Cioni JM , Wong HH , Bressan D , Kodama L , Harris WA , Holt CE .

Wellcome Trust , 322817 European Research Council

Xla Wt + cyfip2 MO (Fig.4.H-K)

	Figure 1. Differential Function of CYFIP1 and CYFIP2 during RGC Axonal Development (A) Sequence analysis of the whole zebrafish embryo injected with cas9 mRNA + cyfip1 or cyfip2 gRNAs. The target site is indicated on the sequence (green), followed by 4 examples of corresponding mutated regions. (B) DiI (red) and DiO (green) fluorescent dyes were injected in the zebrafish embryo retina at 5 dpf. The dashed line denotes the confocal imaging area of the optic tract (OT). (C1–D3′′′) Dorsal (D) (C1′–C3′, D1′–D3′) and Ventral (V) (C1′′–C3′′, D1′′–D3′′) RGC projections were analyzed in control embryos (cas9 mRNA + gRNA control) (C1, D1), cyfip1 CRISPR-injected embryos (cas9 mRNA + gRNA cyfip1) (C2, D2), and cyfip2 CRISPR-injected embryos (cas9 mRNA + gRNA cyfip2) (C3, D3) at 48 hpf (C) and 5 dpf (D). Arrows in (D3′) show missorted dorsal axons in the OT. Yellow lines in (D1)–(D3) indicate the reference line used for quantification of the missorting index (MI). Examples of DiI (dorsal) and DiO signals plotted along the reference line corresponding to sorted (D1′′′, D2′′′) or misprojected (D3′′′) RGC axons (int., intensity; A.U, Arbitrary Units). (E) Quantifications of D and V axonal projection area in the OT at 48 hpf. (F) The missorting index (MI) was quantified as the ratio of the intensity signal of the missorted D (Dm) axons to all the D axons (Dm+Ds). For gRNA cyfip1-injected embryos, only the embryos showing an axon growth phenotype were quantified (n = 18 embryos). Error bars represent SEM. ∗∗p < 0.01, ∗∗∗p < 0.001, n.s., non significant (Mann-Whitney test for E and F). The number of zebrafish analyzed is indicated on the bars. Scale bars: 50 μm (C1–D3). See also Figure S1.
	Figure 2. Dorsal and Ventral RGCs Exhibit Homo- and Heterotypic Axon-Axon Contact Recognition (A) Schematic of the retinotectal projection in Xenopus embryo. Time-lapse imaging of the OT was done from the indicated lateral view. (B1–B3) An example of each observed in vivo axon-axon response is showed first as an initial acquired large field, followed by a time-lapse sequence at high magnification. The position of the ventral (VOT) and dorsal (DOT) optic tract is indicated. (B1) RGC growth cone (GC) crossing the encounter axon shaft. (B2) RGC GC tracking along the encounter axon shaft by multiple filopodia contacts (yellow arrows). (B3) RGC GC growing on the encounter axon, leading to the fasciculation of the two axon shafts (yellow arrowheads). (C) Quantification of the axon-axon responses observed in the optic tract. (D) Assay used to monitor axon-axon interactions in vitro. (E and F) Examples of fasciculation (E) and crossing (F) events observed during homotypic interactions. (G and H) Examples of tracking (G) and retraction (H) events observed during heterotypic interactions. (I) Quantification of the global homotypic and heterotypic responses. (J) Quantification of the axon-axon responses relative to the RGC topographic origin. Time stamps are in the format of min:s. ∗p < 0.05, ∗∗∗p < 0.001 (chi-square test for I and J). Numbers of events analyzed are indicated on the graph (n = 21 independent experiments). Scale bars: 10 μm (B) and 5 μm (E–H).
