Ciliogenesis occurs in vascular endothelial cells (ECs) in AGM. a Three-dimension (3D) confocal imaging showing cilia on ECs in the AGM region using Tg(βact:Arl13b–GFP/kdrl:mCherry/runx1:en-GFP) line at 28 hpf. White squares indicate the ECs with cilia. White bars denote DA or PCV region. DA dorsal aorta, PCV posterior cardinal vein. Scale bars, 10 µm. b The live confocal imaging of kdrl⁺/runx1⁺ or gfi1⁺ HE cells in Tg(βact:Arl13b–GFP/kdrl:mCherry/runx1:en-GFP) (upper panel) or Tg(βact:Arl13b–GFP/gfi1:GFP) at 28 hpf (middle panel). The imaging of gfi1⁺ HE cells sorted by fluorescence-activated cell sorting of dissected trunk region in Tg (gfi1:GFP/βact:Arl13b–GFP) embryos (lower panel). Yellow arrowheads indicate primary cilia in kdrl⁺/runx1⁺ cells; white arrowheads indicate primary cilia in gfi1⁺ HE cells. Scale bars, 5 µm. c Fluorescence in situ hybridization (FISH) result showing the cmyb expression and Ac-tubulin staining showing the cilia in the aorta-gonad-mesonephros (AGM) region at 48 hpf. Yellow arrowhead indicates primary cilia and the white arrowhead indicates the cmyb⁺ HSPC in the AGM region. The cmyb probe was used to examine cmyb expression in Tg (cmyb:EGFP) embryos by FISH. Scale bars, 20 µm. d The live confocal imaging of cilia with kdrl:mCherry/βact:Arl13b–GFP double-transgenic line. White arrow denotes the blood flow direction. Scale bar, 5 µm. e, f The statistical data shows the primary cilia number (e) and length (f) in blood vessels in the AGM region in wild-type embryos. The cilia length presented in each embryo was the average length of all the cilia in the DA of the AGM region calculated per 200 µm. Data represent the analysis results of one-way ANOVA–Sidak test. Error bars, mean ± s.d., n = 10 embryos. ns non-significant, ***P < 0.001

Loss of cilia genes causes primary cilia defects in blood vessels in the aorta-gonad-mesonephros (AGM) region. a Transmission electron microscopy (TEM) imaging of blood vessels (left panel) in the AGM region in control and fsd1-deficient embryos at 28 hpf. The red arrows indicate the ultrastructure of primary cilia in vascular endothelial cells (ECs) (middle panels) and motile cilia in pronephric duct (right panels). Red arrows denote cilia. Scale bars, 5 µm (left panel) and 0.1 µm (right panel). b Visualization of cilia in ECs in the AGM region using kdrl:mCherry/βact:Arl13b–GFP double-transgenic line in control and fsd1 morphants at 28 hpf. The white arrowheads indicate the primary cilia in blood vessels. White bars denote DA or PCV region. Scale bars, 20 µm (left panel) and 5 µm (right panel). c–f The quantification of the primary cilia number and length with kdrl:mCherry/βact:Arl13b–GFP double-transgenic line in control and cilia-impaired embryos at 28 hpf. Data in c, d were analyzed by Student’s t-test (n = 13 embryos). Data in e, f represent the analysis results of one-way ANOVA–Dunnett test (n = 11 embryos). Error bars, mean ± s.d. ns non-significant, *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001

Loss of cilia genes induces hematopoietic stem and progenitor cell (HSPC) defects. a Whole-mount in situ hybridization (WISH) results of HSPC markers (runx1 and cmyb) in the aorta-gonad-mesonephros (AGM) region in control and fsd1 morphants at 36 hpf. The red arrowheads indicate the expression of HSPC markers runx1 and cmyb in DA. b Western blotting showing the protein level of Runx1 in control and fsd1 morphants at 26 hpf. c WISH analysis showing the expression of HSPC markers runx1 and cmyb (red arrowheads) in the DA in fsd1^−/−. d Western blotting showing the protein level of Runx1 in fsd1^−/−. e Representative images showing runx1 and cmyb expression in control, pkd2, kif3a, and ift88 morphants at 33 hpf. The red arrowheads indicate the expression of HSPC markers runx1 and cmyb. f WISH analysis showing the expression of HSPC marker runx1 in the DA in pkd2^−/− or ift88^−/− with a sub-effective dose of pkd2 MO (0.5 ng per embryo, pkd2 MO_low) or ift88 MO (0.8 ng per embryo, ift88 MO_low). The red arrowheads indicate the expression of HSPC marker runx1. Scale bars, 100 µm

