Van Itallie ES , Field CM , Mitchison TJ , Kirschner MW .

R01 HD073104 NICHD NIH HHS , R35 GM131753 NIGMS NIH HHS

             Wnt signaling pathway
             cleavage furrow

	Graphical Abstract.
	Fig. 1. Wnt11b morphant embryos have larger blastopores at the end of gastrulation and posterior bends during the tailbud period. Embryos were injected with a total of 2.5 or 5 ​pmol of Wnt11b Mo into both blastomeres at the 2-cell stage. A. Injected and sibling control embryos were classified when sibling embryos were at Stage 12.5 into two different phenotypes: normal and open blastopores. All conditions are statistically significantly different from each other (Fisher-Freeman-Halton test with BF method for multiple hypotheses; ∗∗ ​= ​p « 0.001). B. The same injected and sibling control embryos from A were classified during the tailbud period into three different phenotypes: normal, posterior bend, ventral bend (not shown). All conditions are statistically significantly different from each other (Fisher-Freeman-Halton test with BF method for multiple hypotheses; ∗∗ ​= ​p « 0.001).
	Fig. 2. Wnt11 morphant embryos have larger blastopores at the end of gastrulation and shortened anterior-posterior axes during the tailbud period. Embryos were injected with 2.5 or 5 ​pmol total of Wnt11 Mo1, Wnt11 Mo2, or a 1:1 mixture of both total into both blastomeres at the 2-cell stage. A. Injected and sibling control embryos were classified when sibling embryos were at Stage 12.5 into four different phenotypes. All injections (except the standard control morpholino) resulted in statistically significantly different proportions of the phenotypes (Chi2 test; ∗∗ ​= ​p « 0.005). The phenotype for the 1:1 mixture of the two morpholinos is weaker than that of either of them alone. B. The anterior-posterior axis lengths of the embryos in A were quantified from still images during the tailbud period. The statistical significance of the difference in the median length between the injected and sibling embryos was tested with the Wilcoxon Rank test using the Bonferroni method to correct for multiple hypothesis testing. The percent reduction of median length is plotted with the marker filled in if the difference is statistically significant (p ​< ​0.05).
	Fig. 3. Wnt11 family morphants embryos have larger blastopores at the end of gastrulation than control morphants and siblings. For four biological replicates, embryos were injected with 10 ​pmol total of either Wnt11 family morpholinos or the control morpholino in both blastomeres at the 2-cell stage. The relative radius of the blastopore to the embryo was quantified using FIJI processing of still images taken when siblings embryos were at Stage 12.5. The difference in relative blastopore radius was statistically significant for all replicates. The sample mean and standard deviation are shown for all biological replicates and experimental conditions. Statistical significance of the difference between the experimental injections and standard control morpholino injection values for each clutch was determined with the student's t-test, and statistically significant perturbation have filled in markers. Multiple hypothesis testing was corrected for using the Bonferroni Method. Representative example blastopores from the different conditions are shown for two biological replicates.
	Fig. 4. Time lapse imaging reveals blastopore lip maturation, bottle cell internalization, and blastopore closure phenotypes associated with the Wnt11 family morphants. A. Kymographs were made from the time lapse images of the vegetal pole during gastrulation. The distance axis is the line across the vegetal pole that passed first through the center of the dorsal lip and then through the center of the eventual ventral blastopore lip. The kymographs were classified into “normal,” “mild perturbation,” and “severe perturbation.” Representative examples of the three classes are shown. In the kymographs for all three phenotypes, the dorsal bottle cells appear and move towards the center of the embryo resulting in an early lip (yellow arrowhead). In the “severe perturbation” kymographs, the movement towards the center is slower (compare i. and ii. to iii.). In the normal kymographs (i.), after the blastopore has moved further, the early lip matures and the color of the dorsal lip line changes to become lighter because the bottle cells have moved inside the embryo (dorsal green arrow). In the mild kymographs (ii.), this happens after transient reversal in the movement of the dorsal lip (dorsal green arrow). In the kymographs for all three phenotypes, the dark ventral lip line appears and also moves towards the center of the embryos (ventral green arrow). In the normal and mild kymographs, the dorsal and ventral lips continue to move closer to each other (pink arrowheads). By contrast, in the severe kymographs, the dorsal lip either reverses and moves away from the ventral line or stalls (dorsal pink arrowhead). B. Results from qualitatively scoring the kymographs from a total of five (Wnt11 family morphants) and six (sibling and control morphants) independent experiments. The Wnt11 family morphants are statistically significantly different than the control morphants and siblings (Fisher-Freeman-Halton test with BF method for multiple hypotheses; ∗∗ ​= ​p « 0.001).
