1. Neuroscience

FUS regulates RAN translation through modulating the G-quadruplex structure of GGGGCC repeat RNA in C9orf72-linked ALS/FTD

  1. Yuzo Fujino
  2. Morio Ueyama
  3. Taro Ishiguro
  4. Daisaku Ozawa
  5. Hayato Ito
  6. Toshihiko Sugiki
  7. Asako Murata
  8. Akira Ishiguro
  9. Tania Gendron
  10. Kohji Mori
  11. Eiichi Tokuda
  12. Tomoya Taminato
  13. Takuya Konno
  14. Akihide Koyama
  15. Yuya Kawabe
  16. Toshihide Takeuchi
  17. Yoshiaki Furukawa
  18. Toshimichi Fujiwara
  19. Manabu Ikeda
  20. Toshiki Mizuno
  21. Hideki Mochizuki
  22. Hidehiro Mizusawa
  23. Keiji Wada
  24. Kinya Ishikawa
  25. Osamu Onodera
  26. Kazuhiko Nakatani
  27. Leonard Petrucelli
  28. Hideki Taguchi
  29. Yoshitaka Nagai  Is a corresponding author
  1. Department of Neurology, Kindai University Faculty of Medicine, Japan
  2. Department of Neurology, Kyoto Prefectural University of Medicine, Japan
  3. Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Japan
  4. Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Japan
  5. Department of Neurology and Neurological Science, Tokyo Medical and Dental University, Japan
  6. School of Life Science and Technology, Tokyo Institute of Technology, Japan
  7. Laboratory of Molecular Biophysics, Institute for Protein Research, Osaka University, Japan
  8. Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and28 Industrial Research, Osaka University, Japan
  9. Research Center for Micro-nano Technology, Hosei University, Japan
  10. Department of Neuroscience, Mayo Clinic, United States
  11. Department of Psychiatry, Osaka University Graduate School of Medicine, Japan
  12. Department of Chemistry, Keio University, Japan
  13. Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Japan
  14. Life Science Research Institute, Kindai University, Japan
  15. Department of Neurology, Osaka University Graduate School of Medicine, Japan
  16. Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
https://doi.org/10.7554/eLife.84338.3
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Cite this article
  1. Yuzo Fujino
  2. Morio Ueyama
  3. Taro Ishiguro
  4. Daisaku Ozawa
  5. Hayato Ito
  6. Toshihiko Sugiki
  7. Asako Murata
  8. Akira Ishiguro
  9. Tania Gendron
  10. Kohji Mori
  11. Eiichi Tokuda
  12. Tomoya Taminato
  13. Takuya Konno
  14. Akihide Koyama
  15. Yuya Kawabe
  16. Toshihide Takeuchi
  17. Yoshiaki Furukawa
  18. Toshimichi Fujiwara
  19. Manabu Ikeda
  20. Toshiki Mizuno
  21. Hideki Mochizuki
  22. Hidehiro Mizusawa
  23. Keiji Wada
  24. Kinya Ishikawa
  25. Osamu Onodera
  26. Kazuhiko Nakatani
  27. Leonard Petrucelli
  28. Hideki Taguchi
  29. Yoshitaka Nagai
(2023)
FUS regulates RAN translation through modulating the G-quadruplex structure of GGGGCC repeat RNA in C9orf72-linked ALS/FTD
eLife 12:RP84338.
https://doi.org/10.7554/eLife.84338.3
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6 figures, 2 tables and 2 additional files

Figures

Figure 1 with 2 supplements
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Screening for RNA-binding proteins (RBPs) that suppress G4C2 repeat-induced toxicity in C9-ALS/FTD flies.

(A) Light microscopic images of the eyes in flies expressing both (G4C2)42 or 89 and the indicated RBPs using the GMR-Gal4 driver. Coexpression of FUS, IGF2BP1, or hnRNPA2B suppressed eye …

Figure 1—source data 1

RNA-binding proteins and their cDNA accession numbers screened in the genetic analyses in Figure 1.

https://cdn.elifesciences.org/articles/84338/elife-84338-fig1-data1-v1.xlsx
Figure 1—source data 2

Summary of the genetic analyses in Figure 1.

https://cdn.elifesciences.org/articles/84338/elife-84338-fig1-data2-v1.xlsx
Figure 1—source data 3

Statistical data related to Figure 1B–E.

https://cdn.elifesciences.org/articles/84338/elife-84338-fig1-data3-v1.xlsx
Figure 1—figure supplement 1
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Characterization of C9-ALS/FTD flies.

