A single-cell transcriptomic and anatomic atlas of mouse dorsal raphe Pet1 neurons

Elife. 2020 Jun 22:9:e55523. doi: 10.7554/eLife.55523.


Among the brainstem raphe nuclei, the dorsal raphe nucleus (DR) contains the greatest number of Pet1-lineage neurons, a predominantly serotonergic group distributed throughout DR subdomains. These neurons collectively regulate diverse physiology and behavior and are often therapeutically targeted to treat affective disorders. Characterizing Pet1 neuron molecular heterogeneity and relating it to anatomy is vital for understanding DR functional organization, with potential to inform therapeutic separability. Here we use high-throughput and DR subdomain-targeted single-cell transcriptomics and intersectional genetic tools to map molecular and anatomical diversity of DR-Pet1 neurons. We describe up to fourteen neuron subtypes, many showing biased cell body distributions across the DR. We further show that P2ry1-Pet1 DR neurons - the most molecularly distinct subtype - possess unique efferent projections and electrophysiological properties. These data complement and extend previous DR characterizations, combining intersectional genetics with multiple transcriptomic modalities to achieve fine-scale molecular and anatomic identification of Pet1 neuron subtypes.

Keywords: Pet1; dorsal raphe; genetics; genomics; mouse; neuronal diversity; neuroscience; serotonin; serotonin neurons; single cell RNA-seq.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Dorsal Raphe Nucleus / anatomy & histology*
  • Dorsal Raphe Nucleus / metabolism
  • Female
  • Gene Expression Profiling
  • Male
  • Mice / anatomy & histology*
  • Mice / genetics*
  • Mice, Inbred C57BL
  • Neurons* / metabolism
  • Single-Cell Analysis
  • Transcription Factors / metabolism
  • Transcriptome*


  • Fev protein, mouse
  • Transcription Factors

Associated data

  • GEO/GSE144980
  • GEO/GSE87758
  • GEO/GSE135132
  • GEO/GSE134163