LivAdapt · Transcriptional adaptation during vertebrate development at the single-cell level

Transcriptional adaptation during vertebrate development at the single-cell level

Understanding how genes are expressed, and in particular how genetic information is translated into proteins, is a fundamental question in biology. During embryonic development, this regulation is especially critical: the precise timing, location, and quantity of protein production determines cell fate decisions, tissue patterning, and the correct formation of organs. Despite decades of progress in measuring gene expression at the RNA level, the dynamics of translation — the step at which messenger RNAs (mRNAs) are decoded by ribosomes to produce proteins — remained largely inaccessible in living vertebrate embryos. This gap represented a major blind spot in our understanding of how embryonic development is controlled at the molecular level. The central motivation of this project was to close this gap by developing, for the first time, a system capable of imaging translation live and in real time within an intact vertebrate embryo. The zebrafish (Danio rerio) was chosen as the model organism of choice: it is genetically tractable, produces optically transparent embryos amenable to high-resolution microscopy, and develops rapidly, making it uniquely suited to live imaging approaches. Prior to this work, live imaging of translation had been demonstrated in unicellular organisms and in cell culture systems, but never in a vertebrate embryo — leaving a fundamental question unanswered: how is protein synthesis regulated in space and time during the development of a complex animal? The project was initially designed around the phenomenon of Transcriptional Adaptation (TA), a form of genetic compensation whereby the mutation or loss of a gene triggers the upregulation of related genes, buffering the organism against genetic perturbation. TA is of broad biological and biomedical relevance, as it underlies many cases where gene knockout animals fail to display the expected phenotypes — a common and poorly understood phenomenon in genetics. The original objectives aimed to dissect TA at the levels of transcription, mRNA localisation, and translation, using live imaging approaches in zebrafish. However, when experimental evidence indicated that the TA response could not be reliably recapitulated under the conditions tested, the project was strategically reoriented — a decision that ultimately led to a stronger and broader scientific outcome. The reorientation focused on deploying the newly developed live translation imaging platform to study bmp2b, a gene encoding a key morphogen involved in dorsoventral patterning and organogenesis. BMP2 acts as a signalling gradient across the embryo, and while its distribution at the mRNA and protein levels had been described, nothing was known about how its translation is regulated in vivo. By applying the new imaging system to this biologically important gene, the project was able to reveal, for the first time, translational regulation of a morphogen gradient in a living vertebrate embryo — including control at the level of translation initiation and in the proportion of mRNAs actively engaged with ribosomes. Beyond this primary finding, the project produced a significant and unexpected discovery: evidence of non-canonical translation occurring in the zebrafish embryo. This refers to translation initiation through mechanisms that deviate from the classical cap-dependent pathway, a phenomenon previously associated with stress responses, viral infection, and cancer, but never before described in the context of normal vertebrate embryogenesis. This discovery opens an entirely new research avenue and reframes fundamental questions about how protein synthesis is controlled during development. The expected impact of this project operates on multiple levels. Technologically, it delivers a versatile live imaging platform — comprising multiple transgenic zebrafish lines with different fluorophores — that can be adopted by the broader zebrafish and vertebrate biology community to study the translation of any gene of interest in a living embryo. The spontaneous requests for tool access already received from two internationally leading research groups (the Pauli lab, Vienna, and the Raz lab, Münster) reflect the community-wide relevance of this resource. Scientifically, the results provide the first direct view of translational regulation during vertebrate embryogenesis, and uncover a previously unknown layer of translational control whose implications extend from developmental biology to disease.

Data: CORDIS, © European Union