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

作者：Gehrig Jochen; Reischl Markus; Kalmar Eva; Ferg Marco; Hadzhiev Yavor; Zaucker Andreas; Song Chengyi; Schindler Simone; Liebel Urban; Mueller Ferenc

来源：Nature Methods, 2009, 6(12): 911-U71.

DOI：10.1038/nmeth.1396

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.

• 出版日期2009-12