PUBLICATION

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

Authors
Gehrig, J., Reischl, M., Kalmar, E., Ferg, M., Hadzhiev, Y., Zaucker, A., Song, C., Schindler, S., Liebel, U., and Muller, F.
ID
ZDB-PUB-091120-40
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
  • Transgenes
  • Animals
  • Enhancer Elements, Genetic*
  • Automation*
  • Zebrafish/genetics*
  • Promoter Regions, Genetic*
(all 6)
PubMed
19898487 Full text @ Nat. Methods
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.
Genes / Markers
Figures
No images available
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
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Citation
Gehrig, J., Reischl, M., Kalmar, E., Ferg, M., Hadzhiev, Y., Zaucker, A., Song, C., Schindler, S., Liebel, U., and Muller, F. (2009) Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos. Nature Methods. 6(12):911-916.