	Figure 3. RGC Axon-Axon Interactions Require CYFIP2 Function (A) Representative western blots and quantification of CYFIP1 and CYFIP2 levels in Xenopus eye lysates at stages 34 and 41 (n = 3, normalized to α-Tubulin). (B) Representative western blots and quantification of CYFIP2 (n = 6, normalized to α-Tubulin) and CYFIP1 (n = 3, normalized to α-Tubulin) levels in CYFIP2MO- compared to CoMO-injected embryos at stage 34. (C) Examples of stalling growth cones (GCs) during homotypic and heterotypic responses after CYFIP2 depletion. (D) Quantification of the homotypic interaction responses after CYFIP2 knockdown. (E and F) Quantification of the number (E) and duration (F) of filopodia contacts during fasciculation and stalling events in CYFIP2MO (n = 7 GC, n = 27 filopodia) compared to CoMO (n = 6 GC, n = 20 filopodia) conditions for homotypic interactions. (G) Quantification of the heterotypic interaction responses after CYFIP2 knockdown. (H and I) Quantification of the number (H) and duration (I) of filopodia contacts during tracking and stalling events in CYFIP2MO (n = 8 GC, n = 26 filopodia) compared to CoMO (n = 5 GC, n = 29 filopodia) conditions for heterotypic interactions. (D and G) Numbers of events analyzed are indicated on the graph (n = 12 independent experiments). (E–I) Error bars represent SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, n.s., non-significant (Mann-Whitney test for A, B, E, F, H and I) and (Fisher’s exact test for D and G). Time stamps are in the format of min:s. Scale bars: 5 μm (C).
	Figure 4. CYFIP2 Regulates Filopodial Dynamics and F-actin in the Growth Cone Peripheral Domain upon Axon-Axon Contact (A) CYFIP2 immunostaining on stage 32 Xenopus retinal growth cone (GC). Arrowheads indicate CYFIP2 in filopodia. (B) Time-lapse imaging of CYFIP2-GFP movements in RGC GC. Arrowheads indicate the accumulation of CYFIP2-GFP. (C) Time-lapse imaging of CYFIP2-GFP movements in an elongating GC filopodia labeled by a membrane marker (blue). Arrowheads indicate CYFIP2-GFP accumulation. (D) Quantification of CYFIP2 signal intensity in GC. (E) Distribution of CYFIP2 signal intensity along RGC axon shaft (last 10 μm) and GC central (C) and peripheral (P) domains. (F) Distribution of CYFIP2-GFP signal intensity along RGC axon shaft (last 10 μm) and GC central (C) and peripheral (P) domains. (G) Scheme illustrating the observed relocalization of CYFIP2 in the GC peripheral domain during axon-contact. (H) Phalloidin immunostaining on isolated or in contact stage 32 Xenopus retinal GCs from CoMO- and CYFIP2MO-injected embryos. (I and J) Quantifications of filopodia length (I) and number (J). (K) Quantification of phalloidin signal intensity in GC. The numbers of GC (D, J, and K) or filopodia (I) analyzed are indicated on the bars. Error bars represent SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, n.s., non-significant (Mann-Whitney test for D–F and I–K). The GC central domain (c.), peripheral domain (p.), and filopodia (f.) are indicated (A–C). Time stamps are in the format of min:s. Scale bars: 5 μm (A, B left panel, and H); 1 μm (B right panels); 2 μm (H). See also Figure S2.
	Figure 5. Subcellular Interactions of CYFIP2 with RNPs and WRC in RGC Axons (A) Immunoprecipitation with anti-GFP was performed on stage 32 Xenopus brains expressing CYFIP2-GFP, and immunoblotted with the indicated antibodies. (B) CYFIP2 and NCKAP1 immunostainings on stage 32 Xenopus retinal cultures. (C) Protein colocalization quantified by Manders’ coefficient. (D and E) CYFIP2 with xFXR (D) or NCKAP1 (E) immunostainings on RGC growth cones. (F) Representative examples of the proximity ligation assay (PLA) obtained between CYFIP2 and NCKAP1, or CYFIP2 and xFXR, in the axon shaft. (G) Representative PLA examples obtained between CYFIP2 and NCKAP1 (G2) or control IgGgoat (G1), and between CYFIP2 and xFXR (G4) or control IgGmouse (G3) in the GC. (H) Quantification of the PLA signals in the axon shaft. (I) Quantification of the PLA signals in the GC. (J) Ratios of the PLA signals in the central (C) and peripheral (P) domain of the GC (Mann-Whitney test, ∗∗∗p < 0.001). Error bars represent SEM. Number of axons analyzed is indicated on the graph. Scale bars: 5 μm.
