1. Cell Biology
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Channel nuclear pore complex subunits are required for transposon silencing in Drosophila

  1. Marzia Munafò
  2. Victoria R Lawless
  3. Alessandro Passera
  4. Serena MacMillan
  5. Susanne Bornelöv
  6. Irmgard U Haussmann
  7. Matthias Soller
  8. Gregory J Hannon  Is a corresponding author
  9. Benjamin Czech  Is a corresponding author
  1. Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, United Kingdom
  2. Department of Life Science, Faculty of Health, Education and Life Sciences, Birmingham City University, United Kingdom
  3. School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, United Kingdom
  4. Birmingham Center for Genome Biology, University of Birmingham, United Kingdom
Research Article
Cite this article as: eLife 2021;10:e66321 doi: 10.7554/eLife.66321
4 figures, 1 table and 4 additional files

Figures

Figure 1 with 3 supplements
Requirement of Nuclear Pore Complex (NPC) subunits for gene regulation and transposon control.

(A) Heatmap summarising literature data for selected Nups and export factors and (B) effects of each knockdown (kd) on cell viability, transposon expression levels with respect to siGFP and Yb-body assembly after 96 hr of siRNA treatment (n = 3; see also Figure 1—figure supplement 2A–E and Figure 1—figure supplement 3). Asterisks denote samples imaged after 48 hr of siRNA treatment because of lethality at later timepoints. (C) Confocal images of Yb and Piwi proteins in ovarian somatic cells (OSCs) upon the indicated kd. Dotted red lines denote nuclear envelope (see also Figure 1—figure supplement 2F). (D–H) MA plots showing mean expression levels (reads per million mapped reads, rpm) against fold-changes of genes and transposable elements (TEs) in RNA-seq from the indicated kd with respect to siGFP control (n = 4). Yellow: genes de-regulated more than fourfold with adjusted p value < 0.05; blue: TEs; blue outlines: genes de-regulated more than fourfold carrying a nearby TE (gypsy, mdg1, 412, or blood) insertion in OSCs; magenta: uni-strand piRNA clusters (20A and flam). (I) Fold-changes in transcript levels upon the indicated kd with respect to siGFP.

Figure 1—figure supplement 1
Yb-body formation is dependent on flam.

(A) Schematic of a Drosophila ovariole, the functional unit of the fly ovary. The follicle cells enclosing egg chambers are highlighted in magenta and cells of the germline are shown in grey. (B) Coverage plots of PIWI-interacting RNAs (piRNAs) and RNA-seq reads uniquely mapped to the uni-strand cluster flam in the indicated genotypes. Dashed lines indicate the location of the P-element insertion in the two flam mutant alleles. The mappability for an average 50 bp read length is shown at the bottom. (C) MA plots showing mean expression levels (rpm) against fold-changes with respect to control (flamBG/+) of genes and TEs in RNA-seq from the indicated genotypes (n = 3). Yellow: genes de-regulated more than fourfold with adjusted p value < 0.05. blue: transposable elements (TEs); magenta: uni-strand piRNA clusters (20A and flam). (D) Volcano plots showing fold-changes and corresponding significance of genes and TEs in RNA-seq from the indicated genotypes. Red: germline TEs; yellow: TEs active in somatic and germline tissue; green: somatic TEs. (E) Confocal images of Yb protein in follicle cells of control and indicated mutant flies. (F) Violin plots showing area of Yb-bodies in follicle cells of indicated genotypes. (G) Western blot showing Piwi and Yb levels in indicated genotypes; asterisk denotes an unspecific band from the anti-Yb antibody. (H) Confocal images of Yb and Piwi proteins in ovarian somatic cells (OSCs) upon the indicated knockdown (maximum intensity projections). Dotted red lines denote the nuclear envelope.

Figure 1—figure supplement 2
Effects of Nuclear Pore Complex subunits on transposable element (TE) silencing and Yb-body assembly in ovarian somatic cells (OSCs).

