Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity

Cell Rep. 2017 Mar 28;18(13):3227-3241. doi: 10.1016/j.celrep.2017.03.004.


The hypothalamus is one of the most complex brain structures involved in homeostatic regulation. Defining cell composition and identifying cell-type-specific transcriptional features of the hypothalamus is essential for understanding its functions and related disorders. Here, we report single-cell RNA sequencing results of adult mouse hypothalamus, which defines 11 non-neuronal and 34 neuronal cell clusters with distinct transcriptional signatures. Analyses of cell-type-specific transcriptomes reveal gene expression dynamics underlying oligodendrocyte differentiation and tanycyte subtypes. Additionally, data analysis provides a comprehensive view of neuropeptide expression across hypothalamic neuronal subtypes and uncover Crabp1+ and Pax6+ neuronal populations in specific hypothalamic sub-regions. Furthermore, we found food deprivation exhibited differential transcriptional effects among the different neuronal subtypes, suggesting functional specification of various neuronal subtypes. Thus, the work provides a comprehensive transcriptional perspective of adult hypothalamus, which serves as a valuable resource for dissecting cell-type-specific functions of this complex brain region.

Keywords: cell heterogeneity; hypothalamus; neuron diversity; oligodendrocyte; single-cell RNA-seq; tanycyte.

Publication types

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

MeSH terms

  • Aging / genetics
  • Animals
  • Cell Differentiation / genetics
  • Ependymoglial Cells / cytology
  • Ependymoglial Cells / metabolism
  • Female
  • Food Deprivation
  • Gene Expression Regulation
  • Hypothalamus / cytology*
  • Hypothalamus / metabolism*
  • Male
  • Mice, Inbred C57BL
  • Neurons / cytology
  • Neurons / metabolism
  • Neuropeptides / metabolism
  • Oligodendroglia / cytology
  • Sequence Analysis, RNA / methods*
  • Single-Cell Analysis / methods*
  • Transcription, Genetic
  • Transcriptome / genetics


  • Neuropeptides