	Fig. 5. Whole embryo fixed immunofluorescence against tubulin and anillin during the formation of the early dorsal blastopore lip. A. Sagittal view of a Stage 10.5 embryo shows membrane proximal anillin (red) localization to dorsal bottle cells and ventral pre-bottle cells. Tubulin (cyan) staining shows the cell outlines revealing bottle cells on the dorsal side of the embryo and elongated cells on the ventral side of the embryo. Schematic highlights the features of interest. Insets show the dorsal and ventral side of the forming blastopore lip at higher magnification. B. Horizontal optical plane views show distinct anillin staining patterns in different parts of the forming dorsal blastopore lip. Three colored planes show the relationship of the horizontal planes to the sagittal plane orientation in A, and the relationship of the horizontal planes to each other. Dorsal is left. Consistent with the sagittal view, anillin has a membrane proximal localization in elongated and apically constricted cells at the dorsal blastopore lip. In the younger, more vegetal region of the lip, the localization of anillin is punctate and in the older, more animal lip, the localization is contiguous and smooth. The z-axis span of the three planes is 90 m.
	Fig. 6. Formation of an early dorsal blastopore lip is perturbed in Wnt11 family morphants. The dorsal blastopore lips of Stage 10.5 embryos were scored using anillin (red) and tubulin (cyan) immunofluorescence into A) Lip, B) Attempted Lip, and C) No lip phenotypes. For the “attempted lip” phenotype, we see lines of anillin, but they are not as strong or contiguous as in the “lip” phenotype. The “no lip” phenotype only has spots of anillin. The results are summarized in D. Wnt11 family morphants are statistically significantly different from the sibling and control morphant embryos (∗∗ ​= ​p« 0.05).
	Fig. 7. Whole embryo fixed immunofluorescence against tubulin and anillin after dorsal lip maturation enables visualization of the extending archenteron. A. Sagittal view of a Stage 11 embryos shows membrane proximal anillin (red) staining along the mature dorsal and immature ventral blastopore lips. There is anillin staining along the animally extending archenteron. Schematics highlight the features of interest. Insets show the dorsal and ventral sides of the blastopore with higher magnification. B. Horizontal optical plane views show the differences in anillin staining and cell shape in different regions of the mature lip and archenteron. As in Fig. 6, the three colored planes show the relationship of the horizontal optical planes to the sagittal plane image in A and the relationship of the horizontal planes to each other. Dorsal is up. At the mature dorsal lip (most vegetal), the anillin staining is often in regions of packed columnar or square cells. In these regions, the anillin appears as a line apically. As the planes move animally, the anillin staining is more spotted, and the cells are various shapes that are neither square nor spherical. When the planes are compared, the span of the anillin arc gets shorter as the planes progress upward from vegetal to animal. The anillin is marking the upwardly extending archenteron. The z-axis span of the three planes is 75 m.