(A) Fold-changes in steady-state RNA levels of the indicated transposons or protein-coding mRNAs in OSCs upon the indicated knockdowns (kd) for 96 or 48 hrs. Values are relative to siGFP control kd and normalised to rp49. Error bars indicate standard deviation (n = 3). p values relative to the siGFP control are indicated above (unpaired t-test). (B) Fold-changes in steady-state RNA levels in OSCs upon the indicated kd for 96 or 48 hrs. Each bar indicates the kd target transcript expression level upon treatment with the respective siRNA. Values are relative to siGFP control and normalised to rp49. Error bars indicate standard deviation (n = 3). p values relative to the siGFP control are indicated above (unpaired t-test). (C) Confocal images of Yb and Piwi proteins and polyA-tail containing transcripts (oligo-dT) in OSCs upon the indicated kd. All kd are analysed after 96 hr unless indicated otherwise. See extended panel in Figure 1—figure supplement 3. (D, E) Violin plots showing area of Yb-bodies in OSCs upon the indicated kd, analysed after 96 (D) or 48 hr (E). ncells = total number of cells analysed. (F) Violin plots showing the area (in µm2) of Yb-bodies in OSCs upon the indicated kd, analysed after 96 hr. ncells = total number of cells analysed. ndots = number of Yb-bodies counted. (G) Quantification of western blots probing Piwi and Yb levels in the indicated kd (n = 4). p values with respect to siGFP control are indicated above (unpaired t-test). A representative western blot is shown on the right.

Figure 1—figure supplement 3
Effects of Nuclear Pore Complex subunits on Yb-body assembly in ovarian somatic cells (OSCs).

Confocal images of Yb and Piwi proteins and polyA-tail containing transcripts (oligo-dT) in OSCs upon the indicated knockdown. All knockdowns are 96 hr unless indicated otherwise.

Figure 2 with 3 supplements
Phenylalanine-glycine (FG) nucleoporins Nup54 and Nup58 function specifically in transposable element (TE) silencing.

(A) Cartoon showing the Nuclear Pore Complex (NPC) structure with nuclear and cytosolic factors involved in flam export; inset shows the domain structure of the Nup62 complex subunits and of Nup93-1. Green boxes: FG-repeats; purple box: Nup54-family domain; grey box: Nic96-family domain. (B) Box plots showing changes in flam RNA levels in the indicated knockdowns (kd) or genotypes. Each datapoint corresponds to a 1 kb bin. Fold-changes were calculated for each bin with respect to the siGFP control. (C) Heatmaps showing changes in flam RNA levels in the indicated kd. Each datapoint corresponds to a 1 kb bin, ordered from 5′ to 3′. Fold-changes were calculated for each bin with respect to the relative siGFP control. (D, E) Coverage plots of piRNAs and RNA-seq reads uniquely mapped to the flam locus or to the protein-coding gene tj upon the indicated kd. The mappability for 25 bp reads is shown at the bottom. (F, G) Scatter plots showing expression levels of PIWI-interacting RNAs (piRNAs) upon the indicated kd. (H) Heatmaps showing changes in flam-derived piRNA levels upon the indicated kd. Each datapoint corresponds to a 1 kb bin, ordered from 5′ to 3′. Fold-changes were calculated for each bin with respect to the siGFP control. (I) Quantification of nuclear and cytoplasmic flam RNA-FISH foci is shown. Nnuc = total number of nuclei analysed; ndots = total number of flam foci counted. (L) Confocal images of flam RNA and polyA-tail containing transcripts (oligo-dT) in ovarian somatic cells (OSCs) upon the indicated kd (full panel in Figure 2—figure supplement 3A). Arrowheads indicate cytosolic flam foci. Dotted line denotes the nuclear envelope based on anti-lamin staining. (M) Confocal images of polyA-tailed transcripts (oligo-dT) in OSCs upon the indicated kd (full panel in Figure 1—figure supplement 2C and Figure 1—figure supplement 3).

Figure 2—figure supplement 1
Effects of Nup54 and Nup58 knockdown (kd) on flam expression.

