Matsuda M , Rozman J , Ostvar S , Kasza KE , Sokol SY .

R35GM122492 U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS), R01NS100759 U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS), R01 NS100759 NINDS NIH HHS , R35 GM138380 NIGMS NIH HHS , R35 GM122492 NIGMS NIH HHS

             neural plate formation

	Fig. 1: Neural plate hinge cells contain heterogeneous apical domains. a, b’ Dorsal view of the middle area of a control Xenopus neural plate stained with phalloidin (a) and the segmented image (a’) at stage 15. The rectangular area in (a), corresponding to the medial hinge, is enlarged in (b). b Cells with small apical domain (red) are interspersed with large cells elongated along the AP axis (green bars). c Rose plots show the orientation of the cells relative to the anteroposterior (AP) axis. n = 929 cells. Data from three stage 15 embryos are combined. d In the dorsolateral hinge region, cells with small apical domain (red) are adjacent to elongated cells (blue). Neuroepithelium (NE) and non-neural ectoderm (N-NE) are in the upper and lower parts of images, respectively. The histogram of apical domain size (e) and cell aspect ratios (f) of cells in stage 11 embryonic ectoderm (green), and cells in the medial or dorsolateral hinge (blue) and non-hinge (red) areas of stage 15 neural plate. Four-to-five rows of cells at the dorsal midline were considered the medial hinge area. The non-hinge areas exclude four-to-five rows of cells from the medial and dorsolateral hinges. Data (means ± s.d.) are combined for three stage 15 embryos and four 11 stage embryos, representative of three independent experiments. Stage 15 hinge, n = 255 cells; stage 15 non-hinge, n = 426 cells; stage 11 ectoderm, n = 1218 cells. The experiments were repeated at least three times. Coefficients of variation (CV) are shown in Supplementary Table 1. One-way ANOVA Kruskal-Wallis test. One-sided. p < 0.0000000001 (e). p < 0.0000000001 (f). Scale bars are 50 μm in (a, a’), 20 μm in (b) and (d).
	Fig. 2: PCP signaling is required for apical domain heterogeneity in the neural plate. a, b’ Representative images of control GFP-injected embryo and vangl2 MO-injected embryo (the injected side marked by GFP). Dorsal view. Control GFP RNA (a, a’), or GFP RNA and 10 ng vangl2 MO (b, b’) were injected into four-cell embryos targeting the presumptive neural plate. Control, n = 6 embryos; vangl2 MO, n = 9 embryos. (c, d) The histogram of apical domain size (c) and cell aspect ratio (d) of uninjected and vangl2 MO-injected cells in (b, b’). The hinge and non-hinge regions were quantified together. Data (means ± s.d.) was quantified with n = 853 cells from three control embryos and n = 359 cells from three vangl2 MO-injected embryos. This represents three independent experiments. The Kolmogorov-Smirnov test. Two-sided. p < 0.00000000001 (c). p = 0.000000004 (d). CVs are shown in Supplementary Table 1. Scale bars are 50 μm in (a, b’).
	Fig. 3: Mechanical model shows that contractile cell subpopulation leads to cell elongation and alignment. a–f 2D vertex model of the neural plate. a Zoom on the neural plate region of the vertex model initial condition. Blue border outlines the posterior neural plate region of the model tissue. Apically constricting cells are in magenta (tissue shown for ). b Model tissue from (a) after relaxation at . Red lines show the direction of cell elongation. c Distribution of angles between the AP axis (horizontal line) and cell elongation direction of non-constricting neural plate cells for the model posterior neural plate in (b); 0° corresponds to perfect alignment. d Central length (along AP) and width (perpendicular to AP) of the model tissue after relaxation as a function of the probability of cell constriction ; values are normalized by length and width if no cells constrict. e Mean angle with the AP axis as a function of the constricting region aspect ratio . Error bars indicate the standard deviation between all non-constricting cells in one instance of the model tissue for each (number of cells in order of increasing ). f Mean cell elongation as a function of the furrow aspect ratio. See Methods for details. e and f are for . g–j Furrow formation in a 3D vertex model simulation of the hinge area. g Initial condition for the 3D vertex model simulation. Hinge region is outlined by a blue border and constricting cells are shown in magenta (tissue shown for ). h Model tissue from (g) after relaxation at time . Red lines show the direction of elongation for the apical side of the cells. i Cross-section view of the model tissue in (h), showing the formation of a shallow furrow. j Cross-section view of a model tissue with .
