A global genomic transcriptional code associated with CNS-expressed genes

Exp Cell Res. 2006 Oct 1;312(16):3108-19. doi: 10.1016/j.yexcr.2006.06.017. Epub 2006 Jun 21.


Highly conserved non-coding DNA regions (HCNR) occur frequently in vertebrate genomes, but their functional roles remain unclear. Here, we provide evidence that a large portion of HCNRs are enriched for binding sites for Sox, POU and Homeodomain transcription factors, and such HCNRs can act as cis-regulatory regions active in neural stem cells. Strikingly, these HCNRs are linked to several hundreds of genes expressed in the developing CNS and they may exert locus-wide regulatory effects on multiple genes flanking their genomic location. Moreover, these data imply a unifying transcriptional logic for a large set of CNS-expressed genes in which Sox and POU proteins act as generic promoters of transcription while Homeodomain proteins control the spatial expression of genes through active repression.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Binding Sites
  • Body Patterning / genetics
  • Cells, Cultured
  • Central Nervous System / metabolism*
  • Chick Embryo
  • Conserved Sequence / genetics*
  • Down-Regulation / genetics
  • Genome / genetics*
  • Genomics
  • High Mobility Group Proteins / metabolism
  • Homeodomain Proteins / genetics
  • Humans
  • Introns / genetics
  • Mice
  • Molecular Sequence Data
  • Neurons / metabolism
  • POU Domain Factors / metabolism
  • Regulatory Sequences, Nucleic Acid / genetics*
  • Tetraodontiformes / genetics
  • Transcription, Genetic / genetics*


  • High Mobility Group Proteins
  • Homeodomain Proteins
  • POU Domain Factors