Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity

Elife. 2019 Jun 21;8:e41266. doi: 10.7554/eLife.41266.


Developmental enhancers integrate graded concentrations of transcription factors (TFs) to create sharp gene expression boundaries. Here we examine the hunchback P2 (HbP2) enhancer which drives a sharp expression pattern in the Drosophila blastoderm embryo in response to the transcriptional activator Bicoid (Bcd). We systematically interrogate cis and trans factors that influence the shape and position of expression driven by HbP2, and find that the prevailing model, based on pairwise cooperative binding of Bcd to HbP2 is not adequate. We demonstrate that other proteins, such as pioneer factors, Mediator and histone modifiers influence the shape and position of the HbP2 expression pattern. Comparing our results to theory reveals how higher-order cooperativity and energy expenditure impact boundary location and sharpness. Our results emphasize that the bacterial view of transcription regulation, where pairwise interactions between regulatory proteins dominate, must be reexamined in animals, where multiple molecular mechanisms collaborate to shape the gene regulatory function.

Keywords: D. melanogaster; Drosophila; chromosomes; computational biology; enhancer; gene expression; systems biology; transcription.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • DNA-Binding Proteins / metabolism*
  • Drosophila Proteins / metabolism*
  • Drosophila*
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental*
  • Homeodomain Proteins / metabolism*
  • Models, Genetic
  • Trans-Activators / metabolism*
  • Transcription Factors / metabolism*
  • Transcription, Genetic


  • DNA-Binding Proteins
  • Drosophila Proteins
  • Homeodomain Proteins
  • Trans-Activators
  • Transcription Factors
  • bcd protein, Drosophila
  • hb protein, Drosophila

Associated data

  • figshare/10.6084/m9.figshare.8235491
  • figshare/10.6084/m9.figshare.8235587
  • figshare/10.6084/m9.figshare.8235614