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
-
- Animals
- Automation*
- Enhancer Elements, Genetic*
- Promoter Regions, Genetic*
- Transgenes
- Zebrafish/genetics*
- PubMed
- 19898487 Full text @ Nat. Methods
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.
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
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping