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Early embryo development requires maternal-to-zygotic transition, during which transcriptionally silent nuclei begin widespread gene expression during zygotic genome activation (ZGA). 1–3 ZGA is vital for early cell fating and germ-layer specification, 3,4 and ZGA timing is regulated by multiple mechanisms. 1–5 However, controversies remain about whether these mechanisms are interrelated and vary among species 6–10 and whether the timing of germ-layer-specific gene activation is temporally ordered. 11,12 In some embryonic models, widespread ZGA onset is spatiotemporally graded, 13,14 yet it is unclear whether the transcriptome follows this pattern. A major challenge in addressing these questions is to accurately measure the timing of each gene activation. Here, we metabolically label and identify the nascent transcriptome using 5-ethynyl uridine (5-EU) in Xenopus blastula embryos. We find that EU-RNA-seq outperforms total RNA-seq in detecting the ZGA transcriptome, which is dominated by transcription from maternal-zygotic genes, enabling improved ZGA timing determination. We uncover discrete spatiotemporal patterns for individual gene activation, a majority following a spatial pattern of ZGA that is correlated with a cell size gradient. 14 We further reveal that transcription necessitates a period of developmental progression and that ZGA can be precociously induced by cycloheximide, potentially through elongation of interphase. Finally, most ectodermal genes are activated earlier than endodermal genes, suggesting a temporal orchestration of germ-layer-specific genes, potentially linked to the spatially graded pattern of ZGA. Together, our study provides fundamental new insights into the composition and dynamics of the ZGA transcriptome, mechanisms regulating ZGA timing, and its role in the onset of early cell fating. [Display omitted] • Whole-embryo and regional EU-RNA-seq determines timing and spatial patterns of ZGA • Maternal-zygotic genes dominate transcriptional output during ZGA • Manipulation of translation and cell division reconciles regulatory mechanisms of ZGA • Timing of germ-layer-specific expression appears sequential in the blastula By profiling the nascent transcriptome during zygotic genome activation (ZGA) from whole Xenopus blastula and dissected subregions, Chen and Good unveil predominant transcription from maternal-zygotic genes and distinct spatial patterns, reconcile regulatory mechanisms of ZGA, and discover a link to sequential activation of germ-layer-specific genes. [ABSTRACT FROM AUTHOR]

Summary Cell division in all eukaryotes depends on function of the spindle, a microtubule-based structure that segregates chromosomes to generate daughter cells in mitosis or haploid gametes in meiosis. Spindle size adapts to changes in cell size and shape, which vary dramatically across species and within a multicellular organism, but the nature of scaling events and their underlying mechanisms are poorly understood. Cell size variations are most pronounced in early animal development, as egg diameters range from tens of microns up to millimeters across animal phyla, and decrease several orders of magnitude during rapid reductive divisions. During early embryogenesis in the model organisms X. laevis and C. elegans , the spindle scales with cell size [ 1, 2 ], a phenomenon regulated by molecules that modulate microtubule dynamics [ 3–6 ], as well as by limiting cytoplasmic volume [ 7, 8 ]. However, it is not known to what extent spindle scaling is conserved across organisms and among different cell types. Here we show that in a range of metazoan phyla, mitotic spindle length decreased with cell size across an ∼30-fold difference in zygote size. Maximum spindle length varied, but linear spindle scaling occurred similarly in all species once embryonic cell diameter reduced to 140 μm. In contrast, we find that the female meiotic spindle does not scale as closely to egg size, adopting a more uniform size across species that most likely reflects its specialized function. Our analysis reveals that spindle morphometrics change abruptly, within one cell cycle, at the transition from meiosis to mitosis in most animals. [ABSTRACT FROM AUTHOR]