Patterned expression of ion channel genes in mouse dorsal raphe nucleus determined with the Allen Mouse Brain Atlas

Brain Res. 2012 May 31;1457:1-12. doi: 10.1016/j.brainres.2012.03.066. Epub 2012 Apr 4.


The dorsal raphe nucleus (DR) is the major source of serotonin (5-hydroxytryptamine, 5-HT) in the forebrain and dysfunction of this midbrain structure is implicated in affective disorders. The DR is composed of several types of 5-HT and non-5-HT neurons and their excitable-membrane properties are heterogeneous and overlapping. In order to understand how these properties may be generated, we examined the mRNA expression patterns of voltage- and ligand-gated ion channels in the DR using the Allen Mouse Brain Atlas. Since DR cytoarchitecture is organized with respect to the midline, we sought to identify genes that were expressed in a pattern with respect to the midline, either enriched or depleted, rather than those that were homogenously expressed throughout the DR. Less than 10% of the screened genes for voltage-gated ion channels showed patterned expression within the DR. Identified genes included voltage-gated sodium channel beta subunits, potassium channels, P/Q-, N-type calcium channels, as well as the alpha2/delta-1 calcium channel. Several voltage-gated chloride channels were also identified, although these may function within intracellular compartments. Of the ligand-gated ion channels examined, 20% showed patterned expression. These consisted primarily of glutamate and GABA-A receptor subunits. The identified genes likely contribute to unique excitable properties of different groups of neurons in the DR and may include novel pharmacologic targets for affective disorders.

Publication types

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

MeSH terms

  • Anatomy, Artistic / methods
  • Animals
  • Atlases as Topic
  • Brain Mapping*
  • Ion Channels / classification
  • Ion Channels / genetics*
  • Ion Channels / metabolism
  • Mice
  • Neurons / metabolism*
  • RNA, Messenger / metabolism
  • Raphe Nuclei / cytology*
  • Raphe Nuclei / physiology*
  • Receptors, GABA / genetics
  • Receptors, GABA / metabolism
  • Receptors, Glutamate / genetics
  • Receptors, Glutamate / metabolism


  • Ion Channels
  • RNA, Messenger
  • Receptors, GABA
  • Receptors, Glutamate