(A) (G4C2)n constructs used in this study. These constructs do not include an ATG start codon downstream of the UAS sequence, and were expressed in a tissue-specific manner using the GAL4-UAS …

Figure 1—figure supplement 1—source data 1

The artificial sequence inserted in the pUAST vector for generation of (G4C2)n flies.

https://cdn.elifesciences.org/articles/84338/elife-84338-fig1-figsupp1-data1-v1.xlsx
Figure 1—figure supplement 1—source data 2

Statistical data related to Figure 1—figure supplement 1C and D.

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Figure 1—figure supplement 2
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Coexpression of FUS suppresses G4C2 repeat-induced toxicity in flies expressing (G4C2)89.

(A) Light microscopic images of the eyes in flies expressing both (G4C2)42 or 89 and FUS using the GMR-Gal4 driver. FUS-2 and FUS-3 are different strains from that in Figure 1. Scale bar: 100 μm. (B)…

Figure 1—figure supplement 2—source data 1

Statistical data related to Figure 1—figure supplement 2B–D.

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Figure 2 with 1 supplement
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FUS suppresses G4C2 repeat-induced toxicity via its RNA-binding activity.

(A) Light microscopic images of the eyes in flies expressing both (G4C2)89 and either FUS or FUS-RRMmut using the GMR-Gal4 driver. Scale bar: 100 μm. (B) Quantification of eye size in the flies of …

Figure 2—source data 1

Statistical data related to Figure 2B–E.

https://cdn.elifesciences.org/articles/84338/elife-84338-fig2-data1-v1.xlsx
Figure 2—figure supplement 1
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Western blot analysis showing expression levels of FUS and FUS-RRMmut proteins.

(A) Western blot analysis of the FUS and FUS-RRMmut proteins in the heads of adult flies expressing EGFP, FUS, or FUS-RRMmut using the GMR-Gal4 driver, with an anti-FUS antibody. The arrowhead …

Figure 2—figure supplement 1—source data 1

Statistical data related to Figure 2—figure supplement 1B.

https://cdn.elifesciences.org/articles/84338/elife-84338-fig2-figsupp1-data1-v1.xlsx
Figure 2—figure supplement 1—source data 2

Source data related to Figure 2—figure supplement 1A.

https://cdn.elifesciences.org/articles/84338/elife-84338-fig2-figsupp1-data2-v1.zip
Figure 3 with 2 supplements
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FUS suppresses RNA foci formation and RAN translation from G4C2 repeat RNA.

(A) Fluorescence in situ hybridization (FISH) analyses of G4C2 repeat RNA in the salivary glands of fly larvae expressing both (G4C2)89 and either FUS or FUS-RRMmut using two copies of the GMR-Gal4 …

Figure 3—source data 1

Statistical data related to Figure 3B, C, E, F, H and I.

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Figure 3—source data 2

Source data related to Figure 3G.

https://cdn.elifesciences.org/articles/84338/elife-84338-fig3-data2-v1.zip
Figure 3—figure supplement 1
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Schema of the LDS-(G4C2)44GR-GFP construct.

Schema of the LDS-(G4C2)44GR-GFP construct containing the (G4C2)44 sequence and 114 nucleotides of the 5′-flanking region of intron 1 of the human C9orf72 G4C2 repeat sequence. A GFP tag in the GR …

Figure 3—figure supplement 2
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Overexpression of FUS does not suppress eye degeneration in dipeptide repeat protein (DPR)-only flies expressing DPRs translated from non-G4C2 RNAs.

Light microscopic images of the eyes in DPR-only flies coexpressing either the poly(GR) or poly(GA) protein, and either FUS or FUS-RRMmut using the GMR-Gal4 driver. Overexpression of FUS did not …

Figure 4 with 1 supplement
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Reduction of endogenous caz expression enhances G4C2 repeat-induced toxicity, RNA foci formation, and dipeptide repeat protein (DPR) aggregation.

