Markéta Kaucká

January 04, 2024

Please refer to or contact Markéta for further information on the project.

List of publications of the group:

If you wish to apply for the position, please contact Markéta Kaucká by email providing a short motivational statement, names of two referees and a short CV (biosketch).

Cell type evolution

The evolution from unicellular to complex multicellular organisms required cells to diversify and acquire unique morphological and functional properties. Such cell diversification powered the emergence of novel functional and morphological traits and enabled series of evolutionary transitions that led to the enormous diversity and complexity of animals we know today. 

From an evolutionary standpoint, cell types are perceived as groups of cells that share morphological and functional features and possess specific gene expression profiles that have arisen through the evolution of a particular regulatory program. Such regulatory programs are assembled through the integration of existing molecular modules, incorporation of novel genes, and evolution of the cis-regulatory landscape. These mechanisms jointly contribute to the emergence of novel cell types and their further radiation.

The evolution of cell types has been conventionally studied by comparing the expression of a relatively small number of mostly conserved marker genes representing a cell type identity. However, a cell expresses thousands of genes, and analysing the evolution of its entire transcriptome provides more detailed insights into the cell type´s origin, and allows to dissect the homology between cell types and the evolutionary relationships

We established a novel approach to investigate the link between the evolution of protein-coding genes and the origin of cell types. We employ single-cell transcriptomics, which provides comprehensive information on the gene expression profile of cell types from any organism. We further use genomic phylostratigraphy, a method known as “gene birthdating”. The combination of the information-rich profile from single-cell transcriptomics together with the knowledge of gene origin enables us to investigate the evolutionary trends and origin of cell types´transcriptomes across the tree of life.

The candidate should have expertise in bioinformatics (R or Python) and a fundamental understanding of molecular biology. The single-cell RNA sequencing data for this project are available. The candidate is expected, to a minor extent, to participate in experimental work as well (for instance, data validation by in situ hybridisation [HCR] and confocal microscopy).

Recommended literature:

Arendt, D. et al. The origin and evolution of cell types. Nat Rev Genet 17, 744-757 (2016).

Zeng, H. K. What is a cell type and how to define it? Cell 185, 2739-2755 (2022).

Arendt, D. The evolution of cell types in animals: emerging principles from molecular studies. Nat Rev Genet 9, 868-882 (2008).

Tarashansky, A. J. et al. Mapping single-cell atlases throughout Metazoa unravels cell type evolution. Elife 10 (2021).

Domazet-Loso, T., Brajkovic, J. & Tautz, D. A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. Trends Genet 23, 533-539 (2007).

Domazet-Loso, T. & Tautz, D. A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature 468, 815-U107 (2010).

Achim, K. & Arendt, D. Structural evolution of cell types by step-wise assembly of cellular modules. Current Opinion in Genetics & Development 27, 102-108 (2014).

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