Transcriptional and epigenetic mechanisms governing sensory and motor neuron specification

Abstract

During nervous system development, a limited pool of progenitors gives rise to a remarkable diversity of neuronal subtypes. The establishment of these distinct identities depends on tightly coordinated transcriptional and epigenetic programs, yet the mechanisms by which transcription factors and cis-regulatory elements cooperate to generate subtype-specific neuronal fates remain incompletely understood. To address this question, I performed two complementary studies in sensory and motor neurons. In the first part, I investigated the role of the transcription factor Isl2 in sensory neuron subtype differentiation. Loss of Isl2 led to a reduction of non-peptidergic sensory neurons, a concomitant expansion of peptidergic identity, and the emergence of hybrid cell populations co-expressing subtype-specific markers. These alterations were accompanied by changes in neuropeptide signaling and downstream defects in peripheral tissue homeostasis, indicating that precise transcription factor-dependent subtype specification is required for normal sensory neuron function. In the second part, I examined the cis-regulatory logic underlying motor neuron subtype diversification. By integrating single-cell transcriptomic and chromatin accessibility analyses, I defined subtype-specific cis-regulatory landscapes in developing spinal motor neurons and identified candidate enhancers associated with distinct motor neuron subtypes. Motif enrichment, footprinting, and functional analyses showed that combinatorial transcription factor binding contributes to subtype-specific regulatory programs. Focusing on the LMC lineage, I further identified and functionally tested candidate enhancers linked to Etv4, a key regulator of limb-innervating motor pools, demonstrating that subtype-resolved chromatin accessibility maps can be used to pinpoint biologically relevant enhancers and infer regulatory mechanisms controlling motor neuron diversification. Together, these findings show that neuronal subtype specification is shaped by both transcription factor function and enhancer-mediated regulatory logic. This work provides an integrated framework for understanding how transcriptional and cis-regulatory mechanisms cooperate to generate neuronal diversity during development.