Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus

Nat Neurosci. 2020 Mar;23(3):456-467. doi: 10.1038/s41593-020-0586-x. Epub 2020 Feb 17.


Mammalian circadian behaviors are orchestrated by the suprachiasmatic nucleus (SCN) in the ventral hypothalamus, but the number of SCN cell types and their functional roles remain unclear. We have used single-cell RNA-sequencing to identify the basic cell types in the mouse SCN and to characterize their circadian and light-induced gene expression patterns. We identified eight major cell types, with each type displaying a specific pattern of circadian gene expression. Five SCN neuronal subtypes, each with specific combinations of markers, differ in their spatial distribution, circadian rhythmicity and light responsiveness. Through a complete three-dimensional reconstruction of the mouse SCN at single-cell resolution, we obtained a standardized SCN atlas containing the spatial distribution of these subtypes and gene expression. Furthermore, we observed heterogeneous circadian gene expression between SCN neuron subtypes. Such a spatiotemporal pattern of gene regulation within the SCN may have an important function in the circadian pacemaker.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Atlases as Topic
  • Circadian Rhythm / physiology
  • Circadian Rhythm Signaling Peptides and Proteins / genetics
  • Gene Expression / physiology*
  • Gene Expression / radiation effects
  • Gene Expression Regulation / physiology
  • Genomics
  • Light
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Neurons / classification
  • Neurons / physiology*
  • Photic Stimulation
  • Single-Cell Analysis*
  • Suprachiasmatic Nucleus / anatomy & histology
  • Suprachiasmatic Nucleus / cytology
  • Suprachiasmatic Nucleus / physiology*


  • Circadian Rhythm Signaling Peptides and Proteins