The words of the regulatory code are arranged in a variable manner in highly conserved enhancers

Dev Biol. 2008 Jun 15;318(2):366-77. doi: 10.1016/j.ydbio.2008.03.034. Epub 2008 Apr 4.


The cis-regulatory regions of many developmental regulators and transcription factors are believed to be highly conserved in the genomes of vertebrate species, suggesting specific regulatory mechanisms for these gene classes. We functionally characterized five notochord enhancers, whose sequence is highly conserved, and systematically mutated two of them. Two subregions were identified to be essential for expression in the notochord of the zebrafish embryo. Synthetic enhancers containing the two essential regions in front of a TATA-box drive expression in the notochord while concatemerization of the subregions alone is not sufficient, indicating that the combination of the two sequence elements is required for notochord expression. Both regions are present in the five functionally characterized notochord enhancers. However, the position, the distance and relative orientation of the two sequence motifs can vary substantially within the enhancer sequences. This suggests that the regulatory grammar itself does not dictate the high evolutionary conservation between these orthologous cis-regulatory sequences. Rather, it represents a less well-conserved layer of sequence organization within these sequences.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Conserved Sequence
  • DNA Mutational Analysis
  • Enhancer Elements, Genetic
  • Forkhead Transcription Factors / metabolism
  • Gene Expression Regulation, Developmental
  • HMGB Proteins / genetics
  • Humans
  • Notochord / metabolism*
  • Promoter Regions, Genetic
  • Regulatory Elements, Transcriptional*
  • SOX9 Transcription Factor
  • Sequence Alignment
  • Zebrafish / genetics
  • Zebrafish / metabolism*
  • Zebrafish Proteins / genetics
  • Zebrafish Proteins / metabolism


  • Forkhead Transcription Factors
  • HMGB Proteins
  • SOX9 Transcription Factor
  • Sox9a protein, zebrafish
  • Zebrafish Proteins
  • foxa2 protein, zebrafish