Blocking formation or function of primary cilia impairs hematopoietic stem and progenitor cell (HSPC) development. a Confocal imaging of cilia in the aorta-gonad-mesonephros (AGM) region in kdrl:mCherry/βact:Arl13b–GFP double-transgenic line with fli1a:ift88-cKO-functional injection, or ciliobrevin D (CBD) treatment at 28 hpf. White arrow denotes the blood flow direction. Scale bar, 5 µm. b, c The quantification of primary cilia number and length in the blood vessels of AGM in a. Data in b, c represent the analysis results of one-way ANOVA–Dunnett test. Error bars, mean ± s.d., n = 10 embryos. ns non-significant, *P < 0.05, ****P < 0.0001. d WISH result of runx1 (red arrowheads) in control and CBD-treated embryos at 31 hpf. The red arrowheads indicate the expression of HSPC marker runx1. Scale bar, 100 µm. e The kdrl:mCherry⁺/cmyb:EGFP⁺ HE cells (white arrowheads) in the AGM region in fli1a:ift88-cKO-injected embryos (left panel) with quantification (right panel) at 36 hpf. Cmlc2:EGFP-negative embryos were used as a negative control (control). Scale bar, 50 µm. Error bars, mean ± s.d., n = 14 embryos. **P < 0.01, Student’s t-test

Cilia are required for hemogenic endothelium (HE) specification. a Whole-mount in situ hybridization (WISH) analysis showing the expression of HE markers, runx1, gata2b, and gfi1aa, in the aorta-gonad-mesonephros (AGM) region at 22, 24, and 26 hpf. Red arrowheads denote the expression of HE markers. b Expression of erythroid marker (gata1), myeloid marker (pu.1) in the caudal hematopoietic tissue (CHT) and T cell marker (rag1) in the thymus at 4 dpf. Red arrowheads mark the corresponding hematopoietic cells. c The expression of HE marker gfi1aa, erythroid marker gata1, and T cell marker rag1 in fsd1^−/−. Red arrowheads mark the corresponding hematopoietic cells. d, e The imaging of kdrl:mCherry⁺/runx1:en-GFP⁺ HE cells (white arrowheads) in the AGM region in control and fsd1 morphants with quantification (e) at 26 hpf. Error bars, mean ± s.d., n = 15 embryos. **P < 0.01, Student’s t-test. f Confocal imaging of HE cells (kdrl:mCherry⁺/cmyb:EGFP⁺) in control and fsd1 morphants at 36 hpf. White arrowheads denote HE cells. g The quantification of kdrl:mCherry⁺/cmyb:EGFP⁺ HE cells in control and fsd1 morphants at 36 hpf. Error bars, mean ± s.d., n = 10 embryos. ***P < 0.001, Student’s t-test. h, i Representative images of runx1 expression (red arrowheads) in control and cilia-impaired embryos with quantification (i) at 28 hpf. Red arrowheads denote runx1⁺ cells in the AGM region. j–l High-resolution imaging of HE cells (kdrl:mCherry⁺/runx1:en-GFP⁺) in control and cilia-impaired embryos with quantification (k, l). White arrowheads indicate kdrl:mCherry⁺/runx1:en-GFP⁺ cells in the AGM region. Data represent the analysis results of one-way ANOVA–Dunnett test. Error bars, mean ± s.d., n = 12, 9, 9, 9, 9 embryos (i). n = 9, 9, 8, 8 embryos (k). n = 8, 10, 10, 9 embryos (l). ***P < 0.001, ****P < 0.0001. Scale bars, 100 µm

