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

Research output: Contribution to journalArticle

Authors

  • J Gehrig
  • M Reischl
  • E Kalmar
  • E Ferg
  • A Zaucker
  • C Song

Abstract

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.

Details

Original languageEnglish
Pages (from-to)911-916
Number of pages6
JournalNature Methods
Volume6
Issue number12
Publication statusPublished - 1 Dec 2009