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

J Gehrig, M Reischl, E Kalmar, Ferenc Mueller, E Ferg, Yavor Hadzhiev, A Zaucker, C Song

    Research output: Contribution to journalArticle

    81 Citations (Scopus)


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


    Dive into the research topics of 'Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos'. Together they form a unique fingerprint.

    Cite this