Notch signaling is downregulated in hemogenic endothelium (HE) cells in primary cilia-impaired embryos. a The gene ontology analysis for the downregulated genes in fsd1 morphants. b Volcano plot showing the dysregulated genes between wild-type embryos and fsd1 morphants at 26 hpf. Endothelial cell markers kdrl and fli1a, arterial markers including ephrinB2a, dll4, and hey2, and Notch signaling components including notch1a, notch2, notch3, maml1, jag1a, and adam10b are highlighted in black. Red arrows denote the gene location site. c qPCR result of Notch target genes in wild-type embryos and fsd1 mutants at 26 hpf. Error bars, mean ± s.d., * P < 0.05, **P < 0.01, ****P < 0.0001, ns non-significant, Student’s t-test. n = 3 biological replicates. d Western blotting showing the protein level of NICD in wild-type embryos and fsd1^−/− at 26 hpf. e Expression of notch1a in kdrl⁺runx1⁺ cells in the AGM in control and fsd1 morphants at 26 hpf. Error bars, mean ± s.d., **P < 0.01, ns non-significant, Student’s t-test. n = 3 biological replicates. f, g Confocal imaging of Tg (tp1:mCherry/fli1a:EGFP) embryos in the AGM region in control and cilia-impaired embryos at 26 hpf. tp1:mCherry⁺/fli1a:EGFP⁺ double positive cells (white arrowheads) were quantified in g. Scale bar, 50 µm. Data represent the analysis results of one-way ANOVA–Dunnett test. Error bars, mean ± s.d., n = 12, 9, 7, 10 embryos, **P < 0.01,***P < 0.001, ****P < 0.0001. h Immunofluorescence staining of RPE-1 cells with acetylated α-tubulin (Ac-tubulin, cilia marker) antibodies and Hoechst (DNA marker) in ciliated and non-ciliated cells treated with siCtrl and siFSD1 respectively. RPE-1 cells were transfected with GFP-NICD plasmid and indicated siRNA. The nuclei were stained with Hoechst (blue) and the cilium was marked by Ac-tubulin (red). The GFP indicated the NICD expression. Scale bar, 5 µm. i Western blotting showing the protein levels of NICD, β-actin and FSD1 in GFP-NICD plasmid transfected in siCtrl or siFSD1 RPE-1 cells. j, k Quantification of GFP-positive cells with nuclear NICD (j) or with primary cilia (k) in h. Data are presented with three independent experiments. Error bars, mean ± s.d., ****P < 0.0001. Student’s t-test. n number of cells

Notch signaling acts downstream of primary cilia in regulating hematopoietic stem and progenitor cell (HSPC) specification. a, b Whole-mount in situ hybridization (WISH) result of runx1 expression in control embryos, fsd1 morphants, fli1a:NICD-EGFP plasmid-injected embryos, and fsd1 morphants injected with fli1a:NICD-EGFP plasmid at 26 hpf and 36 hpf. Red arrowheads denote the runx1⁺ cells in the AGM region. c Quantification of runx1⁺ cells in the aorta-gonad-mesonephros (AGM) region in b. Data represent the analysis results of two-way ANOVA–Tukey test for multiple comparisons. Error bars, mean ± s.d., n = 15, 17, 17, 6 embryos. **P < 0.01, ****P < 0.0001. d WISH result of runx1 expression (red arrowheads) in control embryos, fsd1 morphants, hs:NICD-EGFP plasmid injected embryos, and fsd1 morphants injected with hs:NICD-EGFP at 36 hpf. These embryos were heat shocked for 30 min at 42 °C from 20 hpf. e Expression of runx1 (red arrowheads) in control, morphants, and fli1a:NICD-EGFP injected morphants at 36 hpf. Scale bars, 100 µm

ZFIN is incorporating published figure images and captions as part of an ongoing project. Figures from some publications have not yet been curated, or are not available for display because of copyright restrictions.