Gene expression programs underlying spinal commissural neuron differentiation and axon growth across the midline

The shared transcriptional programs for axonal midline crossing and the divergent gene expression signatures that define C-neuron subtypes have remained largely elusive, as lineage-based methods for accessing these neurons are hindered by their extensive heterogeneity.

Here, we combined a genetic labeling strategy with single-cell RNA sequencing and complementary methods to study gene expression in developing C-neurons. We identify molecularly distinct C-neuron subtypes that reveal stratification of this neuronal class beyond progenitor identity and birthdate. We also uncover a large-scale gene expression switch that coincides with commissural axon growth across the midline and underlies differential axonal protein expression for guidance towards and away from the midline.