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 early embryonic development will be found in uncovering molecular mechanisms of gene regulation and deciphering the regulatory circuitry underlying pluripotency, regional specification and patterning. These processes are essential for our understanding of congenital disease and cancer and for developing the potential of regenerative medicine.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)
Epigenetics of cell identity
We are using human and mouse stem cells and Xenopus embryos to increase our understanding of what defines cell identity and to probe the mechanisms involved in cellular transitions. We study these mechanisms using chromatin immunoprecipitation in combination with Next Generation deep sequencing (ChIP-seq), chromatin accessibility assays (ATAC-seq), single cell transcriptomic profiling 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.
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.
TBP family-insensitive network during early development (Gazdag et al., 2016)
Comparative approaches in the analysis of regulatory elements are quite powerful as it can provide information on the conservation of gene regulation as well as 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, can provide insight into mechanisms of genomic evolution.
Comparison of the gene-regulatory landscape of the two X.laevis hoxb4 homeologs at an early gastrula stage (Session et al., 2016)