Formation of tissue boundaries during zebrafish embryogenesis

Projektinformationen

DevBoundaries

ID Finanzhilfevereinbarung: 101031809

DOI

10.3030/101031809

Projekt abgeschlossen

EK-Unterschriftsdatum 7 April 2021

Startdatum 1 September 2022

Enddatum 31 August 2024

Finanziert unter

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Gesamtkosten

€ 191 149,44

EU-Beitrag

€ 191 149,44

Koordiniert durch

UNIVERSITAT BASEL
Switzerland

Periodic Reporting for period 1 - DevBoundaries (Formation of tissue boundaries during zebrafish embryogenesis)

Berichtszeitraum: 2022-09-01 bis 2024-08-31

Zusammenfassung vom Kontext und den Gesamtzielen des Projekts

Separation of different cell types by tissue boundaries is a hallmark of all multi-cellular organisms. During animal development, boundaries between tissues not only arise to achieve physical and functional segregation between neighbouring groups of embryonic cells, but also serve as signalling centres that control downstream patterning events . Changes in the location or integrity of tissue boundaries often lead to severe defects in development, and the underlying cellular behaviours are also profoundly linked to disease states like cancer formation and metastasis . However, the mechanisms underlying tissue boundary formation are poorly understood: Successful formation of tissue boundaries requires a tight coordination between acquisition of cell fate and regulation of cellular properties responsible for morphogenesis, such as cell division, motility, polarity, and adhesion . It has been challenging to analyse how gene expression, cell lineages and cell movement coordinate in space and time.

The overarching goal of this project is to probe the in vivo mechanisms of tissue boundary formation using the zebrafish embryonic shield region as a model system. I will generate a dynamic atlas characterizing the (1) cellular and (2) molecular basis of boundary formation, and (3) identify key regulators and their mechanism in cell differentiation and morphogenesis during boundary formation. This region has been of long-standing interest because it corresponds to the Mangold-Spemann organizer, but only now has it become tractable as a model system to study tissue boundary formation between multiple diverse cell types through the advent of technological revolutions in live imaging (Aim 1), spatial transcriptomics (Aim 2) and genome editing (Aim 3)

Arbeit, die ab Beginn des Projekts bis zum Ende des durch den Bericht erfassten Berichtszeitraums geleistet wurde, und die wichtigsten bis dahin erzielten Ergebnisse

Spatiotemporal patterns of gene expression underlie embryogenesis. Despite progress in single-cell genomics, mapping these patterns across whole embryos with comprehensive gene coverage and at high resolution has remained elusive. Here, we introduce a whole-embryo imaging platform using multiplexed error-robust fluorescent in-situ hybridization (weMERFISH). We quantified the expression of 495 genes in whole-mount zebrafish embryos at subcellular resolution. Integration with single-cell multiomics data generated an atlas detailing the expression of 25,872 genes and the accessibility of 294,954 chromatin regions, explorable with an online interface MERFISHEYES (beta version). We found that temporal gene expression aligns with cellular maturation and morphogenetic movements, diverse expression patterns correspond to composites of tissue-specific accessible elements, and changes in gene expression generate sharp boundaries during gastrulation. These results establish a novel approach for whole-organism spatial transcriptomics, provide a comprehensive spatially resolved atlas of gene expression and chromatin accessibility, and reveal the diversity, precision and emergence of embryonic patterns.

Fortschritte, die über den aktuellen Stand der Technik hinausgehen und voraussichtliche potenzielle Auswirkungen (einschließlich der bis dato erzielten sozioökonomischen Auswirkungen und weiter gefassten gesellschaftlichen Auswirkungen des Projekts)

Aim 1 and aim 2 are largely completed. Interesting genes will be identified for mutagenesis in Aim3

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