Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos.
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.
Gehrig
Jochen
J
Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, Eggenstein-Leopoldshafen, Germany.
Reischl
Markus
M
Kalmár
Eva
E
Ferg
Marco
M
Hadzhiev
Yavor
Y
Zaucker
Andreas
A
Song
Chengyi
C
Schindler
Simone
S
Liebel
Urban
U
Müller
Ferenc
F
D000818:Animals; D001331:Automation; D004742:Enhancer Elements, Genetic; D011401:Promoter Regions, Genetic; D019076:Transgenes; D015027:Zebrafish / Q000235:genetics*