During embryonic development, gene expression patterns are tightly controlled in space and time, which gives rise to the rich structures of multicellular organisms. As genes are activated or deactivated in a restricted spatiotemporal window, it has been hypothesized that the position and timing of gene activity encode embryonic body plans. To test this idea, various genetic tools have been developed, including tissue-specific promoters, recombinase systems and drug-inducible gene expression systems, which permit gene-specific perturbations to be introduced in developing embryos. For example, a drug-inducible Cre-recombinase driven by tissue-specific promoters is a standard tool for loss-of-function analysis in the field of developmental biology. Combinations of these technologies have allowed the artificial control of gene activity in developing tissues; however, spatiotemporal accuracy remains poor. These drawbacks hamper the dissection of highly dynamic events in embryos, such as oscillatory gene expression of transcription factors with 2–3 h periodicity.