(A) Light microscopic images of the eyes in flies expressing (G4C2)89 using the GMR-Gal4 driver, with knockdown of caz. Scale bar: 100 μm. (B) Quantification of eye size in flies of the indicated …

Figure 4—source data 1

Statistical data related to Figure 4B, D, F, G and I.

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Figure 4—figure supplement 1
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Endogenous caz is a functional homologue of FUS for the suppression of G4C2 repeat-induced toxicity.

(A) Light microscopic images of the eyes in flies expressing both (G4C2)42 or 89 and either caz (FLAG-caz) or FUS-4 (FLAG-FUS) using the GMR-Gal4 driver. FUS-4 is a different strain from those used …

Figure 4—figure supplement 1—source data 1

Statistical data related to Figure 4—figure supplement 1B–D.

https://cdn.elifesciences.org/articles/84338/elife-84338-fig4-figsupp1-data1-v1.xlsx
Figure 5 with 2 supplements
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FUS directly binds to and modulates the G-quadruplex structure of G4C2 repeat RNA, resulting in the suppression of RAN translation in vitro.

(A) Analysis of the binding of His-tagged FUS proteins to biotinylated (G4C2)4 RNA by the filter binding assay. The nitrocellulose membrane (left) traps RNA-bound FUS proteins, whereas unbound RNAs …

Figure 5—source data 1

Statistical data related to Figure 5G.

https://cdn.elifesciences.org/articles/84338/elife-84338-fig5-data1-v1.xlsx
Figure 5—source data 2

Source data related to Figure 5F.

https://cdn.elifesciences.org/articles/84338/elife-84338-fig5-data2-v1.zip
Figure 5—figure supplement 1
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FUS colocalizes with G4C2 RNA foci.

Combined fluorescence in situ hybridization (FISH) and immunohistochemical analyses of G4C2 repeat RNA and FUS in the salivary glands of flies expressing both (G4C2)89 and FUS using two copies of …

Figure 5—figure supplement 2
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FUS modulates the G-quadruplex structure of G4C2 repeat RNA.

(A–C) CD spectra of (G4C2)4 RNA incubated with or without FUS in the presence of 150 mM KCl (A), NaCl (B), or LiCl (C). CD spectra of (G4C2)4 RNA alone (black), FUS alone (green), sum of (G4C2)4 RNA …

Figure 6
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Identification of G-quadruplex-targeting RNA-binding proteins (RBPs) that suppress G4C2 repeat-induced toxicity in C9-ALS/FTD flies.

(A) Light microscopic images of eyes in flies expressing both (G4C2)89 and the indicated G-quadruplex-targeting RBPs using the GMR-Gal4 driver. Scale bar: 100 μm. (B) Quantification of eye size in …

Figure 6—source data 1

RNA-binding proteins and their cDNA accession numbers screened in the genetic analyses in Figure 6.

https://cdn.elifesciences.org/articles/84338/elife-84338-fig6-data1-v1.xlsx
Figure 6—source data 2

Statistical data related to Figure 6B–D, F.

