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Fig. 6 | Genome Biology

Fig. 6

From: Transcriptomic signatures shaped by cell proportions shed light on comparative developmental biology

Fig. 6

Cusp proportions estimated with a simple model recapitulate time ordering on first PCA axis and upper–lower heterochrony. a Cusp patterning in the lower molar, from one to six main cusps, which corresponds to its adult morphology. The timing and sequence of cusp addition reflects observations based on the analysis of in situ hybridization data using the cusp tip marker Fgf4 (see “Methods” and Fig. 5e). b Model of cusp proportion for the lower molar without maturation. The contribution of each cusp to a final proportion of “cusp tissue” (represented by the last stage) is modeled with a simple grid. In this model, the total contribution is achieved as soon as the cusp has been patterned. Time for cusp patterning is derived from bench data in (a). c Model of cusp proportion for the lower molar with maturation. In this model, the contribution of each cusp to a final proportion of “cusp tissue” increases following patterning. “Cusp tissue” expands at the same speed in all cusps. The average shade of gray of grid unit, at each developmental stage, gives a visual impression on the average degree of the expansion of the cusp tissue territory, from unpatterned cusp (white) to just-patterned cusp (light gray) and fully expanded cusp (black). We computed cusp expansion in each tooth based on this model, 0 corresponding to no cusp patterned (all white), and 1 to a complete expansion (all black). d Top: Relationship between the number of cusps, as shown in (a) and the coordinate on the first PCA axis (developmental stages are indicated). Dashed lines: glm model in which PCA1 explains cusp number (corresponding P value = 0.003). Bottom: Relationship between cusp proportions, estimated using model 2 (shown in (c)), and the coordinate on the first PCA axis (developmental stages are indicated). Dashed lines: glm model in which PCA1 explains cusp proportion (corresponding P value = 1e-12). e Lower/upper difference as estimated in terms of cusp number (as in (a)), cusp proportion estimated with model 1 in (b), cusp proportion estimated with model 2 in (c), and coordinates on PCA axis 1. Model (c) recapitulates best the heterochrony measured on PCA1. f Relationship between the proportion of “cusp tissue,” estimated using the maturation model in (c), and the proportion of “epithelial cusp tissue” estimated by deconvolutions. Six markers from bite-it (Bmp7, Edar, Fgf9, Cdkn1a, Wnt10b, Shh) were chosen, because their expression territory is large and therefore may well reflect the advancement of cusp expansion. g Proportions of “epithelial cusp tissue” estimated by deconvolution as in (f) for upper (black) and lower (gray) samples, at each developmental stage. RNA-seq samples of mesenchyme isolated from lower and upper molar germs [45] serve as negative controls (“mes”)

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