Fig. 4: Gene modules defining cell fate choice and commitment along the differentiation trajectories.

a–i Analysis of the bifurcations of the differentiation tree representing cell fate selection between distinct neuronal cell lineages: I_c versus I_a/I_b/II (a–c), II versus I_a/I_b (d–f) and I_a versus I_b (g–i). a, d, g Scatter plots show average expression of lineage-specific modules in each cell along the trajectory. Early competing modules show gradual co-activation, followed by selective upregulation of one fate-specific module and downregulation of the alternative fate-specific module. Late modules show almost mutually exclusive expression within the two lineages after bifurcation reflecting commitment to either fate. Colors encode tree branches as in Fig. 2a. b, e, h Representative genes in each module; asterisks highlight TFs (see also Supplementary Data 7). c, f, i Average local correlations of early gene modules with branch-specific correlations, in cells with similar developmental pseudotime (in black on the trajectories); the difference between intra- and inter-module correlations is shown in the upper right corner of the correlation plots and would reflect the repulsion between modules. j Summary scheme of the cellular diversification of developing SGNs via distinct trajectories. The transcriptional regulators predicted to be involved in the unfolding of the different lineages are represented on the different trajectories and are derived from the analysis of Figs. 2–4. Genes in colored boxes indicate TFs of early modules from the bifurcation analysis and potentially driving specific cell fate choice (arrows). The arrow symbols after the genes indicate an upregulation or downregulation within a trajectory, while they indicate a high or low expression, respectively, in the final states (I_a, I_b, I_c and II states at the far-right end of the differentiation tree). Int., intermediate.