Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos

Nat Methods. 2009 Dec;6(12):911-6. doi: 10.1038/nmeth.1396. Epub 2009 Nov 8.


Zebrafish embryos offer a unique combination of high-throughput capabilities and the complexity of the vertebrate animal for a variety of phenotypic screening applications. However, there is a need for automation of imaging technologies to exploit the potential of the transparent embryo. Here we report a high-throughput pipeline for registering domain-specific reporter expression in zebrafish embryos with the aim of mapping the interactions between cis-regulatory modules and core promoters. Automated microscopy coupled with custom-built embryo detection and segmentation software allowed the spatial registration of reporter activity for 202 enhancer-promoter combinations, based on images of thousands of embryos. The diversity of promoter-enhancer interaction specificities underscores the importance of the core promoter sequence in cis-regulatory interactions and provides a promoter resource for transgenic reporter studies. The technology described here is also suitable for the spatial analysis of fluorescence readouts in genetic, pharmaceutical or toxicological screens.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Automation*
  • Enhancer Elements, Genetic*
  • Promoter Regions, Genetic*
  • Transgenes
  • Zebrafish / genetics*