Single-nucleus RNA sequencing of developing superior colliculus identifies neuronal diversity and candidate mediators of circuit assembly

Cell Rep. 2023 Sep 26;42(9):113037. doi: 10.1016/j.celrep.2023.113037. Epub 2023 Aug 24.


The superior colliculus (SC) is a sensorimotor structure in the midbrain that integrates input from multiple sensory modalities to initiate motor commands. It undergoes well-characterized steps of circuit assembly during development, rendering the mouse SC a popular model to study establishment of neural connectivity. Here we perform single-nucleus RNA-sequencing analysis of the mouse SC isolated at various developmental time points. Our study provides a transcriptomic landscape of the cell types that comprise the SC across murine development with particular emphasis on neuronal heterogeneity. We report a repertoire of genes differentially expressed across the different postnatal ages, many of which are known to regulate axon guidance and synapse formation. Using these data, we find that Pax7 expression is restricted to a subset of GABAergic neurons. Our data provide a valuable resource for interrogating the mechanisms of circuit development and identifying markers for manipulating specific SC neuronal populations and circuits.

Keywords: CP: Neuroscience; axon growth; axon guidance; axon regeneration; axon targeting; circuit assembly; retinal ganglion cells; single-cell RNA sequencing; single-nucleus RNA sequencing; superior colliculus.

Publication types

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

MeSH terms

  • Animals
  • GABAergic Neurons*
  • Gene Expression Profiling
  • Mice
  • Sequence Analysis, RNA
  • Superior Colliculi* / physiology
  • Transcriptome / genetics