	Fig. 8. Archenteron extension in perturbed in Wnt11 family morphants. Archenteron extension in Stage 11 embryos was scored using anillin (red) and tubulin (cyan) immunofluorescence. The embryos were classified into A) Extension and B) No extension phenotypes (two different examples). By contrast to the “extension” phenotype, the “no extension” embryos do not have arcs of membrane proximal anillin staining in the more animal planes; only cytoplasmic anillin signal is seen in the zoom insets. The top “no extension” example shows evidence of a late forming “early lip.” However, no archenteron extension is seen. The lower example is more representative of what is seem in the Wnt11 family morphants. The z-axis span of the three planes is 85 m. The results of scoring sibling, control morphant, and Wnt11 family morphants are summarized in C. Wnt11 family morphants are statistically significantly different from the sibling and control morphant embryos (∗∗ ​= ​p« 0.05).
	Fig. 9. Comparison of external and internal phenotypes observed in sibling and Wnt11 family morphants. Top panel shows the vegetal view of the embryos with the externally visible phenotype, and the bottom panel shows cartoons of a cross sectional view with internal events indicated. A. During Stage 10.5, we observe the dorsal blastopore lip moving vegetally (upper panel, purple). This is due to epiboly (bottom panel, pink) and vegetal rotation (bottom panel, blue) that move the marginal zone mesendoderm deeper in the embryo (bottom panel, orange). B. During Stage 11, we observe the dorsal blastopore lip continuing to move vegetally (upper panel, purple), and the vegetal material moves animally and dorsally under the dorsal blastopore lip. The blastopore lip movement is now largely due to convergent extension (bottom panel, green). Continuing vegetal rotation movements (upper panel, blue) drive the vegetal material under the dorsal blastopore lip. The archenteron has extended and bottle cells remain at the animal extent. C. In the Wnt11 family morphants, we observe moderate vegetal movement of the dorsal blastopore lip (upper panel, small purple arrow) before and during Stage 10.5, and very little after Stage 11. The vegetal material does move animally and dorsally (upper panel, brown arrow) and overflows the dorsal blastopore lip. We also observed that the archenteron does not extend, and the bottle cells remain at the surface of the embryo. The dashed lines indicate processes that are likely affected by knockdown of the Wnt11 family ligands (convergent extension - green, vegetal rotation - blue).
	Supplemental Figure 1. The Xenopus laevis and Danio rerio (zebrafish) genomes both encode two Wnt11 family proteins. A. Xenopus laevis Wnt11 and Wnt11b are more similar in protein sequence identity to their Danio rerio homologs (77.6%, 69.2%) than they are to each other (63.3%). B. Multiple sequence alignment of the Xenopus laevis and Danio rerio Wnt11 family members shows that despite the closer homology between the Wnt11s and Wnt11b/Wnt11f2, there are regions of 100% similarity between all four proteins across the entire protein sequence. The first ~20 amino acids are a signal peptide that is cleaved in the forming of mature proteins. (Geneious Prime 2020; https://www.geneious.com)
	Supplemental Figure 2. Recently published transcriptomics and proteomics data shows that both Wnt11b and Wnt11 increase in mRNA and protein level during gastrulation. Developmental time series transcriptomics and proteomics data both include multiple time points just before and during the gastrulation period (orange boxes; Stages 9, 10, and 12 for transcriptomics and Stages 9 and 12 for proteomics). Note the much smaller y-axis scale for Wnt11 than Wnt11b for both mRNA and protein. There are two alloalleles of Wnt11: Wnt11.L and Wnt11.S. TPM counts for both Wnt11.L and Wnt11.S are combined. The peptides measured for Wnt11 do not allow us to distinguish between Wnt11.L and Wnt11.S.
