Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos
Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos
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DOI：
10.1038/nmeth.1396
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发表时间：
2009-12-01
期刊：
影响因子：
48
通讯作者：
Mueller, Ferenc
中科院分区：
文献类型：
--
作者：
Gehrig, Jochen;Reischl, Markus;Mueller, Ferenc
斑马鱼胚胎为各种表型筛选应用提供了高通量能力和脊椎动物复杂性的独特组合。然而，需要自动化成像技术来开发透明胚胎的潜力。在这里，我们报道了一个高通量管道，用于在斑马鱼胚胎中注册域特异性报告基因表达，目的是绘制顺式调控模块和核心启动子之间的相互作用。自动显微镜加上定制的胚胎检测和分割软件，基于数千个胚胎的图像，可以对202个增强子-启动子组合的报告子活性进行空间注册。启动子-增强子相互作用特异性的多样性强调了核心启动子序列在顺式调控相互作用中的重要性，并为转基因报告子研究提供了启动子资源。这里描述的技术也适用于基因、药物或毒理学筛选中荧光读数的空间分析。
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.