Embryonic development is a study in contrasts between variation and stability. On the one hand, generation of complex spatial patterns proceeds with striking precision: the different tissues and organs are generally formed at the correct position, at the right time, and with a defined size. On the other hand, regulation should also not be too rigid, since embryos need to flexibly adjust to environmental perturbations and correct errors caused by noisy gene expression. We study the interplay between variation and stability by using the zebrafish as a model system. We aim to understand the stochastic mechanisms that underlie phenotypic diversity in isogenic populations, and to identify the error repair mechanisms that ensure robust pattern formation in the presence of perturbations.

Systematic investigation of variability and robustness during vertebrate organ formation requires development of novel approaches for spatially-resolved gene expression profiling and lineage analysis, ideally on the single cell level. We previously developed a method for spatially-resolved transcriptomics called ‘tomo-seq’, and we recently established a strategy for massively-parallel single cell lineage analysis based on CRISPR/Cas9 technology. We use these approaches in combination with light microscopy and tools from zebrafish developmental biology. Our work combines biophysics, systems biology and developmental biology.

cartoon methods
Experimental methods. A. Tomo-seq method for spatially resolved transcriptomics (Junker et al., Cell, 2014). Three individual zebrafish embryos are sectioned along the three main body axes. By sequencing the mRNA from each slice we obtain three spatially-resolved datasets in 1D. We use computational approaches to then reconstruct the original 3D image. B. Massively parallel single-cell lineage tracing (Spanjaard et al., Nature Biotechnology, 2018). With the help of CRISPR/Cas9 technology, we introduce molecular barcodes into single cells at around the 1000 cell stage. Barcoded cells are indicated as circles with different colors. Barcodes are transmitted to the progeny of the labeled cells, and can be read out by single-cell RNA-seq of dissociated fish.



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