	Supplemental Figure 3. Schematic explaining the modified RNase Protection Assay to assay for changes in ribosome protected mRNA fragments. Since translation blocking morpholinos are thought to decrease protein levels by perturbing translation initiation, the number of coding sequence bound ribosomes on the mRNA of interest should decrease with translation blocking morpholino treatment. To assay for the ribosome protected mRNA fragments of interest, first, stabilized polysomes are digested into monosomes with RNase. The resulting monosomes and the protected mRNA footprints are purified first by sedimentation and then by phenol-chloroform and spin-column methods. This part of the protocol is the same as the first part of the established protocol for ribosome profiling [1,2], but uses a lysis buffer very similar to one previously established for polysome profiling in Xenopus laevis [3]. Next, an RNase Protection Assay is performed with the purified RNA [4]. Briefly, the purified RNA is hybridized with radioactive probes that are synthesized antisense to a portion of the coding sequence of the mRNA of interest. More RNase is then added under conditions that promote digestion of single stranded RNA and not hybrids. The portions of the radioactive probes that are either hybridized to footprints or self-hybridized are protected from digestion. The resulting RNA is visualized after gel separation using autoradiography.
	Supplemental Figure 4. Validation that the modified RPA assay confirms expected decrease in ribosomes associated with targeted mRNA using the positive control beta-catenin (Ctnnb1) morpholino. Heasman et al. showed that injection of the Ctnnb1 morpholino resulted in reduced Ctnnb1 protein levels and no decrease in mRNA levels in Xenopus laevis [5]. Thus, we chose to use the Ctnnb1 morpholino, which is sold by GeneTools as the Xenopus laevis positive control, to validate our modified RPA assay. Sets of 15 embryos were either not injected (siblings or sibs), injected with a total of 2.5 picomoles of the standard negative control morpholino, or injected with 1.25 picomoles or 2.5 picomoles of Ctnnb1 Mo and collected at Stage 10. This was repeated for a total of three biological replicates. Samples were processed to isolate RNA as described in Supplemental Methods with 1250 U of RNase1. 10 ug of RNA was probed with the 5’ CDS Ctnnb1 probes. 15 ug of RNA was probed with the 3’ CDS Ctnnb1 probes. For both sets of probes the concentration of each .L and .S probe in final hybridization reaction was 7 uM and the gels were exposed for 24 hours. The region of the film designated by the white box was quantified using ImageJ. The mean signal relative to siblings for the three repeats and the standard deviation are reported for both probes and all the experimental conditions. The red asterisk signifies that some of the sample was lost and not run on the gel.
	Supplemental Figure 5. Modified RPA assay shows a Wnt11b morpholino dependent decrease in Wnt11b coding sequence fragments bound by ribosomes. Embryos were injected as described previously with different doses of the Wnt11b morpholino (10, 5, or 2.5 picomoles) or the standard negative control morpholino (10 picomoles). Embryos were collected at Stage 11 and Stage 13. Samples were processed to isolate RNA as described in Supplemental Methods with 2000 U RNase1. 10 ug of input RNA was probed with anti-sense probes against two different portions of the Wnt11b mRNA coding sequence. (For the probe self-hybridization controls and the synthesized positive control, yeast RNA was added such that the total RNA amount was 10 ug.) The positive control is a synthesized 30 nt sense RNA from the Wnt11b sequence that overlaps with the probes. The two doses are 10x10-18 moles and 100x10-18 moles. At the higher dose the positive control footprints are detected. The gel was exposed for 37 hours. The region of the film designated by the white box was quantified using ImageJ and the relative signal compared to the Stage 11 sibling samples was quantified for each lane (yellow numbers). All of the Wnt11b morpholino treated samples have less signal than the sibling and negative control morpholino injected samples.
