Transcriptional Landscape of the Dorsal Raphe Nucleus

Abstract

The dorsal raphe nucleus (DRN) is a major source of neuromodulators in the brain that has been implicated in a wide range of neurological and psychiatric disorders. However, little is known about how dysfunction of DRN neurons causes behavioral deficits. The DRN is the largest of the serotonergic nuclei housing approximately a third of all serotonergic neurons (5-HT neurons). Although it is further comprised of many other cell types that interact with 5-HT neurons, complexities at the molecular level have impeded efforts to identify and isolate specific subsets of DRN cells to study their unique contributions to the regulation of behavior. Here we used single-cell RNA sequencing (scRNA-seq) to assess the cell type composition of the mouse DRN. We identified at least 17 major cell types and 18 distinct neuron subtypes in the DRN, of which 5 are subtypes of 5-HT neurons. We showed that these subtypes differ in their anatomical distribution and axonal projections, and described a specific 5-HT neuron subtype that is poised to regulate both motor and cognitive functions via modulation of basal ganglia circuits. This study provides a resource that lays out the cellular organization of the DRN to guide the design of molecular and genetic strategies for functional studies of the DRN and its subcircuits. Additionally, we used scRNA-seq to characterize transcriptional changes that occur in the DRN during viral infection. Here we describe the changes in cell type composition resulting from infiltration by leukocytes, as well as both global and cell type-specific changes in gene expression mediating the antiviral inflammatory response. These results provide further insights into distinct functions performed by various non-neuronal cell types to mediate different facets of the immunological response. Collectively, this dissertation provides an updated molecular and anatomical map of the DRN, which will serve as a framework for the molecular and genetic dissection of its diverse functions. Finally, we outline a roadmap for the continued investigation of the distinct functions of each DRN cell type and their interactions in mediating state-dependent changes in behavior.