA663907
SRA SRP282626

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
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
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Processed data are available on Series record
Processed data provided as supplementary file
Raw data are available in SRA

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