The group is broadly interested in how changes in genome regulation contributed to animal evolution. To fill this fundamental gap, the group focuses on two distinct groups of organisms with informative phylogenetic positions: Choanoflagellates, the closest relatives of animals and cnidarians (jellyfish, corals, sea anemones) which are the sister group to the Bilateria, a group consisting of the majority of animal species including humans and all established animal model systems.

Investigating the role of chromatin during cell differentiation in choanoflagellates, the closest relatives of animals

In the first project, funded by an ERC starting grant, we aim to reconstruct the origin and evolution of cell type-specific gene expression by investigating the gene-regulatory mechanisms that drive life history transitions in choanoflagellates. Choanoflagellates are unicellular and the closest living relatives of animals. They are, therefore, extremely informative for dissecting the earliest stages of animal evolution. The primary species utilized in the lab is Salpingoeca rosetta. S. rosetta is a very useful and informative model for several reasons. Firstly, it has a complex life cycle with several different life stages which allow us to compare gene expression and chromatin in different cell types. S. rosetta also has a small genome (~55 Mb) and a chromosome level assembly is available. In addition, work in recent years has led to the development of transgenesis and genome editing in S. rosetta allowing us to perform functional experiments. Although S. rosetta is our primary model we are also interested in expanding our models to include new choanoflagellates and beyond…

Dissecting gene regulation in the sea anemone Nematostella vectensis

In a second project, we use the sea anemone Nematostella to investigate chromatin function during development and differentiation. Nematostella is part of the phylum cnidaria, the sister group to the majority of animals and thus in a pivotal phylogenetic position for understanding early animal evolution. We work to dissect chromatin regulation during development and cell differentiation, using the nervous system as a model. In doing so we aim to understand how the processes underlying developmental gene regulation in more “complex” animals first evolved while simultaneously addressing more general questions about the role of chromatin in development and differentiation.

Fig 3. The sea anemone Nematostella vectensis (top left). Transgenics labelling neurons (top middle) or stinging cells (tog right) can be FACS-sorted and used for different omics-based epigenomic analyses (bottom panel).

Experimental Approaches

We use a variety of approaches to address our questions. We use omics tools to probe transcription and chromatin, e.g., RNAseq, ATACseq, ChIPseq, and microscopy to visualize cells and their chromatin. We also use both transgenesis and CRISPR-Cas9 genome editing to both overexpress proteins for functional characterization and generate loss-of-function mutants to study gene function. We are also excited to expand our experimental toolbox as time goes by!