Precise gene expression during embryonic development is crucial to generate the numerous cell types and tissues that build the animal body plan. This patterning is driven by developmental genes that are often expressed in a complex and conserved fashion. Gene expression patterns are instructed by regulatory sequences in the genome, the so-called enhancers. Enhancers act as switches in the genome that can modulate gene expression levels and turn a gene on or off. Given this important function for gene regulation, it is surprising that enhancers are often not conserved at the sequence level and act rather as seemingly variable entities during genome evolution. However, the mechanisms that allow this regulatory plasticity during evolution, but also maintenance of conserved genes expression during development are not well understood. Enhancers together with their target genes are spatially organized into conserved 3D chromatin structures, suggesting that spatial conformation within the nucleus is the missing link between less conserved enhancers and conserved target gene expression during animal development.
This project aims to understand the functional relationship between enhancers, conserved gene expression patterns and 3D chromatin structure during vertebrate development and evolution. As sequence conservation of enhancers is extremely limited, we applied innovative approaches to identify and systematically compare the functional response of enhancers and gene expression across different animal lineages. We identified functionally conserved enhancers and their target genes in the distantly related vertebrate model organisms, zebrafish (Danio rerio) and the western clawed frog (Xenopus tropicalis). Assessing the underlying 3D chromatin architecture, we deciphered the chromatin structures at orthologous genomic regions and enriched our understanding of how the cis-regulatory information of enhancers and genome structure translate into function. Although enhancers are not constrained by sequence conservation, they are constrained by conserved structural properties in the nucleus. Our data pave the way towards a deeper understanding of cis-regulatory mechanisms during development and evolution but also towards a better evaluation of regulatory mutations that are frequently detected in human congenital disease and cancer.