	Supplemental Figure 6. The location of the targets of Wnt 11 Mo1 and Wnt11 Mo2 in the 5’UTR of Wnt11.S. (Geneious Prime 2020; https://www.geneious.com)
	Supplemental Figure 7. Additional control morpholino experiments provide further evidence for Wnt11 morpholino phenotype specificity. For three biological replicates, we injected both blastomeres of two-cell embryos with five picomoles total of one of four different morpholinos: Wnt11 Mo-2 (introduced in this paper), the Wnt11 morpholino introduced in Garriock et al. [6,7], five base pair mismatch control morpholino for Wnt11 Mo-2 that has the same GC content as Wnt11 Mo-2, and a sequence reverse mismatch control morpholino for Wnt11 Mo-2. As expected, both the Wnt11 Mo-2 and Garriock et al. Mo injected embryos are statistically significantly different than the un-injected sibling embryos (red asterisks, p << 0.005). The five base-pair mismatch control morpholino is not statistically significantly different than the un-injected embryos. The reverse control morpholino is statistically significantly different that the un-injected embryos. However, ninety percent of reverse control injected embryos have the normal Stage 12.5 phenotype compared to thirty-three and thirteen percent of the on-target designed morpholinos. We ascribe the phenotype from this morpholino to be due to toxicity because it is the only morpholino in this comparison with the severely open phenotype, even though it is a small number of embryos and does not repeat over all three experiments. The phenotype results for Wnt11 Mo-2 and Garriock et al. Mo are also statistically significantly different (black asterisks, p = 0.005). This is consistent with the fact that the Garriock et al. Mo targets both Wnt11.L and Wnt11.S whereas the Wnt11 Mo-2 (and Wnt11 Mo-1) only target Wnt11.S.
	Supplemental Figure 8. Wnt11 family morphants do not close their blastopores completely during neurulation. Images of sibling and Wnt11 family morphant embryos during neurulation from two experiments corresponding to Experiments 1 and 2 in Figure 3.
	Supplemental Figure 9. Strength of the ten picomole Wnt11 family morpholino phenotype cannot be attributed to toxicity from the total morpholino amount. For three biological replicates, we injected both blastomeres of two-cell embryos with either the five base-pair mismatch control morpholino, the Wnt11 family morpholinos, or a combination of the two. The total morpholino dose was between nine and ten picomoles. The embryos injected only with the high dose of the control morpholino are not statistically significantly different than the un-injected embryos. Embryos injected with either of the Wnt11 family containing morpholinos are statistically significantly different than the un-injected embryos (red asterisks), but the embryos injected with only five picomoles of the Wnt11 family morpholinos are also statistically significantly different than the embryos injected with ten picomoles of the Wnt11 family morpholinos. The majority of the embryos injected with less of the Wnt11 family morpholinos have the moderately closed phenotype compared to the larger dose of Wnt11 family morpholinos that have the severely open phenotype. We take these results as evidence that the strength of the ten picomole Wnt11 family phenotype is not the result of morpholino toxicity effects.
	Supplemental Figure 10. Custom imaging apparatus enables inverted high-resolution multiplexed imaging. More information, including files for making the custom apparatus components, can be found on GitHub. A. Custom embryo holders were laser cut to fit inside the chambers of an eight-chamber slide. Embryos are placed inside the wells and are stable when the microscope stage moves. B. The chamber slide is then inserted into a custom 3D printed slide holder. This slide holder is important because the flat surface of the chamber slide is too small to fit on the stage.
	Supplemental Figure 11. Quantitative analysis of time-lapse imaging of blastopore closure after dorsal lip maturation. (i) Wnt11 family morphant embryos have larger blastopores at the time when the dorsal lip matures in sibling morphants and less blastopore closure during the second half of gastrulation than sibling and control morphant embryos. Quantification of the decrease in normalized blastopore radius for the sibling, control morphant, and Wnt11 family morphants during gastrulation. Quantification starts when sibling embryos form a mature blastopore lip, as determined by inspection of movie frames. For control morphant and Wnt11 family morphant embryos, quantification begins at the expected time of lip maturation as determined by the mean of the matched sibling maturation times. Wnt11 family morphants have larger blastopore radii when quantification begins and show only limited blastopore closure afterwards. In addition to Wnt11 family morphant phenotypes, control morphant embryos have, on average, larger blastopores at the expected time of lip maturation than siblings. This is consistent with the expected delay of gastrulation caused by any morpholino injection. However, the blastopores of control morphants do close over a similar time period as the sibling embryos. (ii, iii) Still images for a sibling embryo and Wnt11 family morphant embryo at the beginning of quantification and one and two hours later. Progressive closure of the blastopore is seen in the sibling embryo. For the Wnt11 family embryo, the blastopore has formed by the expected lip maturation time, but the dorsal bottle cells are entirely visible. At the one hour timepoint the blastopore is slightly smaller, but the dorsal lip has still not matured. After two hours the dorsal vegetal material has extruded above the dorsal lip instead of being internalized.
