The BEAF-32 insulator coordinates genome organization and function during the evolution of Drosophila species

Genome Res. 2012 Nov;22(11):2199-207. doi: 10.1101/gr.142125.112. Epub 2012 Aug 15.


Understanding the relationship between genome organization and expression is central to understanding genome function. Closely apposed genes in a head-to-head orientation share the same upstream region and are likely to be coregulated. Here we identify the Drosophila BEAF-32 insulator as a cis regulatory element separating close head-to-head genes with different transcription regulation modes. We then compare the binding landscapes of the BEAF-32 insulator protein in four different Drosophila genomes and highlight the evolutionarily conserved presence of this protein between close adjacent genes. We find that changes in binding of BEAF-32 to sites in the genome of different Drosophila species correlate with alterations in genome organization caused by DNA rearrangements or genome size expansion. The cross-talk between BEAF-32 genomic distribution and genome organization contributes to new gene-expression profiles, which in turn translate into specific and distinct phenotypes. The results suggest a mechanism for the establishment of differences in transcription patterns during evolution.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Binding Sites
  • DNA-Binding Proteins / genetics*
  • DNA-Binding Proteins / metabolism
  • Drosophila / genetics*
  • Drosophila Proteins / genetics*
  • Drosophila Proteins / metabolism
  • Evolution, Molecular*
  • Eye Proteins / genetics*
  • Eye Proteins / metabolism
  • Gene Rearrangement
  • Genome, Insect*
  • Insulator Elements
  • Phenotype
  • Species Specificity
  • Transcription, Genetic


  • BEAF-32 protein, Drosophila
  • DNA-Binding Proteins
  • Drosophila Proteins
  • Eye Proteins