Transcriptional code and disease map for adult retinal cell types

Nat Neurosci. 2012 Jan 22;15(3):487-95, S1-2. doi: 10.1038/nn.3032.


Brain circuits are assembled from a large variety of morphologically and functionally diverse cell types. It is not known how the intermingled cell types of an individual adult brain region differ in their expressed genomes. Here we describe an atlas of cell type transcriptomes in one brain region, the mouse retina. We found that each adult cell type expressed a specific set of genes, including a unique set of transcription factors, forming a 'barcode' for cell identity. Cell type transcriptomes carried enough information to categorize cells into morphological classes and types. Several genes that were specifically expressed in particular retinal circuit elements, such as inhibitory neuron types, are associated with eye diseases. The resource described here allows gene expression to be compared across adult retinal cell types, experimenting with specific transcription factors to differentiate stem or somatic cells to retinal cell types, and predicting cellular targets of newly discovered disease-associated genes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cluster Analysis
  • Connexins / genetics
  • Eye Proteins / genetics
  • Eye Proteins / metabolism
  • Flow Cytometry
  • Gene Expression / genetics
  • Gene Library
  • Membrane Potentials / genetics
  • Mice
  • Mice, Inbred C57BL
  • Mice, Transgenic
  • Microarray Analysis / methods
  • Mutation / genetics
  • Nerve Tissue Proteins / genetics
  • Nerve Tissue Proteins / metabolism*
  • Neurons / classification*
  • Neurons / physiology*
  • Patch-Clamp Techniques
  • Potassium Channels, Voltage-Gated / genetics
  • Receptors, Kainic Acid / genetics
  • Retina / cytology*
  • Retinal Diseases / genetics*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*
  • Visual Pathways / metabolism


  • Connexins
  • Eye Proteins
  • Gja10 protein, mouse
  • Gluk2 kainate receptor
  • Nerve Tissue Proteins
  • Potassium Channels, Voltage-Gated
  • Receptors, Kainic Acid
  • Transcription Factors