	Fig. 4: Lmo7-expressing ectoderm as a model of apical domain heterogeneity. a Scheme of the experiment. GFP-Lmo7 RNA (1 ng) was injected in two oppositely localized animal blastomeres in four-cell stage embryos. Adapted from Xenopus illustrations © Natalya Zahn (2022), Xenbase (www.xenbase.org RRID:SCR_003280)75. b Representative GFP-Lmo7-expressing embryo at stage 11. Hyperpigmentation was observed in 90–95% embryos (n > 100). c Still image from Movie 1 shows GFP-Lmo7 fluorescence from the embryo in (b). d Segmented image of the rectangular area in (c). e Representative rose plot from n = 792 cells from one embryo depicts cell orientation with respect to the injection axis (white arrow connecting red and blue dots in c–e). The data represent at least three experiments. Scale bars are 100 μm in (b, c) and 50 μm in (d).
	Fig. 5: Apical domain heterogeneity in ectoderm cells expressing Lmo7. a Scheme of the experiment. GFP-Lmo7 (100 pg) or GFP-ZO1 RNA (150 pg) was injected into four animal blastomeres of 4–8-cell embryos for live imaging at stage 11. Uniform fluorescence has been confirmed in stage 11 ectoderm. Adapted from Xenopus illustrations © Natalya Zahn (2022), Xenbase (www.xenbase.org RRID:SCR_003280)75. b-d’ Time-lapse imaging of GFP-Lmo7 embryos for ~4 h. Apically constricting (AC) and expanding (AE) cells are marked by red and blue, respectively. Areas in (b) and (b’”) are enlarged in (c, d) and (c’, d’), respectively. Quantification of apical domain dynamics in GFP-Lmo7 (e) and GFP-ZO1 (f) cells in one representative embryo. Each line represents apical domain size changes of individual cells for ~4 h. The cells were scored as AC (red) or AE (blue) if they had more than 20% decrease or increase in their apical domain size, respectively. The remaining cells were designated as ‘no change’ (green). n = 50 cells for GFP-Lmo7. n = 49 cells for GFP-ZO1. g Frequencies of cells with different changes in apical domain size are shown for embryos in (e) and (f). The Freeman-Halton extension of Fisher’s exact test. Two-sided. p = 2.383 E-13. These experiments were repeated 3–5 times. Scale bars are 40 μm in (b) and 20 μm in (c, d).
	Fig. 6: Mosaic expression of Lmo7 causes apical constriction. a Scheme of the experiment. GFP-ZO1 RNA (100 pg) and Flag-Lmo7 RNA (100 pg) were coinjected into one ventral blastomere of 16-cell stage embryos. Adapted from Xenopus illustrations © Natalya Zahn (2022), Xenbase (www.xenbase.org RRID:SCR_003280)75. b–g’ Representative images of GFP-ZO1 cells co-expressing Flag-Lmo7 in “sheet” (b, c’) or in “isolated” from Movies 4 and 5. Time-lapse imaging was initiated at stage 11. AC and AE cells are marked by red and blue, respectively. Asterisks show cells undergoing mitosis during the imaging. Rectangular areas in (b, b’ and d), d’ are enlarged in (c, c’) and (e–g’), respectively. Scale bars are 30 μm in (b, d) and 10 μm in (c, e–g). Experiments are repeated 3–5 times. Apical domain dynamics in the “sheet” (h) and “isolated” ectoderm (i). Each line represents apical domain size changes of an individual cell over 1.5–2 h. AC, AE, and “no change” cells (see Fig. 5 legend) are shown in red, blue, and green, respectively. Quantification was based on n = 66 cells from one Flag-Lmo7 (sheet) embryo and n = 20 cells from three Flag-Lmo7 (isolated) embryos. j Frequency (%) of AC, AE and “no change” cells in (h and i). These experiments were repeated 3–5 times. The Freeman–Halton extension of Fisher’s exact test. Two-sided. p = 0.00242.
