Transcriptional profiling reveals strict boundaries between hippocampal subregions

J Comp Neurol. 2001 Dec 17;441(3):187-96. doi: 10.1002/cne.1406.


The hippocampus consists of distinct anatomic regions that have been demonstrated to have different biological functions. To explore the molecular differences between hippocampal subregions, we performed transcriptional profiling analysis by using DNA microarray technology. The cRNA derived from the CA1, CA3, and dentate gyrus regions of the hippocampus and from spinal cord was hybridized to Affymetrix high-density oligo arrays. This systematic approach revealed sets of genes that were expressed specifically in subregions of the hippocampus corresponding to predefined cytoarchitectural boundaries, which could be confirmed by in situ hybridization and Real Time quantitative polymerase chain reaction. The relative enrichment and absence of genes in the hippocampal subregions support the conclusion that there is a molecular basis for the previously defined anatomic subregions of the hippocampus and also reveal genes that could be important in defining the unique functions of the hippocampal subfields.

Publication types

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

MeSH terms

  • Animals
  • Computer Systems
  • Dentate Gyrus / physiology
  • Gene Expression
  • Gene Expression Profiling*
  • Hippocampus / anatomy & histology*
  • Hippocampus / physiology
  • In Situ Hybridization
  • Male
  • Mice
  • Oligonucleotide Array Sequence Analysis
  • Polymerase Chain Reaction
  • RNA, Complementary / genetics
  • Spinal Cord / physiology
  • Transcription, Genetic*


  • RNA, Complementary