	Supplemental Figure 12. Antibodies against anillin (red) and microtubules (cyan) have the expected localizations related to the cell cycle. Inset panels show examples of cells in interphase (anillin in the nucleus), metaphase (microtubules spindle), anaphase (microtubule spindles separating on either side of the anillin localized cleavage furrow), and the end of cytokinesis (anillin in the microtubule midbody structure).
	Supplemental Figure 13. Drawings and schematics showing two views of embryos at Stages 10.5 and 11. On the left, external vegetal views and on the right internal cross-section views. The schematics show the locations of the structures discussed in the main text; bottle cells, blastopore lips, and the archenteron. The red box shows the relationship of the vegetal view drawing to the cross-section schematic before a 90-degree upwards rotation. A. At Stage 10.5 the early blastopore lip has formed on the dorsal side of the embryo. The lip is dark in color because bottle cell apices are at the lip. There are elongated pre-bottle cells where the dorsal lip will form. B. At Stage 11 the dorsal blastopore is mature. The external color of the mature dorsal blastopore lip has changed because the bottle cells have left the blastopore lip and moved animally. The bottle cells are at the animal extent of the archenteron which is lined by the epithelial cells that were formally above and below the early blastopore lip. Bottle cells have formed on the ventral side of the embryo resulting in an early blastopore lip. Vegetal rotation (dorsal animal movement of the vegetal endoderm; blue arrows) is occurring internally as early as Stage 10, but it is clearly visible from movies of the exterior of the embryos at Stage 11. Cross-section drawings are based on drawings by P Hausen and M Riebesell [8].
	Supplemental Figure 14. Horizontal plane optical section images of whole-mount immunofluorescence against anillin (red) and NaK-ATPase (cyan). Staining against NaK-ATPase (an integral membrane protein) is seen at the membrane of many cells in the embryo. There is also moderately enhanced staining at the dorsal blastopore lip where membrane proximal anillin staining is also seen.
	Supplemental Figure 15. Wnt11 family morphant embryos at Stage 11.5 still show no evidence of archenteron extension. Whole-mount immunofluorescence against anillin (red) and tubulin (cyan) of matched sibling (A) and Wnt11 family morphant (B) embryos scored in Figure 8. This set developed the furthest before fixation. In the sibling embryo, archenteron morphogenesis has proceeded past the initial upward movement. Anillin staining can still be seen in the membrane proximal location (yellow arrows). We see no evidence of this in the morphant embryo. In both embryos, anillin staining can also be seen at the small part of the blastopore lip visible in this cross-section (blue arrows).
	Supplemental Figure 16. Anillin staining persists in the archenteron and blastopore through the end of gastrulation. Whole-mount immunofluorescence against anillin (red) and tubulin (cyan) of un-injected Stage 12.5 embryos. A. Two different optical sections of the same embryo (dorsal up, blastopore left). The expanding anterior archenteron is visible on the right. The higher magnification insets show that there is membrane proximal anillin staining (yellow arrows). B. Vegetal view of the blastopore. Anillin is enriched on the apical side of epithelial cells at the blastopore. C. Pre-fixation external view of an embryo at the same timepoint.
	Supplemental Figure 17. Horizontal plane optical section images of whole-mount immunofluorescence against anillin (red) and ERM family proteins (cyan). Staining against ERM family proteins is highly specific for cells at the blastopore, similar to anillin.

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