ZFIN ID: ZDB-PUB-091120-40
Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos
Gehrig, J., Reischl, M., Kalmar, E., Ferg, M., Hadzhiev, Y., Zaucker, A., Song, C., Schindler, S., Liebel, U., and Muller, F.
Date: 2009
Source: Nature Methods   6(12): 911-916 (Journal)
Registered Authors: Ferg, Marco, Gehrig, Jochen, Hadzhiev, Yavor, Liebel, Urban, Müller, Ferenc, Schindler, Simone, Zaucker, Andreas
Keywords: none
MeSH Terms:
  • Animals
  • Automation*
  • Enhancer Elements, Genetic*
  • Promoter Regions, Genetic*
  • Transgenes
  • Zebrafish/genetics*
PubMed: 19898487 Full text @ Nat. Methods
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.