	Fig. 7: Modulation of the apical domain by Shroom3. a Scheme of the experiment for G–I. Shroom3 (80 pg) and myrGFP (50 pg) RNA were co-injected into one animal blastomere of 16-cell stage embryos. Stage 10.5 embryos were fixed, stained with phalloidin and the animal pole ectoderm was imaged. Adapted from Xenopus illustrations © Natalya Zahn (2022), Xenbase (www.xenbase.org RRID:SCR_003280)75. b, c’ Shroom3 cells (yellow) with adjacent wild-type cells (blue) are shown. Rectangular areas in B and B’ are enlarged in (c) and (c’). Cell orientation is shown by green bars. d Apical domain size of Shroom3 cells and the adjacent wild-type cells. e Cell aspect ratios for Shroom3 cells and the adjacent wild-type cells. n = 114 (Shroom3 cells) and n = 105 (adjacent wild-type cells) from 5 embryos were analyzed for (c) and (e). The Kolmogorov-Smirnov test. Two-sided. p < 0.000000001 (d). p = 0.0266 (e). Experiments were repeated three times. f Model of neural plate bending. A subset of cells at neural plate hinge lines are selected to undergo PCP-dependent isotropic apical constriction (red arrows). Due to the geometry of the neural plate, the adjacent cells passively respond to the pulling forces exerted by their constricting neighbors by elongating along the anteroposterior axis (blue arrows). This cell alignment promotes neural plate folding and preserves tissue length. Scale bars are 50 μm in (b) and 20 μm in (c).
	Supplementary Figure 1. PCP-dependent cell heterogeneity in the anterior and posterior neural plate. (a-b’) Representative images of injected embryos. GFP RNA and vangl2 MO or control GFP RNA was injected into one dorsal blastomere of 4-cell stage embryos. Embryos at stage 15-16 were stained with phalloidin. The approximate locations of posterior and anterior NP images in Figs. 2a-b’ and S1c-c’ and are indicated in white boxes. The midline is indicated by white arrowheads. (c, c’) vangl2 knockdown increased apical domain size and decreased cell aspect ratio in the anterior neural plate. Scale bars are 100 µm in a, b and 50 µm in c. Experiments were repeated three times. (d) Comparison of apical domain size in vangl2 MO-injected and control cells. See Methods. n=283 cells for control. N=110 cells for vangl2 MO. (e) Cell aspect ratio for cells in c. (f) Apical domain size in the vangl2 MO-injected and control epidermis. Note that epidermis in vangl2 MO has smaller apical domains than control epidermis. (g) Cell aspect ratio in the vangl2 MO injected and control epidermal cells. n=209, for control cells from 6 embryos. n=246, for vangl2 MO containing cells from 9 embryos. Experiments were repeated three times. Statistical significance was assessed using the KolmogorovSmirnov test. p<0.0000000001 (d). p=0.000000939 (e). p=0.000002587 (f). p=0.0027 (g).