	Figure 6. CYFIP2-RNP Recruitment in Growth Cones on Axon-Axon Contact (A) Time-lapse sequence showing the transport of CYFIP2-GFP in Cy3-UTP-RNA-granules in RGC axon shaft, highlighted by arrowheads. (B) Quantification of the CYFIP2-GFP containing RNPs motions in the RGC axon shaft. (C) Example of CYFIP2-GFP and Cy3-UTP-RNA granules signals in a RGC growth cone (GC). (D) Assay used to follow Cy3-UTP-RNA granules movements during axon-axon interactions. (E) Example of a time-lapse sequence showing the recruitment of Cy3-UTP-RNA granules in the peripheral domain of the GC in response to a heterotypic contact. (F–H) Quantifications of the relative Cy3-UTP-RNA granules distribution for each time point in isolated GCs (F) (n = 3 experiments), after heterotypic interactions (G) (n = 5 experiments) or homotypic interactions (H) (n = 5 experiments). T = 0 correspond to the cell-contact point. (I–K) Quantification of Cy3-UTP-RNA granules anterograde transport over time in isolated (I) (n = 3 experiments), after heterotypic interactions (J) (n = 4 experiments) or homotypic interactions (K) (n = 4 experiments), normalized to the average anterograde transport for each axon. Error bars represent SEM. ∗p < 0.05 (Mann-Whitney test for F–K). Time stamps are in the format of min:s. Scale bars: 3 μm (A) and 5 μm (C and E).
	Figure 7. CYFIP2 Regulation of the WRC Mediates Axon Sorting in the Tract (A) Schematic illustrating CYFIP2’s regulatory domains and mutations. (B) Representative examples of CYFIP2WT-GFP (n = 9 GC), CYFIP2ΔCTD-GFP (n = 11 GC), and CYFIP2mutE-GFP (n = 13 GC) expression in Xenopus retinal cultures (n = 4 experiments). Arrows indicate CYFIP2-GFP accumulation in the growth cone peripheral domain and filopodia. (C1–C5) Lateral-view of whole-mount 5 dpf zebrafish embryos injected with DiI and DiO in the dorsal and ventral retina, respectively. Co-injection of CYFIP2MO + CYFIP2WT (C3) or CYFIP2mutE (C4), but not CYFIP2ΔCTD (C5), mRNAs rescue the pre-sorting defect observed in CYFIP2MO-injected embryos (C2) compared to CoMO-injected embryos (C1). (D) Quantification of the Missorting Index (Mann-Whitney test, ∗∗∗p < 0.001, n.s., non-significant). Error bars represent SEM. The number of zebrafish analyzed is indicated on the bars. Scale bars: 5 μm (B) or 50 μm (C). See also Figures S3 and S4.
	Figure 1. Differential Function of CYFIP1 and CYFIP2 during RGC Axonal Development(A) Sequence analysis of the whole zebrafish embryo injected with cas9 mRNA + cyfip1 or cyfip2 gRNAs. The target site is indicated on the sequence (green), followed by 4 examples of corresponding mutated regions.(B) DiI (red) and DiO (green) fluorescent dyes were injected in the zebrafish embryo retina at 5 dpf. The dashed line denotes the confocal imaging area of the optic tract (OT).(C1–D3′′′) Dorsal (D) (C1′–C3′, D1′–D3′) and Ventral (V) (C1′′–C3′′, D1′′–D3′′) RGC projections were analyzed in control embryos (cas9 mRNA + gRNA control) (C1, D1), cyfip1 CRISPR-injected embryos (cas9 mRNA + gRNA cyfip1) (C2, D2), and cyfip2 CRISPR-injected embryos (cas9 mRNA + gRNA cyfip2) (C3, D3) at 48 hpf (C) and 5 dpf (D). Arrows in (D3′) show missorted dorsal axons in the OT. Yellow lines in (D1)–(D3) indicate the reference line used for quantification of the missorting index (MI). Examples of DiI (dorsal) and DiO signals plotted along the reference line corresponding to sorted (D1′′′, D2′′′) or misprojected (D3′′′) RGC axons (int., intensity; A.U, Arbitrary Units).(E) Quantifications of D and V axonal projection area in the OT at 48 hpf.(F) The missorting index (MI) was quantified as the ratio of the intensity signal of the missorted D (Dm) axons to all the D axons (Dm+Ds). For gRNA cyfip1-injected embryos, only the embryos showing an axon growth phenotype were quantified (n = 18 embryos).Error bars represent SEM. ∗∗p < 0.01, ∗∗∗p < 0.001, n.s., non significant (Mann-Whitney test for E and F). The number of zebrafish analyzed is indicated on the bars. Scale bars: 50 μm (C1–D3). See also Figure S1.
