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Early embryogenesis requires rapid division of pluripotent blastomeres, regulated genome activation, precise spatiotemporal signaling to pattern cell fate, and morphogenesis to shape primitive tissue architectures. The complexity of this process has inspired researchers to move beyond simple genetic perturbation into engineered devices and synthetic biology tools to permit temporal and spatial manipulation of the control systems guiding development. By precise alteration of embryo organization, it is now possible to advance beyond basic analytical strategies and directly test the sufficiency of models for developmental regulation. Separately, advances in micropatterning and embryoid culture have facilitated the bottom-up construction of complex embryo tissues allowing ex vivo systems to recapitulate even later stages of development. Embryos fertilized and grown ex vivo offer an excellent opportunity to exogenously perturb fundamental pathways governing embryogenesis. Here we review the technologies developed to thermally modulate the embryo cell cycle, and optically regulate morphogen and signaling pathways in space and time, specifically in the blastula embryo. Additionally, we highlight recent advances in cell patterning in two and three dimensions that have helped reveal the self-organizing properties and gene regulatory networks guiding early embryo organization. [ABSTRACT FROM AUTHOR]

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]