From Wiring to Firing: Collapse of embryonic identities and emergence of functional diversity during motor neuron maturation

Abstract

Neurons born in the embryo undergo a protracted process of maturation during which time they project axons to their specific targets, integrate into circuits, refine synapses, and acquire unique electrophysiological properties. The molecular strategies that individual neuron types deploy to complete this complex process remain poorly understood. In this work, we used single nucleus multiome sequencing (RNA-seq and ATAC-seq) to track the transition from specification to functional maturation in mouse skeletal motor neurons (SMNs). Our data show that individual SMNs undergo significant transcriptional changes as they mature, but more strikingly, we find that diversity within SMNs fluctuates dramatically as the functional needs of these cells change over time. At embryonic day E15.5, when motor axons are innervating their specific muscle targets, SMNs can be subdivided into dozens of transcriptional subclusters. These embryonic subclusters represent known motor columns and pools, which utilize column- and pool-specific genes to innervate unique muscle targets. About a week later, at postnatal day 3 (P3) many column- and pool-specific genes are downregulated or become broadly expressed and SMNs coalesce on the molecular level into a more homogenous state. These neurons then undergo a second round of diversification during the first two weeks of postnatal life (P3-P13), acquiring gene expression patterns that divide them into the functionally distinct alpha, gamma, and type3 subtypes found in adults. The fluctuations in SMN diversity go hand-in-hand with changes in accessible chromatin regions and transcription factor (TF) expression. Differential ATAC-seq peaks that define embryonic diversity are lost over time while new peaks that control expression in adult subtypes are gained. TFs that are known to regulate embryonic diversity are also downregulated over time, as a separate set of TFs that likely regulate adult subtype identities are upregulated. Our work uncovers a novel maturation trajectory for postmitotic neurons where extensive spatial diversity is first acquired in the embryo to ensure proper circuit wiring; this diversity is then lost as maturing neurons re-diversify into functional identities required for proper circuit firing in postnatal life. Therefore, all aspects of a neurons identity - its morphology, circuitry, and electrophysiologically - may not be fully described by its gene expression program at adulthood, but instead is a culmination of transcriptional events that occur throughout its specification and maturation trajectory as the functional needs of the cells evolve.