Xu et al., Supplementary Figures 1-7
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1 Xu et al., Supplementary Figures 1-7 Supplementary Figure 1. PIPKI is required for ciliogenesis. (a) PIPKI localizes at the basal body of primary cilium. RPE-1 cells treated with two sirnas targeting to human PIPKI (sipipki -O1, sipipki -O2) or negative control sirna (sinc) were serum starved to induce primary ciliogenesis and stained with appropriate antibodies. (b) Knockdown of PIPKI was validated by immunoblotting. (c) PIPKI exhibits basal body localization in multiple types of ciliated cells. (d, e) PIPKI and PIPKI antibodies yielded no cilium-related signal. Serum starved RPE-1 cells were fixed with methanol (d) or 1 P a g e
2 paraformaldehyde (PFA) (e) and stained with appropriate antibodies. (f) PIPKIγ forms a ring-like structure at the ciliary base. RPE-1 cells co-stained with anti-pipki and anti-plk4 antibodies were examined by 3D-SIM microscopy. (g-i) PIPKI depletion substantially inhibits primary ciliogenesis in RPE-1, NIH3T3, and RCTE cells. (g) RPE-1 cells treated with negative control (sinc) or sirnas against PIPKI (sipipki -O1 and sipipki -O2), PIPKI (sipipki ), or PIPKI (sipipki ) were serum starved to induce ciliogenesis and stained with anti-acetylated -tubulin antibody (Ac-tub). (h) NIH3T3 cells were treated with sinc or mouse PIPKI -specific (sipipki -O3) sirnas. (i) RCTE cells treated with sinc or two PIPKI -specific sirnas were analyzed as described in (a). The percentage of ciliated cells (n > 200) in each group was quantified from at least three independent experiments and plotted. Error bars represent s.d. ***P < (j) Severe ciliary defect was observed in ppk-1-null C. elegans. With dye-filling assay, ppk-1-null worms exhibited complete dye-filling minus phenotype. Brackets indicate ciliated Amphid neurons. (k) Genotyping results of ppk-1-null worms. Actin was used as a loading control. Nuclei were visualized by DAPI staining (blue). Insets show magnified images of primary cilia. Ac-tub, acetylated -tubulin. Glu-tub, polyglutamylated tubulin. -tub, -tubulin. Scale bars are 0.5 μm in (f) and 5 μm in other panels. 2 P a g e
3 Supplementary Figure 2. PIPKI functions downstream of basal-body membrane docking and upstream of TZ formation. RPE-1 cells treated with negative control (sinc) or PIPKI (sipipki ) sirna were serum starved and stained with the appropriate antibodies. Percentage of cells (n > 200) showing positive staining of indicated proteins was quantified from at least three experiments. Error bars represent standard deviation (s.d.). N.S., no statistically significant difference. -tub, -tubulin. Scale bars, 0.5 μm. 3 P a g e
4 Supplementary Figure 3. PIPKI promotes the recruitment of TTBK2 to the M-centriole/basal body. (a) CP110 retained at the M-centriole in serum-starved, PIPKI -depleted RPE-1 cells. Arrowheads point to the basal body. (b) TTBK2 recruitment to the M-centriole induced by serum starvation was impaired in RPE-1 cells when PIPKI was knocked down. Percentage of cells (n > 200) exhibiting CP110 on both centrioles (a), or TTBK2 at the M-centriol/basal body (b) was quantified from at least three independent experiments. Glu-tub, polyglutamylated tubulin. -tub, -tubulin. (c) PIPKI overexpression promotes TTBK2 recruitment to the centrosome in a PIPKI kinase activity dependent manner. RCTE cells stably expressing GFP-TTBK2 were transfected with empty vector 4 P a g e
5 (Control), wild-type (WT), or kinase-dead (KD) HA-PIPKI i3 for 8 h without serum starvation. Cep83 was used as a centrosome marker. (d) RCTE cells were transfected with empty vector (Control), HA- PIPKI, and HA-PIPKI CT. The percentage of ciliated cells (n > 20) in each group was quantified from at least three independent experiments and plotted. Error bars represent standard deviation (s.d.). ***P < N.S., no statistically significant difference. Scale bars, 0.5 μm. 5 P a g e
6 Supplementary Figure 4. INPP5E inhibits ciliogenesis by suppressing CP110 removal from the basal body. IMCD3 Cells transfected with empty vector (Control), or Flag-INPP5E were serum starved and stained with indicated antibodies. Percentage of cells with CP110 on both centrioles (a, n > 100) and ciliated cells (b, n > 200) was quantified from at least three independent experiments. Error bars represent s.d. ***P< P a g e
7 Supplementary Figure 5. Localization of PI variants in cell. (a, b) IMCD3 cells were stained with indicated antibodies, and nuclei were visualized by DAPI staining. Anti-PtdIns(4)P (PI(4)P) (a) and anti-ptdins(4,5)p 2 (PIP2) (b) antibodies were pre-absorbed with control PolyPIPosomes (Control), or PolyPIPosomes containing 5% of PI(4)P or PIP2 before adding onto samples for immunostaining. (c, d) IMCD3 cells transfected with the PI(3)P probe GFP-FYVE, or the PI(5)P probe GFP-PHD were processed for immunofluorescence microscopy. Scale bars: green, 5 μm; white, 0.5 μm. 7 P a g e
8 Supplementary Figure 6. CEP164 and TTBK2 contain evolutionarily conserved PI binding motifs. The protein sequences of Cep164 (a) and TTBK2 (b) orthologs were analyzed by MULTALIN alignment software. Evolutionarily conserved PI-binding motifs with lysine/arginine-rich patches were highlighted. (c, d) PolyPIPosome pull-down assay. HEK293T Cells transfected with 8 P a g e
9 wild-type (WT) Myc-CEP164 or GFP-TTBK2, or mutated Myc-CEP164 (9A) and GFP-TTBK2 (ΔPI) were subjected to pull-down assay with PolyPIPosomes containing PI(4)P. The resulting precipitates and cell lysates (Input) were immunoblotted with indicated antibodies. 9 P a g e
10 Supplementary Figure 7. Uncropped images of immunoblotting results for Figs P a g e
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SUPPLEMENTARY INFORMATION Legends for Supplementary Tables. Supplementary Table 1. An excel file containing primary screen data. Worksheet 1, Normalized quantification data from a duplicated screen: valid
Supplemental Material
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Figure 1: TDP-43 is subject to lysine acetylation within the RNA-binding domain a) QBI-293 cells were transfected with TDP-43 in the presence or
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