Collapse of embryonic identities and emergence of functional diversity during motor neuron maturation

Post-mitotic neurons undergo a protracted maturation period as they extend axons to their targets, form synapses, and refine electrophysiological properties. We use temporal single-nucleus multiome sequencing to map molecular underpinnings of maturation in mouse skeletal motor neurons (SMNs). Our data show that SMNs undergo transcriptional changes as they mature, but more strikingly, we find that diversity within SMNs changes dramatically as they transition from axon targeting to forming functional circuits. Embryonic SMNs comprise dozens of transcriptional subclusters representing known motor columns and pools, which utilize specific transcriptional programs to innervate unique muscle targets. However, this transcriptional diversity is largely lost by early postnatal life, and SMNs re-diversify into adult alpha, gamma, and type3 identities, which innervate different fibers within each muscle to regulate movement. This work shows that transcriptional subtype diversity within a neuron type, and the underlying regulatory programs, can transform completely during maturation to accommodate changing functional needs.