	Figure 2. Dorsal and Ventral RGCs Exhibit Homo- and Heterotypic Axon-Axon Contact Recognition(A) Schematic of the retinotectal projection in Xenopus embryo. Time-lapse imaging of the OT was done from the indicated lateral view.(B1–B3) An example of each observed in vivo axon-axon response is showed first as an initial acquired large field, followed by a time-lapse sequence at high magnification. The position of the ventral (VOT) and dorsal (DOT) optic tract is indicated. (B1) RGC growth cone (GC) crossing the encounter axon shaft. (B2) RGC GC tracking along the encounter axon shaft by multiple filopodia contacts (yellow arrows). (B3) RGC GC growing on the encounter axon, leading to the fasciculation of the two axon shafts (yellow arrowheads).(C) Quantification of the axon-axon responses observed in the optic tract.(D) Assay used to monitor axon-axon interactions in vitro.(E and F) Examples of fasciculation (E) and crossing (F) events observed during homotypic interactions.(G and H) Examples of tracking (G) and retraction (H) events observed during heterotypic interactions.(I) Quantification of the global homotypic and heterotypic responses.(J) Quantification of the axon-axon responses relative to the RGC topographic origin. Time stamps are in the format of min:s. ∗p < 0.05, ∗∗∗p < 0.001 (chi-square test for I and J). Numbers of events analyzed are indicated on the graph (n = 21 independent experiments).Scale bars: 10 μm (B) and 5 μm (E–H).
	Figure 3. RGC Axon-Axon Interactions Require CYFIP2 Function(A) Representative western blots and quantification of CYFIP1 and CYFIP2 levels in Xenopus eye lysates at stages 34 and 41 (n = 3, normalized to α-Tubulin).(B) Representative western blots and quantification of CYFIP2 (n = 6, normalized to α-Tubulin) and CYFIP1 (n = 3, normalized to α-Tubulin) levels in CYFIP2MO- compared to CoMO-injected embryos at stage 34.(C) Examples of stalling growth cones (GCs) during homotypic and heterotypic responses after CYFIP2 depletion.(D) Quantification of the homotypic interaction responses after CYFIP2 knockdown.(E and F) Quantification of the number (E) and duration (F) of filopodia contacts during fasciculation and stalling events in CYFIP2MO (n = 7 GC, n = 27 filopodia) compared to CoMO (n = 6 GC, n = 20 filopodia) conditions for homotypic interactions.(G) Quantification of the heterotypic interaction responses after CYFIP2 knockdown.(H and I) Quantification of the number (H) and duration (I) of filopodia contacts during tracking and stalling events in CYFIP2MO (n = 8 GC, n = 26 filopodia) compared to CoMO (n = 5 GC, n = 29 filopodia) conditions for heterotypic interactions.(D and G) Numbers of events analyzed are indicated on the graph (n = 12 independent experiments).(E–I) Error bars represent SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, n.s., non-significant (Mann-Whitney test for A, B, E, F, H and I) and (Fisher’s exact test for D and G). Time stamps are in the format of min:s. Scale bars: 5 μm (C).
	Figure 4. CYFIP2 Regulates Filopodial Dynamics and F-actin in the Growth Cone Peripheral Domain upon Axon-Axon Contact(A) CYFIP2 immunostaining on stage 32 Xenopus retinal growth cone (GC). Arrowheads indicate CYFIP2 in filopodia.(B) Time-lapse imaging of CYFIP2-GFP movements in RGC GC. Arrowheads indicate the accumulation of CYFIP2-GFP.(C) Time-lapse imaging of CYFIP2-GFP movements in an elongating GC filopodia labeled by a membrane marker (blue). Arrowheads indicate CYFIP2-GFP accumulation.(D) Quantification of CYFIP2 signal intensity in GC.(E) Distribution of CYFIP2 signal intensity along RGC axon shaft (last 10 μm) and GC central (C) and peripheral (P) domains.(F) Distribution of CYFIP2-GFP signal intensity along RGC axon shaft (last 10 μm) and GC central (C) and peripheral (P) domains.(G) Scheme illustrating the observed relocalization of CYFIP2 in the GC peripheral domain during axon-contact.(H) Phalloidin immunostaining on isolated or in contact stage 32 Xenopus retinal GCs from CoMO- and CYFIP2MO-injected embryos.(I and J) Quantifications of filopodia length (I) and number (J).(K) Quantification of phalloidin signal intensity in GC.The numbers of GC (D, J, and K) or filopodia (I) analyzed are indicated on the bars. Error bars represent SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, n.s., non-significant (Mann-Whitney test for D–F and I–K). The GC central domain (c.), peripheral domain (p.), and filopodia (f.) are indicated (A–C). Time stamps are in the format of min:s. Scale bars: 5 μm (A, B left panel, and H); 1 μm (B right panels); 2 μm (H). See also Figure S2.
