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Series GSE131950 Query DataSets for GSE131950
Status Public on Jul 09, 2019
Title Nuclear RNA export factor variant initiates piRNA-guided co-transcriptional silencing
Organism Drosophila melanogaster
Experiment type Expression profiling by high throughput sequencing
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–piRISC complexes) to preserve genomic integrity by repressing transposable elements (TEs). Among PIWI-clade proteins in Drosophila, Piwi transcriptionally silences its targets via heterochromatin formation characterised by H3K9me3 marks and the linker histone H1. Recent studies have shown that Panoramix (Panx) interacts with Piwi–piRISC complexes to induce transcriptional repression of targets mediated by the recruitment of H3K9me3 marks. Here, we identified Nxf2, a nuclear RNA export factor (NXF) variant, as a protein that forms a complex with Panx and Piwi. Nxf2 further associates with p15 (Nxt1), a co-adaptor for nuclear RNA export. However, unlike Nxf1 that plays a major role in mRNA export, Nxf2–p15 instead transcriptionally regulates TEs in the Piwi–piRNA pathway. Panx–Nxf2–p15 complex formation is necessary in the silencing by stabilizing protein levels of Nxf2 and Panx. Notably, ectopic targeting of Nxf2 initiates co-transcriptional repression of the target reporter in a manner independent of H3K9me3 marks or H1. However, continuous silencing requires HP1a and H1. The amino-terminal domain of Nxf2 harbouring RNA binding activity is essential for recruitment of the Piwi–piRISC complex to target TEs. Indeed, Nxf2 directly interacts with target TE transcripts in a Piwi-dependent manner. These findings suggest a model in which the Nxf2–Panx–p15 complex enforces the association of Piwi with target transcripts to trigger co-transcriptional repression, prior to heterochromatin formation in the nuclear piRNA pathway. Our results provide an unexpected connection between an NXF variant and small RNA-mediated co-transcriptional silencing.
Overall design mRNA levels, H3K9me3 occupancy, Nxf2 or Piwi associated RNA, and Piwi associated smRNA in ovarian somatic cells (OSC).
Contributor(s) Murano K, Iwasaki YW, Siomi H
Citation(s) 31368590
Submission date May 30, 2019
Last update date Jul 03, 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)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
GPL21306 Illumina HiSeq 4000 (Drosophila melanogaster)
Samples (31)
GSM3831467 RNA-seq from Control(EGFP)-KD rep1
GSM3831468 RNA-seq from Piwi-KD rep1
GSM3831469 RNA-seq from Panx-KD rep1
BioProject PRJNA545425
SRA SRP199841

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Supplementary file Size Download File type/resource
GSE131950_processed_Nxf2CLIPseq_KD.txt.gz 3.0 Kb (ftp)(http) TXT
GSE131950_processed_Nxf2CLIPseq_UV.txt.gz 2.3 Kb (ftp)(http) TXT
GSE131950_processed_PiwiCLIPseq.txt.gz 2.0 Kb (ftp)(http) TXT
GSE131950_processed_RNAseq.txt.gz 4.4 Kb (ftp)(http) TXT
GSE131950_processed_smRNAseq.txt.gz 1.9 Kb (ftp)(http) TXT
GSE131950_siNxf2_H3K9_merge_peaks.bed.gz 50.0 Kb (ftp)(http) BED
GSE131950_siPanx_H3K9_merge_peaks.bed.gz 57.4 Kb (ftp)(http) BED
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Processed data are available on Series record

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