https://cdn.elifesciences.org/articles/84338/elife-84338-fig6-data2-v1.xlsx

Tables

Table 1
Association (ka) and dissociation (kd) rate and dissociation constants (KD) between FUS and (G4C2)4 RNA in different buffers as assessed by surface plasmon resonance (SPR) analysis.
Bufferka (M–1s–1) × 106kd (s–1) × 10–3KD (M)
KCl1.4221.5 × 10–8
NaCl0.41541.3 × 10–7
LiCl0.0018251.4 × 10–5
Key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Strain, strain background (Drosophila melanogaster)UAS-(G4C2)n, UAS-FUS-2, UAS-FUS-RRMmutThis paperN/ASee ‘Generation of constructs and transgenic flies’
Strain, strain background (D. melanogaster)UAS-RBP
(FUS-3; IGF2BP1; hnRNPA2B1; hnRNPR; SAFB2; SF3B3; hnRNPA1; hnRNPL; DHX30; SAFB; DHX15; ILF2; DDX21; hnRNPK; SFPQ; ILF3; NONO; ELAVL1; DDX3X; DDX5; DDX17; DHX9; DHX36)		This paperN/ASee ‘Generation of constructs and transgenic flies’
Strain, strain background (D. melanogaster)UAS-LDS-(G4C2)44GR-GFPGoodman et al., 2019 (PMID::31110321)FLYB: FBtp0135960
Strain, strain background (D. melanogaster)UAS-FUSIshiguro et al., 2017 (PMID::28343865)FLYB: FBtp0117594
Strain, strain background (D. melanogaster)UAS-FUS-4 (UAS-FLAG-FUS)Wang et al., 2011 (PMID::21881207)FLYB: FBtp0070284
Strain, strain background (D. melanogaster)UAS-caz (UAS-FLAG-caz)Wang et al., 2011 (PMID:21881207)FLYB: FBtp0070279
Strain, strain background (D. melanogaster)caz2Frickenhaus et al., 2015 (PMID::25772687)FLYB: FBal0323133
Strain, strain background (D. melanogaster)UAS-TDP-43Ishiguro et al., 2017 (PMID::28343865)FLYB: FBtp0117592
Strain, strain background (D. melanogaster)GMR-GAL4 driverYamaguchi et al., 1999 (PMID:10597285)FLYB: FBtp0010074
Strain, strain background (D. melanogaster)Elav-GAL4 driver: P{w[+mC]=GAL4-elav.L}2/CyOBloomington Drosophila Stock CenterBDSC: 8765; FLYB: FBst0008765
Strain, strain background (D. melanogaster)Elav-GeneSwitch GAL4 driver: y(1) w[*]; P{w[+mC]=elav-Switch.O}GSG301Bloomington Drosophila Stock CenterBDSC: 43642; FLYB: FBst0043642
Strain, strain background (D. melanogaster)UAS-EGFP: w[*]; P{w[+mC]=UAS-2xEGFP}AH2Bloomington Drosophila Stock CenterBDSC: 6874; FLYB: FBst0006874
Strain, strain background (D. melanogaster)UAS-DsRed: w[*]; P{w[+mC]=UAS-AUG-DsRed}ABloomington Drosophila Stock CenterBDSC: 6282; FLYB: FBst0006282
Strain, strain background (D. melanogaster)UAS-EWSR1: w[1118]; P{w[+mC]=UAS-EWSR1.C}26MBloomington Drosophila Stock CenterBDSC: 79592; FLYB: FBst00079592
Strain, strain background (D. melanogaster)UAS-(GR)36: w[1118]; P{{y[+t7.7] w[+mC]=UAS-poly-GR.PO-36}attP40Bloomington Drosophila Stock CenterBDSC: 58692; FLYB: FBst00058692
Strain, strain background (D. melanogaster)UAS-(GA)36: w[1118]; P{{y[+t7.7] w[+mC]=UAS-poly-GA.PO-36}attP40Bloomington Drosophila Stock CenterBDSC: 58693; FLYB: FBst00058693
Strain, strain background (D. melanogaster)UAS-(GR)100: w[1118]; P{{y[+t7.7] w[+mC]=UAS-poly-GR.PO-100}attP40Bloomington Drosophila Stock CenterBDSC: 58696; FLYB: FBst00058696
Strain, strain background (D. melanogaster)UAS-(GA)100: w[1118]; P{{y[+t7.7] w[+mC]=UAS-poly-GA.PO-100}attP40Bloomington Drosophila Stock CenterBDSC: 58697; FLYB: FBst00058697
