High-multiplexity imaging reveals that temporal-to-spatial patterning of embryonic structures can involve active transformation of temporal information rather than direct mapping

Abstract

How spatial patterns arise during embryonic development is classically explained by the French Flag model, in which cells acquire positional identities by interpreting morphogen concentration thresholds. However, in many developmental systems, spatial patterns instead emerge progressively through temporal programs of gene expression that are transformed into spatial organization. For example, in the short-germ insect Tribolium castaneum, both periodic pair-rule gene expressions that generate body segments and non-periodic gap gene expressions that establish regional identities arise sequentially at the posterior and propagate anteriorly in waves across the developing embryo. Understanding how such temporal gene expression programs are translated into spatial patterns remains a major challenge. To address this problem, we developed a sequential multiplexed imaging strategy based on hybridization chain reaction (HCR), enabling visualization of up to ten anterior-posterior (AP) patterning genes within the same Tribolium embryo. By combining this approach with intronic-exonic labeling, we established a framework to infer gene expression dynamics and propagatory behavior during AP patterning. Using this framework, we show that gap gene expression domains remain dynamic and continue to propagate during tissue elongation, indicating that spatial patterns are actively remodeled throughout development. We then directly compared temporal gene activation at the posterior with the resulting spatial organization of pair-rule and gap genes. Surprisingly, while primary pair-rule genes preserve their temporal phase relationships in space, gap genes do not. Instead, the relative positioning of gap gene domains progressively changes as they move anteriorly, indicating that the final spatial organization of gap genes is actively reshaped during propagation rather than being directly inherited from the initial temporal sequence. The continued propagatory behavior of gap gene domains suggests that such reshaping could arise through differential propagation dynamics between genes and/or through progressive reconfiguration of underlying gene regulatory interactions during pattern formation. Together, these findings reveal that temporal-to-spatial patterning can involve active transformation of temporal information rather than a simple mapping from time into space.