RNA FISH to Study Zygotic Genome Activation in Early Mouse Embryos

Characterizing the maternal-to-zygotic transition (MZT) is a central question in embryogenesis, and is critical for our understanding of early post-fertilization events in mammals. High-throughput RNA sequencing (RNA Seq) of mouse oocytes and early embryos has recently revealed that elaborate transcription patterns of genes and repeats are established post-fertilization. This occurs in the context of the gradually depleted maternal pool of RNA provided by the oocyte, which can confound the accurate analysis of the zygotic genome activation when the mRNA population is sequenced. In this context, and given the limited amounts of material available from embryos, particularly when studying mutants, as well as the cost of sequencing, an alternative, complementary single cell approach is RNA FISH. This approach can assay the expression of specific genes or genetic elements during preimplantation development, in particular during the MZT. Here, we describe how RNA FISH can be applied to visualize nascent transcription at specific genomic loci in embryos at different stages of preimplantation development and also discuss possible analytical methods of RNA FISH data.