Alternatively spliced insertions in the paired domain restrict the DNA sequence specificity of Pax6 and Pax8

EMBO J. 1997 Nov 17;16(22):6793-803. doi: 10.1093/emboj/16.22.6793.


Transcription factors of the Pax family bind to their target genes via the paired domain which is known to be composed of two subdomains each recognizing distinct half-sites in adjacent major grooves of the DNA helix. We now demonstrate that the mammalian Pax8 gene gives rise, by alternative mRNA splicing, to a protein isoform containing an extra serine residue in the recognition alpha-helix 3 of the paired domain. This Pax8(S) protein does not interact with bipartite paired domain-binding sites, indicating that inactivation of the N-terminal DNA-binding motif severely restricts the sequence specificity of the paired domain. However, the Pax8(S) protein binds in vitro and in vivo to the 5aCON sequence which was previously identified as a high-affinity binding site for the Pax6(5a) splice variant carrying a 14-amino-acid insertion in the paired domain. The 5aCON sequence is shown to consist of four interdigitated 5' half-sites of the bipartite consensus sequence and is thus bound by four Pax8(S) molecules via the intact C-terminal DNA-binding motif of the paired domain. Together these data suggest that inactivation of the N-terminal region of the paired domain by alternative splicing is used in vivo to selectively target Pax transcription factors to gene regulatory regions containing highly specialized 5aCON-like sequences.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing*
  • Amino Acid Sequence
  • Animals
  • Binding Sites / genetics
  • Consensus Sequence
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • Eye Proteins
  • Genes, Reporter
  • Homeodomain Proteins*
  • Humans
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Proteins*
  • PAX6 Transcription Factor
  • PAX8 Transcription Factor
  • Paired Box Transcription Factors
  • Protein Conformation
  • Repressor Proteins
  • Serine / genetics
  • Trans-Activators / genetics
  • Trans-Activators / metabolism*
  • Transcription, Genetic


  • DNA-Binding Proteins
  • Eye Proteins
  • Homeodomain Proteins
  • Nuclear Proteins
  • PAX6 Transcription Factor
  • PAX6 protein, human
  • PAX8 Transcription Factor
  • PAX8 protein, human
  • Paired Box Transcription Factors
  • Pax6 protein, mouse
  • Pax8 protein, mouse
  • Repressor Proteins
  • Trans-Activators
  • Serine