	Supplementary Figure 2. Quantification of bicellular junction length and phalloidin intensity in Vangl2-depleted and wild-type neuroepithelial cells. (a-b”) Quantification of bicellular junction (BJ) length and the average relative phalloidin intensity in the area bordering the anterior and the posterior regions of NP. Two different embryos are shown in a and b. The uninjected control side (blue in a, a”, b, b”). vangl2 MO-injected side (orange in a’, a”, b’, b”). Individual dots represent individual BJs. n=1121 cells for uninjected in a, a”. n=856 cells for vang2 MO in a’, a”. n=571 cells for uninjected in b, b”, n=307 cells for vangl2 MO in b’, b”. BJs were used for quantification to avoid the complexity of tricellular junction regulation
	Supplementary Figure 3. Effects of Vangl2 depletion on apical domain size. Embryos were injected at the 8-16 cell stage with vangl2 MO to achieve mosaic depletion. (a) Representative image of phalloidin-stained anterior neuroectoderm with mosaic vangl2 depleted cells (asterisks in a, green in a’). GFP was co-injected with vangl2 MO as a tracer. (b) Quantification of apical domain size in mosaic vangl2 MO cells (red) and the adjacent wild-type control cells (blue). n=162 for vangl2 MO cells and n=151 for adjacent wile-type cells from three embryos. som: somite, nt: notochord, ne: neuroectoderm, n-ne: non-neuroectoderm. The Kolmogorov-Smirnov test. p<0.0000000001. Scale bar: 20 µm.
	Supplementary Figure 4. Targeting of neuroectoderm by microinjection and the quantification of the body length in mosaic Vangl2 morphants. Representative cross-section of phalloidin-stained stage 15 embryo (dorsal region) that was injected in a dorsal animal blastomere at the 4-8-cell stage with 50 pg of GFP RNA as a lineage tracer. GFP fluorescence is imaged directly after cryosectioning. b and b’, separate channels, b”, merged channels. Experiments were repeated three times. Scale bar: 50 µm. (c) Quantification of the body length of mosaic vangl2 morphants at stages 16-17. n=11, for control GFP expressing embryos. n=11, for vangl2 MO+GFP embryos. The Student’s t-test. Two-sided. p=0.0089.
	Supplementary Figure 5. Effect of the external region on cell alignment in simulations. (a, b) Model tissue after relaxation (a) and distribution of angles between the AP axis (horizontal line) and cell elongation direction (b) at � = 2000 for �′! = 100 and �′" = 34. (c, d) Model tissue after relaxation (c) and distribution of angles between the AP axis and cell elongation direction (D) at � = 2000 for �′! = 100 and �′" = 100. (e, f) Model tissue after relaxation (e) and distribution of angles between the AP axis and cell elongation direction (f) at � = 20000 for �′! = 180 and �′" = 180. (g) Central length (along the AP axis) and width (perpendicular to the AP axis) of the model tissue, relative to those lengths at the start of the simulation, as a function of �′" at � = 2000, keeping �′! = 100.
	Supplementary Figure 6. Apically constricting ‘hinge cells’ contribute to neural plate cell morphology and orientation. (a) Zoom on the neural plate region of the vertex model initial condition with separate dorsolateral hinge regions. Blue border outlines the hinges, whereas a red border outlines the region between them. Constricting cells are shown in magenta for the hinges and in cyan for the remainder of the model posterior neural plate (tissue shown for �# = 0.5 and �$ = 0.2). (b) Model tissue from panel a after relaxation at � = 2000. Red lines show the direction of cell elongation. (c, d) Distribution of angles between the AP axis (horizontal line) and cell elongation direction for the model tissue in panel b for non-constricting cells in the hinges (c) and in the remainder of the neural plate (d).
