Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo

Elife. 2015 Aug 12;4:e07956. doi: 10.7554/eLife.07956.

Abstract

Metazoan genes are embedded in a rich milieu of regulatory information that often includes multiple enhancers possessing overlapping activities. In this study, we employ quantitative live imaging methods to assess the function of pairs of primary and shadow enhancers in the regulation of key patterning genes-knirps, hunchback, and snail-in developing Drosophila embryos. The knirps enhancers exhibit additive, sometimes even super-additive activities, consistent with classical gene fusion studies. In contrast, the hunchback enhancers function sub-additively in anterior regions containing saturating levels of the Bicoid activator, but function additively in regions where there are diminishing levels of the Bicoid gradient. Strikingly sub-additive behavior is also observed for snail, whereby removal of the proximal enhancer causes a significant increase in gene expression. Quantitative modeling of enhancer-promoter interactions suggests that weakly active enhancers function additively while strong enhancers behave sub-additively due to competition with the target promoter.

Keywords: D. melanogaster; biophysics; developmental biology; quantitative imaging; stem cells; structural biology; transcription.

Publication types

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

MeSH terms

  • Animals
  • DNA-Binding Proteins / biosynthesis*
  • DNA-Binding Proteins / genetics
  • Drosophila / embryology*
  • Drosophila Proteins / biosynthesis*
  • Drosophila Proteins / genetics
  • Embryonic Development
  • Enhancer Elements, Genetic*
  • Evaluation Studies as Topic
  • Gene Expression Regulation, Developmental*
  • Optical Imaging
  • Promoter Regions, Genetic
  • Repressor Proteins / biosynthesis*
  • Repressor Proteins / genetics
  • Snail Family Transcription Factors
  • Transcription Factors / biosynthesis*
  • Transcription Factors / genetics

Substances

  • DNA-Binding Proteins
  • Drosophila Proteins
  • Repressor Proteins
  • Snail Family Transcription Factors
  • Transcription Factors
  • hb protein, Drosophila
  • kni protein, Drosophila
  • sna protein, Drosophila