	Figure 5. Subcellular Interactions of CYFIP2 with RNPs and WRC in RGC Axons(A) Immunoprecipitation with anti-GFP was performed on stage 32 Xenopus brains expressing CYFIP2-GFP, and immunoblotted with the indicated antibodies.(B) CYFIP2 and NCKAP1 immunostainings on stage 32 Xenopus retinal cultures.(C) Protein colocalization quantified by Manders’ coefficient.(D and E) CYFIP2 with xFXR (D) or NCKAP1 (E) immunostainings on RGC growth cones.(F) Representative examples of the proximity ligation assay (PLA) obtained between CYFIP2 and NCKAP1, or CYFIP2 and xFXR, in the axon shaft.(G) Representative PLA examples obtained between CYFIP2 and NCKAP1 (G2) or control IgGgoat (G1), and between CYFIP2 and xFXR (G4) or control IgGmouse (G3) in the GC.(H) Quantification of the PLA signals in the axon shaft.(I) Quantification of the PLA signals in the GC.(J) Ratios of the PLA signals in the central (C) and peripheral (P) domain of the GC (Mann-Whitney test, ∗∗∗p < 0.001).Error bars represent SEM. Number of axons analyzed is indicated on the graph. Scale bars: 5 μm.
	Figure 6. CYFIP2-RNP Recruitment in Growth Cones on Axon-Axon Contact(A) Time-lapse sequence showing the transport of CYFIP2-GFP in Cy3-UTP-RNA-granules in RGC axon shaft, highlighted by arrowheads.(B) Quantification of the CYFIP2-GFP containing RNPs motions in the RGC axon shaft.(C) Example of CYFIP2-GFP and Cy3-UTP-RNA granules signals in a RGC growth cone (GC).(D) Assay used to follow Cy3-UTP-RNA granules movements during axon-axon interactions.(E) Example of a time-lapse sequence showing the recruitment of Cy3-UTP-RNA granules in the peripheral domain of the GC in response to a heterotypic contact.(F–H) Quantifications of the relative Cy3-UTP-RNA granules distribution for each time point in isolated GCs (F) (n = 3 experiments), after heterotypic interactions (G) (n = 5 experiments) or homotypic interactions (H) (n = 5 experiments). T = 0 correspond to the cell-contact point.(I–K) Quantification of Cy3-UTP-RNA granules anterograde transport over time in isolated (I) (n = 3 experiments), after heterotypic interactions (J) (n = 4 experiments) or homotypic interactions (K) (n = 4 experiments), normalized to the average anterograde transport for each axon.Error bars represent SEM. ∗p < 0.05 (Mann-Whitney test for F–K). Time stamps are in the format of min:s. Scale bars: 3 μm (A) and 5 μm (C and E).
	Figure 7. CYFIP2 Regulation of the WRC Mediates Axon Sorting in the Tract(A) Schematic illustrating CYFIP2’s regulatory domains and mutations.(B) Representative examples of CYFIP2WT-GFP (n = 9 GC), CYFIP2ΔCTD-GFP (n = 11 GC), and CYFIP2mutE-GFP (n = 13 GC) expression in Xenopus retinal cultures (n = 4 experiments). Arrows indicate CYFIP2-GFP accumulation in the growth cone peripheral domain and filopodia.(C1–C5) Lateral-view of whole-mount 5 dpf zebrafish embryos injected with DiI and DiO in the dorsal and ventral retina, respectively. Co-injection of CYFIP2MO + CYFIP2WT (C3) or CYFIP2mutE (C4), but not CYFIP2ΔCTD (C5), mRNAs rescue the pre-sorting defect observed in CYFIP2MO-injected embryos (C2) compared to CoMO-injected embryos (C1).(D) Quantification of the Missorting Index (Mann-Whitney test, ∗∗∗p < 0.001, n.s., non-significant).Error bars represent SEM. The number of zebrafish analyzed is indicated on the bars. Scale bars: 5 μm (B) or 50 μm (C). See also Figures S3 and S4.

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