Strain, strain background (D. melanogaster)RNAi of GFP: w[1118]; P{w[+mC]=UAS-GFP.dsRNA.R}142Bloomington Drosophila Stock CenterBDSC: 9330; FLYB: FBst0009330
Strain, strain background (D. melanogaster)RNAi of caz: P{KK107486}VIE-260BVienna Drosophila Resource CenterVDRC: v100291; FLYB: FBst0472165
AntibodyRat monoclonal anti-poly(GR) antibody (5A2)MilliporeCar# MABN778;
RRID:AB_2728664		IHC(1:1000), WB(1:1000)
AntibodyMouse monoclonal anti-poly(GA) antibody (5E9)MilliporeCar# MABN889;
RRID:AB_2728663		IHC(1:1000)
AntibodyRabbit polyclonal anti-poly(GA) antibodyCosmo BioCat# CAC-TIP-C9-P01IHC(1:1000)
AntibodyRabbit polyclonal anti-poly(GP) antibodyNovus BiologicalsCat# NBP2-25018;
RRID:AB_2893239		IHC(1:1000)
AntibodyRabbit polyclonal anti-FUS antibodyBethyl LaboratoriesCat# A300-302A;
RRID:AB_309445		IHC(1:1000), WB(1:1000)
AntibodyMouse monoclonal anti-EGFP antibodyClontechCat# 632569WB(1:1000)
AntibodyMouse monoclonal anti-actin antibody (AC-40)Sigma-AldrichCat# A4700; RRID:AB_476730WB(1:1000)
AntibodyMouse monoclonal anti-c-Myc antibody (9E10)WakoCat# 017-21876WB(1:3000)
Recombinant DNA reagentpcDNA5/FRT-C9orf72 intron1-(G4C2)80 (plasmid)This paperSee ‘RNA synthesis for in vitro translation’
Sequence-based reagent(G4C2)n_F(1)This paperPCR primersATGAATGGGAGCAGTGGTGG
Sequence-based reagent(G4C2)n_R(1)This paperPCR primersTGTTGAGAGTCAGCAGTAGCC
Sequence-based reagent(G4C2)n_F(2)This paperPCR primersCCCAATCCATATGACTAGTAGATCC
Sequence-based reagent(G4C2)n_R(2)This paperPCR primersTGTAGGTAGTTTGTCCAATTATGTCA
Sequence-based reagentgal4_FLi et al., 2008 (PMID:18449188)PCR primersTTGAAATCGCGTCGAAGGA
Sequence-based reagentgal4_RLi et al., 2008 (PMID:18449188)PCR primersGGCTCCAATGGCTAATATGCA
Peptide, recombinant proteinHis-FUSThis paperN/ASee ‘Filter binding assay’
Peptide, recombinant proteinHis-FUS-RRMmutThis paperN/ASee ‘Filter binding assay’
Peptide, recombinant proteinFUS (not tagged)This paperN/ASee ‘Preparation of recombinant FUS protein’
Peptide, recombinant proteinFUS-RRMmut (not tagged)This paperN/ASee ‘Preparation of recombinant FUS protein’
Commercial assay or kitIn-Fusion Cloning systemTaKaRa BioCat# Z9645N
Commercial assay or kitEZ-Tn5<KAN-2>Insertion KitEpicentreCat# EZI011RK
Commercial assay or kitQuantiTect Reverse Transcription KitQIAGENCat# 205314
Commercial assay or kitmMESSAGE mMACHINE T7 Transcription KitThermo Fisher ScientificCat# AM1344
Commercial assay or kitFlexi Rabbit Reticulocyte Lysate SystemPromegaCat# L4540
Chemical compound, drugRU486 (mifepristone)WakoM3321; CAS: 84371-65-3
Chemical compound, drugFormula 4-24 Instant Drosophila mediumWakoCat# 534-20571
Software, algorithmZEN imaging softwareZeissRRID:SCR_013672; https://www.zeiss.com/microscopy/en/products/software/zeiss-zen.html
Software, algorithmImageJSchneider et al., 2012 (PMID:22930834)RRID:SCR_003070; https://imagej.nih.gov/ij/
Software, algorithmGraphPad Prism version 8.4.3GraphPad Software Inc.RRID:SCR_002798; https://www.graphpad.com

Additional files

Supplementary file 1

Full genotypes of the fly lines and their cultured temperatures.

https://cdn.elifesciences.org/articles/84338/elife-84338-supp1-v1.xlsx
MDAR checklist
https://cdn.elifesciences.org/articles/84338/elife-84338-mdarchecklist1-v1.docx

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