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