(A) Volcano plots showing fold-changes and corresponding significance of genes and transposable elements (TEs) in RNA-seq from the indicated kd. Red: germline TEs; yellow: TEs active in somatic and germline tissue; green: somatic TEs. (B–D) Coverage plots of PIWI-interacting RNAs (piRNAs) and RNA-seq reads uniquely mapped upon the indicated kd. The mappability for 50 bp reads is shown at the bottom. (E) Heatmap showing changes in flam RNA levels in indicated genotypes. Each datapoint corresponds to a 1 kb bin, ordered from 5′ to 3′. Fold-changes were calculated for each bin with respect to the flamBG/+ control. The blue arrow indicates the P-element insertion in the flamKG allele, which disrupts flam transcription. (F) Changes in flam RNA levels in the indicated kd (100 kb sliding windows, ordered from 5′ to 3′, n = 396 windows). Dotted lines represent linear regression fits between log2 FC and transcript coordinates with Pearson’s r and significance (p) shown. (G) Coverage plots of piRNAs, RNA-seq, and PRO-seq reads (in rpm) uniquely mapped upon the indicated kd. The mappability for 50 bp reads is shown at the bottom. (H, I) Box plots showing changes in PRO-seq signal upon the indicated kd (n = 2). Each datapoint for flam and 20A corresponds to a 1 kb bin. Fold-changes were calculated for each bin with respect to the siGFP control.

Figure 2—figure supplement 2
Nup54 and Nup58 are required for PIWI-interacting RNA (piRNA) production from flam.

(A) Bar plots showing small RNA size profiles of transposable element (TE)-mapped reads upon the indicated knockdowns (kd). Counts are normalised to 1 million mapped miRNAs. Red: antisense; blue: sense. (B) Bar plots showing the genomic source of the sense and antisense TE-mapped small RNAs shown in (A) upon the indicated kd. Counts are normalised to 1 million mapped miRNAs. (C) Coverage plot showing piRNA levels over the uni-strand cluster 20A. (D) Scatter plot showing expression levels of piRNAs upon the indicated kd. (E) Box plots showing changes in flam piRNA and siRNA levels upon the indicated kd (1 kb bins).

Figure 2—figure supplement 3
Nup54 and Nup58 are required for flam export.

(A) Confocal images of flam RNA and polyadenylated mRNAs (oligo-dT) upon the indicated knockdown (kd). Arrowheads indicate cytosolic flam foci. (B) Schematic of the probes used for flam DNA-FISH. (C, D) Confocal images of flam DNA and Yb protein signal in ovarian somatic cells (OSCs) (C) and ovaries (D).

Figure 3 with 2 supplements
Nup54 and Nup58 are specifically required for flam export and processing into PIWI-interacting RNAs (piRNAs).

(A) Schematic of the Nup54 and Nup58 domain structure and the deletion constructs used in rescue experiments and co-immunoprecipitation assays. Green box: phenylalanine-glycine (FG)-repeats; purple box: Nup54-family domain. (B) Western blots of FLAG-tag co-immunoprecipitates from lysates of S2 cells transfected with the indicated constructs. IN: input; UB: unbound; IP: immunoprecipitate. (C) Fold-changes in steady-state RNA levels of the mdg1 transposon in ovarian somatic cells (OSCs) nucleofected with the indicated siRNAs and rescue constructs. Values are relative to siGFP and normalised to rp49. Error bars indicate standard deviation (n = 4). p values indicated next to each bar were calculated with respect to the relative mCherry control (unpaired t-test). (D) Schematic of the nup54MB allele. The dashed box indicates the portion that is absent in the mutant (purple box: Nup54 family domain). (E) Western blots of FLAG-tag co-immunoprecipitates from lysates of S2 cells transfected with the indicated constructs. (F) Box plots showing changes in piRNA cluster transcript levels in the indicated genotypes. Each datapoint corresponds to a 1 kb bin. (G) Steady-state levels of transposable element (TE) transcripts in the indicated genotypes. (H) Confocal images of Yb protein in follicle cells of the indicated genotypes (full panel in Figure 3—figure supplement 2).

