To understand how the genome directs development, we need to know the cell-to-cell changes in genomic activity at individual loci and how changes are regulated. Advances in single-cell profiling provide a new ability to determine the regulatory configuration of individual cells genome-wide through profiling gene expression and chromatin accessibility. However, determining the connections between mother and daughter cells remains difficult. The invariant and known cell lineage of C. elegans solves this problem, making it possible with single-cell profiling to determine locus-specific activity in every cell from the zygote to the differentiated state. In Aim 1 we study the early events of genome quiescence, zygotic genome activation (ZGA), and lineage commitment by profiling all cells from the zygote to the 26-cell stage, and germ cells through their later ZGA. In Aim 2 we use the 20-cell intestine as a paradigm to study progression through a complete developmental trajectory. We will investigate mechanisms of key transitions and further study the relationship of activity patterns to genome 3D structure. In Aim 3, we focus on the impacts and regulation of active and PRC2/Polycomb chromatin domains. Our work will impact understanding of core principles of genome regulation relevant across animals. During animal development, the single celled embryo has the remarkable ability to give rise to all of the different cells and tissues of the organism, directed by instructions in the genome sequence. As new cells are produced, their identities are progressively defined by patterns of activation and repression of the genome, which generates correct gene expression programmes. We do not yet know this progressive series of events in any animal. Recent technical advances have made it possible to map which regions of the genome are active in individual cells (single-cell profiling). We will use this technology to study development in the nematode C. elegans, which has just 959 body cells. We will study the precise cell-to-cell changes in genome activity along development, revealing how specific information in the genome sequence is progressively read to produce correct cell types. Our findings will illuminate core principles of development relevant across animals.