	Supplementary Figure 7. Heterogeneous response of ectodermal cells to Lmo7. (a, b) Quantification of apical domain size dynamics in GFP-CAAX (a) or GFP-Lmo7 (b) embryos. GFP-CAAX or Lmo7 RNA was injected into four animal blastomeres of 4-8- cell embryos as shown in Fig. 5a. Each line represents apical domain size change of an individual cell over 4-5 hours. AC (red) and AE (blue) cells show more than 20% decrease or increase in their apical domain size, respectively. Cells with less than 20% changes (‘no change’) are shown in green. Grey lines indicate cells which had the apical domain smaller than 150 µm2 at the beginning of time-lapse imaging and remained small. Data for 71 GFP-CAAX cells are from 3 embryos. Data for 112 GFPLmo7 cells are from 4 embryos. (c) Percentage of AC, AE and ‘no change’ cells in a and b. Repeated at least three times. The Freeman-Halton extension of Fisher’s exact test. p= 2.081 E-16.
	Supplementary Figure 8. Cell segmentation and cell tracking in Lmo7-expressing and control ectoderm. Representative still images of stage 11-12 ectoderm expressing GFP-Lmo7 (a-a”’) and GFP-ZO1 (c-c”’) from time-lapse imaging. Segmented images of a-a”’ and c-c”’ are shown in b-b”’ and d-d”’, respectively. See Movie 2 and Movie 3. For details of segmentation and cell tracking, see Methods. Experiments were repeated at least three times. Scale bars are 40 µm.
	Supplementary Figure 9. Non-homogeneous distribution of lmo7l transcripts in late gastrulae. Whole mount in situ hybridization was carried out with lmo7l antisense and sense probes using stage 11.5 embryos. Representative embryo images are shown. (a,b) lmo7l antisense probe. Dorsal view (a). Vegetal view (b). (c) lmo7 sense probe. Dorsal view. A: anterior. P: posterior. Scale bar: 200 µm
	Supplementary Figure 10. Apical constriction of mosaically expressing Lmo7 cells. (a) Scheme of the experiment. myrBFP RNA (50 pg) was injected into two ventral blastomeres of 4-cell stage embryos. GFP-Lmo7 RNA (100 pg) was subsequently injected into one ventral blastomere of 16-cell stage embryos. The animal ectoderm was imaged at stage 11. Adapted from Xenopus illustrations © Natalya Zahn (2022), Xenbase (www.xenbase.org RRID:SCR_003280) 1. (b) Representative image of myrBFP and GFP-Lmo7 expressing embryos. (c-d”) Representative still images of GFPLmo7 (c-c”) and myrBFP (d-d”) cells from time-lapse imaging. (e, f) Quantification of apical domain size dynamics in myrBFP (e) and GFP-Lmo7 (f) cells. Each line represents apical domain size changes of individual cells over 2 hrs. n=20 cells for myrBFP only and n=39 for myrBFP+GFP-Lmo7 from three embryos. (g) Percentage of AC (red), AE (blue) and ‘no change’ (green) cells (See Fig. 5 legend) is shown in e and f. the Freeman-Halton extension of Fisher’s exact test. p= 0.000065. The data represents 3-5 independent experiments.
	Supplementary Figure 11. Shroom3 promotes apical domain heterogeneity. (a) Scheme of the experiment for b-e. myc-Shroom3 (40 pg) and myrRFP (50 pg) RNAs were co-injected into two opposing animal blastomeres of 4-8 cell stage embryos. Animal pole ectoderm was imaged at stage 11. Adapted from Xenopus illustrations © Natalya Zahn (2022), Xenbase (www.xenbase.org RRID:SCR_003280) 1. (b, b’) Representative segmented Shroom3-expressing ectoderm. Rectangular area in b is enlarged in b’. (c) Rose plot depicting cell orientation of Shroom3 cells in b and b’. n=161 cells from one embryo. (c, e) Quantification of apical domain size (d) and cell aspect ratio (e) of myrRFP cells and myrRFP+Shroom3 cells. n=332 cells for myrRFP and n=260 cells (myrRFP+Shroom3). Two embryos each. The Kolmogorov-Smirnov test. p<0.000000001 (d). p<0.000000001 (e). Experiments were repeated three times. Scale bars are 50 µm in b and 20 µm in b’.

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