During embryonic development gene expression patterns progressively emerge as cell fates are determined and the embryo takes form. The emergence of these expression patterns is coincident with changes in the spatial distributions of transcription factors, chromatin remodelers, and transcriptional machinery within nuclei. The mechanisms that drive these changes in spatial distributions and their functional implications are not well understood. I will discuss the application of high-resolution light-sheet microscopy and single-molecule tracking in live pre-implantation mouse embryos and blastoderm stage Drosophila embryos to understand the emergence and functional implications of nuclear protein distribution patterns during development. I will show data and simulations on the molecular diffusion and binding kinetics that underlie the appearance of high-local concentrations of transcription factors, repressive complexes, and transcriptional machinery, and the functional impact of these high-local concentrations on transcription regulation during development. Finally, I will discuss how our new insights on how the molecular kinetics of regulatory nuclear proteins drive changes in their spatial distributions challenge current models of transcription regulation and nuclear organization.