Figure 3—figure supplement 1
Effect of nup54MB mutants on gene expression.

(A) Fold-changes in steady-state RNA levels of the gypsy transposon or act5c gene in ovarian somatic cells (OSCs) nucleofected with the indicated siRNAs and rescue constructs. Values are relative to siGFP control knockdown and normalised to rp49. Error bars indicate standard deviation (n = 4). p values indicated next to each bar were calculated with respect to the relative mCherry control (unpaired t-test). (B) Coverage plots of RNA-seq reads over the nup54 locus. (C) Brightfield images showing ovary size and morphology in the indicated genotypes. (D) MA plots showing mean expression levels (rpm) and fold-changes with respect to control (w1118) of genes and transposable elements (TEs) in RNA-seq from the indicated genotypes (n = 3). Yellow: genes de-regulated more than fourfold with adjusted p value < 0.05; blue: TEs; magenta: uni-strand PIWI-interacting RNA (piRNA) clusters (20A and flam). (E) Heatmaps showing fold-changes in the RNA expression levels of various nucleoporins (Nups) and export factors in the indicated genotypes. (F) Heatmap showing changes in flam RNA levels in the indicated genotypes. Each datapoint corresponds to a 1 kb bin, ordered from 5′ to 3′. Fold-changes were calculated for each bin with respect to the w1118 control.

Figure 3—figure supplement 2
Effect of nup54MB mutants on Yb-body assembly.

Confocal images of Piwi and Yb proteins in ovaries of the indicated genotypes. Quantification of the size of Yb-bodies in the indicated genotypes is shown to the right. ndots = number of Yb-bodies counted; negg ch = number of egg chambers analysed.

Figure 4 with 1 supplement
Nup54 and Nup58 coordinate export and licensing of flam via Nxf1 and Yb.

(A, B) Volcano plots showing enrichment and corresponding significance of biotinylated proteins identified via proximity labelling, followed by mass spectrometry (PL-MS) from ovarian somatic cells (OSCs) expressing the indicated constructs against control (n = 3). NPC subunits: green; Yb: magenta; Nxf1: blue; bait protein: yellow. (C, D) Confocal images of Yb protein and TurboID-Nup54/Nup58 or phenylalanine-glycine nucleoporins (FG-Nups) in OSCs. Arrowheads indicate Yb-bodies juxtaposed to Nup foci. (E, F) Western blots of FLAG-tagged co-immunoprecipitates from cells transfected with the indicated constructs and siRNAs. (G) Proposed model of flam export-coupled licensing in OSCs.

Figure 4—figure supplement 1
Nup54/Nup58 coordinate flam export and licensing by bridging Nxf1 and Yb.

(A) Coverage plot of the indicated CLIP-seq reads over the first 50 kb of the flam locus (n = 3). The mappability for 50 bp reads is shown at the bottom. (B) Volcano plot showing enrichment and corresponding significance of biotinylated proteins identified via proximity labelling, followed by mass spectrometry (PL-MS) from ovarian somatic cells (OSCs) expressing BASU-Yb against control (n = 2). Cytosolic PIWI-interacting RNA (piRNA) pathway factors: magenta; nucleoporins: green; mitochondrial piRNA biogenesis factors: brown; bait protein: yellow. (C) Confocal images of Yb protein and TurboID-Nup54/Nup58 or phenylalanine-glycine nucleoporins (FG-Nups) in OSCs. Arrowheads indicate Yb-bodies juxtaposed to Nup foci. (D–F) Western blots of FLAG-tag co-immunoprecipitates from lysates of cells transfected with the indicated constructs. IN: input; UB: unbound; IP: immunoprecipitate. (G) Western blots of HA-tag co-immunoprecipitates from lysates of cells transfected with the indicated constructs. IN: input; UB: unbound; IP: immunoprecipitate.

