Visualizing Zygotic Genome Activation In Single Cells of Early Embryos

Early embryogenesis requires the maternal-to-zygotic transition (MZT) that necessitates the zygotic genome activation (ZGA). During ZGA, hundreds to thousands of genes are transcribed, which is essential for various processes in early embryo development, including maintaining embryonic survival, cell fate specification, and germ layer formation. One major challenge in studying ZGA has been to directly visualize ZGA in individual cells of early embryos. Here, we describe a method to directly visualize ZGA in single cells of early embryos by metabolic labeling of nascent transcripts using 5-ethynyl uridine (5-EU), followed by conjugating the nascent EU-RNAs with fluorophores via click chemistry and visualizing them in whole-mount embryos by confocal microscopy, using Xenopus laevis as a model. This method enabled us to track single-cell ZGA in whole-mount embryos and to reveal the heterogeneous onset of ZGA in space and time during early embryogenesis. It can be used in other embryonic systems or tissues to study gene transcription and genome regulation at the single-cell level.