Gene expression of cartilage and bone (precursor) cells is affected in foxe1 mutants. (A-I) Relative gene expression of tgfβ3, wnt5a, sp7, col2a1, col1a2, runx2b, dlx2a, sox9a and fgfr2 in mutants versus wild types. Axis description from (A) applies to all graphs. (J) dlx2a positive post migratory neural crest cells at 24 hpf (Prim-5) in wild types, 20% of the heterozygous- and 60% of the homozygous mutants. Asterisks indicate the level of significance: * = p< 0.05, ** = p< 0.01, *** = p< 0.001, **** = p< 0.0001 (n = 10–15). Data were assessed for normality with the D’Agostino-Pearson normality test. Normally distributed data were analyzed using a one-way ANOVA and post-hoc Tukey test. Non-parametric data were compared with a Kruskal–Wallis test with post-hoc Dunn’s Multiple comparison test. Error bars indicate standard deviation. Scale bar 100 µm.

a, b Cell trajectories suggested by pseudotime analysis with Monocle 3. Shown on a UMAP, the starting point of each trajectory was labeled with a number. The pseudotime is shown as a heatmap in a. Red arrows and letters highlight different branches in b. Clusters are labeled in the same number and color as in Fig. 2c. c Schematic of transgenic lines and experimental design to define the origin of aEPCs. 4HT was used at 10 μM. d Section images of 3 dpa hearts carrying the tcf21:Switch; tcf21:CreERt2; col12a1bEGFP reporters. 4HT treatment was performed as indicated in c. mCherry and EGFP are shown in magenta and green, respectively in the merged image. Single-channel images are shown in grayscale. Arrows indicate representative EGFP+mCherry+ cells. White dashed lines indicate the injury sites. Scale bar, 100 μm. e fn1a expression shown on the pseudotime UMAP. The mural cell trajectories are circled with red dashed lines. f Whole-mount images of the ventricular surface showing expression of pdgfrb:EGFP (green) and tcf21:H2R (magenta) in transgenic lines at 7 dpa. The framed regions are enlarged to show details on the right, with single-channel images shown in grayscale. Arrows indicate representative EGFP+mCherry+ cells. Scale bar, 100 μm. g Schematic of transgenic lines and experimental design to define the fate of aEPCs. 4HT was used at 5 μM. h Whole-mount images of the ventricular surface from hearts carrying the ubi:Switch; ptx3a:CreERt2 reporters. pdgfrb expression is detected by HCR staining (green). mCherry is shown in magenta, and nuclei were stained with DAPI (blue). Arrows indicate representative pdgfrb+mCherry+ cells. A maximum projection image is shown on the left. Z-stack images of the numbered frames are shown on the right. Scale bar, 50 μm.

Ectopic accumulation of urotensin neuropeptides is associated with spine curvature in zebrafish ciliary mutants.(A) Representative images of wild type and scoliosis zebrafish mutants. Micro-CT images are shown on the bottom. (B) qPCR analysis showing the expression of urotensin genes in the heads of wild type and scoliosis mutants. (C) Enlarged views of the head regions of wild type, ccdc57, and uts2r3 mutants. (D, E) Statistical analysis of the dorsal curvature angles in different mutants as indicated. The angles were measured between the direction of the parasphenoid bone and the Weberian vertebrae as illustrated in the diagram (D). (F) In situ hybridization results showing the expression of urp2 in the brains of wild type and uts2r3 mutant as indicated. (G) Expression of urp2 in the spinal cords of wild type and uts2r3 mutant. The strongly increased expression of the urp2 in the tail region was shown on the enlarged views. (H) Dissected spinal cords from wild type and uts2r3 mutants as indicated. The two boxed regions correspond to those in panel G. Scale bars: 1 cm in panels A and H. The data underlying the graphs shown in the figure can be found in S1 Data.

Chd7 knockout suppressed OPC migration. (a) Representative image of dorsally migrated olig2+ cells at 3, 4, 5, and 6 dpf between chd7+/+ and chd7−/− groups. Scale bar: 100 μm. (b) The number of dorsally migrated olig2+ cells at 3, 4, 5, and 6 dpf decreased in chd7−/− group. Data shown as mean ± sem. 3 dpf, ** p = 0.0023; 4 dpf, **** p < 0.0001; 5 dpf, **** p < 0.0001; 6 dpf, p = 0.7349, ns: not significant, unpaired Student’s two-tailed t-test. (c) Representative image of total and dorsally migrated olig2+ cells at 4 dpf between chd7+/+ and chd7−/− group. Scale bar: 10 μm. (d) The number of total olig2+ cells at 4 dpf did not differ significantly between the two groups, ns: not significant. The number of dorsally migrated olig2+ cells at 4 dpf decreased in chd7−/− group. ** p = 0.0075, unpaired Student’s two-tailed t-test.