Tables

Key resources table
Reagent type
(species) or resource
DesignationSource or referenceIdentifiersAdditional information
Gene (Drosophila melanogaster)fs(1)YbFlyBaseFBgn0000928
Gene (Drosophila melanogaster)flamencoFlyBaseFBgn0267704
Gene (Drosophila melanogaster)Nup54FlyBaseFBgn0033737
Gene (Drosophila melanogaster)Nup58FlyBaseFBgn0038722
Gene (Drosophila melanogaster)ElysFlyBaseFBgn0031052
Gene (Drosophila melanogaster)Nup43FlyBaseFBgn0038609
Gene (Drosophila melanogaster)Nup214FlyBaseFBgn0010660
Gene (Drosophila melanogaster)Nup62FlyBaseFBgn0034118
Gene (Drosophila melanogaster)Nup93-1FlyBaseFBgn0027537
Gene (Drosophila melanogaster)Nup98-96FlyBaseFBgn0039120
Gene (Drosophila melanogaster)Nxf1/SbrFlyBaseFBgn0003321
Gene (Drosophila melanogaster)Nxt1FlyBaseFBgn0028411
Gene (Drosophila melanogaster)laminFlyBaseFBgn0002525
Gene (Drosophila melanogaster)Nup107FlyBaseFBgn0027868
Gene (Drosophila melanogaster)Nup154FlyBaseFBgn0021761
Gene (Drosophila melanogaster)ZucFlyBaseFBgn0261266
Gene (Drosophila melanogaster)tjFlyBaseFBgn0000964
AntibodyAnti-Piwi (Rabbit polyclonal)DOI:10.1016/j.cell.2007.01.043IF(1:500)
WB(1:5000)
AntibodyAnti-Yb (Mouse monoclonal)DOI:10.1101/gad.1989510IF(1:500)
WB(1:1000)
AntibodyAnti-Yb (Rabbit polyclonal)DOI:10.1038/emboj.2011.308WB(1:1000)
AntibodyAnti-tubulin (Rabbit polyclonal)AbcamCat# ab18251,
RRID:AB_2210057
WB(1:5000)
AntibodyAnti-HA (Rabbit monoclonal)Cell Signaling TechnologyCat# 3724,
RRID:AB_1549585
WB(1:1000)
AntibodyAnti-HA (Rabbit polyclonal)AbcamCat# ab9110,
RRID:AB_307019
WB(1:1000)
AntibodyAnti-FLAG (Mouse monoclonal)SigmaCat# F1804,
RRID:AB_262044
WB(1:1000)
AntibodyAnti-lamin (Mouse monoclonal)Developmental Studies Hybridoma BankCat# adl67.10,
RRID:AB_528336
IF(1:200)
AntibodyAnti-Nuclear Pore Complex Proteins (Mouse monoclonal)BiolegendCat# 902907,
RRID:AB_2565026
IF(1:500)
AntibodyAnti-Mouse IgG Alexa Fluor-488 (Goat polyclonal)Thermo Fisher ScientificCat# A-11029,
RRID:AB_2534088
IF(1:500)
AntibodyAnti-Rabbit IgG Alexa Fluor-647 (Goat polyclonal)Thermo Fisher ScientificCat# A-21245,
RRID:AB_2535813
IF(1:500)
AntibodyGFP-Booster Atto-488 (Alpaca monoclonal)ChromotekCat# gba488-100,
RRID:AB_2631386
IF(1:500)
Commercial assay or kitIRDye 800CW StreptavidinLI-CORCat# 926-32230WB(1:4000)
Commercial assay or kitStreptavidin, Alexa Fluor 555 ConjugateThermo Fisher ScientificCat# S-21381IF(1:500)
Commercial assay or kitMouse monoclonal anti-FLAG M2 magnetic beadsSigma-AldrichCat# CatM8823,
RRID:AB_2637089
Commercial assay or kitDynabeads MyOne Streptavidin C1Thermo Fisher ScientificCat# 65001
Commercial assay or kitPierce IP Lysis Buffer-100 mlThermo Fisher ScientificCat# 87787
Commercial assay or kitRIPA Lysis and Extraction BufferThermo Fisher ScientificCat# 89901
Commercial assay or kitThermo Scientific Pierce anti-HA magnetic beadsThermo Fisher ScientificCat# 88836
Commercial assay or kitcOmplete, Mini, EDTA-free Protease Inhibitor CocktailSigma-AldrichCat# 11836170001
Commercial assay or kitRNasin Plus RNase InhibitorPromegaCat# N2615
