One of the most profound and intriguing questions in biology concerns the relationships between genetic diversity, morphology and function. This complex biology arises during embryonic development. The key to understanding development and differentiation will be found in uncovering molecular mechanisms of gene regulation and deciphering the regulatory circuitry underlying pluripotency, lineage commitment, regional specification and patterning. These processes in their relation to gene regulatory networks play out in development and evolution over short and long time scales respectively. Understanding these relationships is essential to combat congenital disease and cancer, and for developing the potential of regenerative medicine.

Epigenetics of cell identity and lineage commitment

We are using human and mouse stem cells, differentiating human cardiomyocytes, and vertebrate embryos to increase our understanding of what defines cell identity and to probe the mechanisms involved in cellular transitions. These important transitions include the exit of pluripotency and lineage commitment, patterned differentiation, multi-lineage interactions and cellular maturation. We study these mechanisms using single cell transcriptomic profiling, chromatin immunoprecipitation (ChIP-seq), chromatin accessibility assays (ATAC-seq), and mass spectrometry. In combination with gene perturbation experiments we aim to uncover how chromatin state contributes to transitions in cellular identity and potential and how this is regulated at the molecular level. One particular mechanism we are interested in involves the targeting of chromatin-modifying enzymes to specific genes in the genome. For example, the Polycomb PRC2 complex is a complex of proteins involved in repression of cell lineage identity genes. This complex prevents ectopic expression of master regulators outside their lineage.

Gene-regulatory networks

Based on the conceptually simple premise that transcription factors (TFs) bind their cognate motifs in regions with accessible chromatin, it is possible to construct gene-regulatory networks by integrating results from ATAC-seq, RNA-seq and underlying genomic sequence. We are using these networks to model gene regulatory dynamics, spatial gene regulation and developmental transitions. This approach can be applied to many experimental systems for which chromatin accessibility and transcriptome data can be obtained. Furthermore, in combination with single cell analyses of cell populations it can be inferred which regulatory factors play important roles in cellular transitions.

Equally interesting is how regulatory networks compare between species: Much can be learned from the deeply conserved master control switches of development and differentiation. Such comparative approaches in the analysis of regulatory elements can not only provide information on the conservation of gene regulation, but also on the extent to which gene regulation is rewired in different systems or species. For example, we have studied gene-regulatory elements in Xenopus laevis embryos, a long-standing model for vertebrate embryogenesis. Interestingly, the genome of Xenopus laevis has been subject to a whole genome duplication event, followed by selective loss of genes and regulatory regions. The analysis of the two subgenomes of X.laevis and the comparison with the closest diploid relative, X. tropicalis, provides insight into mechanisms of genomic evolution.

Model systems

*Mouse and human embryonic stem cells, iPS cells, and differentiating cardiomyocytes: Studies of epigenetic mechanisms, epigenetic stability, lineage commitment and differentiation
*X. tropicalis embryos: Studies of epigenetics and gene-regulatory networks of development

Chromatin state, as defined by chromosome topology, chromatin accessibility and epigenetic modifications, can act as a filter of genomic information influencing lineage commitment and epigenetic stability (Perino and Veenstra, 2016)

TBP family-insensitive network during early development (Gazdag et al., 2016)

Comparison of the gene-regulatory landscape of the two X.laevis hoxb4 homeologs at an early gastrula stage (Session et al., 2016)
Radboud University Faculty of Science Radboud Institute for Molecular Life Sciences Dept. Molecular Developmental Biology