Enhancer dynamics and cellular architecture in the human spinal cord

Studies of neurodegenerative disease mechanisms require an understanding of the cellular complexity of the healthy human spinal cord. Here, we report the spatial organization of RNA transcription and associated enhancer dynamics in the adult human spinal cord at single-cell and single-molecule resolution. We expand traditional multi-omic measurements and identify epigenetically poised and bivalent active transcriptional enhancer states that define cell-type specification. Simultaneous detection of chromatin accessibility and histone modifications in spinal cord nuclei reveals previously unobserved cell-type-specific masked enhancer activity, in which transcriptional activation is uncoupled from chromatin accessibility. Such masked enhancers define both stable cell-type identity and transitions between cells undergoing differentiation. We also define gene regulatory networks in glial cells that reorganize along the rostrocaudal axis, demonstrating anatomical differences in gene regulation. Finally, we identify the spatial organization of cells into distinct cellular networks and address the functional significance of this observation in the context of paracrine signaling. We conclude that cellular diversity in the spinal cord is best captured through the lens of enhancer state and intercellular interactions that drive transitions in cellular state.