Commercial assay or kitEffectene Transfection ReagentQiagenCat# 301427
Commercial assay or kitNucleofector Kit VLonzaCat# VVCA-1003
Commercial assay or kitDNase I, Amplification GradeThermo Fisher ScientificCat# 18068015
Commercial assay or kitRNaseOUT Recombinant Ribonuclease InhibitorThermo Fisher ScientificCat# 10777019
Commercial assay or kitMagne HaloTag Beads,20% SlurryPromegaCat# G7282
Commercial assay or kitDeoxynucleotide Solution Set (100 mM; 25 μmol each)New England BiolabsCat# N0446S
Commercial assay or kitSuperScript III Reverse TranscriptaseThermo Fisher ScientificCat# 18080085
Commercial assay or kitChloroform anhydrous 99+%Sigma-AldrichCat# 288306
Commercial assay or kitTRIzol ReagentThermo Fisher ScientificCat# 15596026
Commercial assay or kitInsulin solution humanSigma-AldrichCat# I9278
Commercial assay or kitFibronectin from human plasma 0.1% solutionSigma-AldrichCat# F0895
Commercial assay or kitProLong Diamond Antifade MountantThermo Fisher ScientificCat# P36961
Commercial assay or kitFly ExtractDrosophila Genomics Resource CenterCat# 1645670
Commercial assay or kitSMARTer RNA Unique Dual Index Kit – 24UClontechCat# 634451
Commercial assay or kitRiboPOOL 10 nM for DrosophilaCambridge Bioscience
Commercial assay or kitD-Biotin solutionThermo Fisher ScientificCat# B20656
Commercial assay or kitShields and Sang M3 Insect MediumSigmaCat# S3652
Commercial assay or kitLibrary Quantification KitKapa BiosystemsCat# KK4873
Commercial assay or kitProTEV PlusPromegaCat# V6101
Commercial assay or kitParaformaldehyde, 16% w/v aq. soln., methanol freeAlfa AesarCat# 043368.9M
Commercial assay or kitRNase A (affinity purified)1 mg/mlThermo Fisher ScientificCat# AM2271
Commercial assay or kitNuPAGE 4–12%, Bis-Tris,1.5 mm, Mini Protein Gel, 10-wellThermo Fisher ScientificCat# NP0335BOX
Commercial assay or kitXfect Transfection ReagentTakara BioCat# 631318
Commercial assay or kitPierce Protein A/G Magnetic BeadsThermo Fisher ScientificCat# 88802
Commercial assay or kitAgencourt RNAClean XP beadsBeckman CoulterCat# A63987
Commercial assay or kitNEBNext Ultra Directional RNA Library Prep Kit for IlluminaNew England BiolabsCat# E7420L
Commercial assay or kitSMARTer Stranded RNA-Seq KitTakara BioCat# 634839
Commercial assay or kitRNeasy Mini KitQiagenCat# 74104
Commercial assay or kitCell Line Nucleofector kit VLonzaCat# VVCA-1003
Commercial assay or kitNucleofector II deviceLonzaCat# AAB-1001
Cell line (Drosophila melanogaster)S2 cellsThermo Fisher ScientificCat# R69007,
RRID:CVCL_Z232
Cell line (Drosophila melanogaster)Ovarian somatic cells (OSCs)DOI:10.1038/nature08501RRID:CVCL_IY73
Software, algorithmFijiImageJRRID:SCR_002285
Software, algorithmProteome Discoverer 2.1Thermo Fisher ScientificRRID:SCR_014477
Software, algorithmSTARDOI:10.1093/bioinformatics/bts635RRID:SCR_015899
Software, algorithmDEseq2DOI:10.1186/s13059-014-0550-8RRID:SCR_015687
Software, algorithmImage Studio LiteLI-CORRRID:SCR_013715

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