High Conservation of Transcription Factor Binding and Evidence for Combinatorial Regulation Across Six Drosophila Species

Nat Genet. 2011 May;43(5):414-20. doi: 10.1038/ng.808. Epub 2011 Apr 10.

Abstract

The binding of some transcription factors has been shown to diverge substantially between closely related species. Here we show that the binding of the developmental transcription factor Twist is highly conserved across six Drosophila species, revealing strong functional constraints at its enhancers. Conserved binding correlates with sequence motifs for Twist and its partners, permitting the de novo discovery of their combinatorial binding. It also includes over 10,000 low-occupancy sites near the detection limit, which tend to mark enhancers of later developmental stages. These results suggest that developmental enhancers can be highly evolutionarily constrained, presumably because of their complex combinatorial nature.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Animals
  • Base Sequence
  • Binding Sites / genetics
  • Conserved Sequence
  • DNA / genetics
  • DNA / metabolism
  • Drosophila / embryology
  • Drosophila / genetics*
  • Drosophila / metabolism*
  • Drosophila Proteins / chemistry
  • Drosophila Proteins / genetics*
  • Drosophila Proteins / metabolism*
  • Drosophila melanogaster / genetics
  • Drosophila melanogaster / growth & development
  • Drosophila melanogaster / metabolism
  • Enhancer Elements, Genetic
  • Molecular Sequence Data
  • Sequence Homology, Amino Acid
  • Snail Family Transcription Factors
  • Species Specificity
  • Transcription Factors / chemistry
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Twist-Related Protein 1 / chemistry
  • Twist-Related Protein 1 / genetics*
  • Twist-Related Protein 1 / metabolism*

Substances

  • Drosophila Proteins
  • Snail Family Transcription Factors
  • Transcription Factors
  • Twi protein, Drosophila
  • Twist-Related Protein 1
  • sna protein, Drosophila
  • DNA