GENE-TUNE · Genome Enhancer Network Exploration – Tuning expression through enhancer collaboration

Enhancers are the central regulators of temporal and spatial gene expression patterns, but how enhancers control their target genes from vast distances remains enigmatic. Individual enhancers do not work in isolation but are embedded into the genomic context, often together with other enhancer elements. The synergy arising from multiple enhancers can activate a target gene across distances that the individual elements cannot bridge. Therefore, the synergy of enhancers plays an essential role in gene regulation, but the nature of this synergy and how it affects gene expression is not understood. We have recently established a unique synthetic platform that allows for the efficient interrogation of individuals and combinations of enhancers from different distances to a target promoter. We aim to refine this platform by incorporating large-scale analysis to decode distance-dependent activation and enhancer synergy patterns. This rich dataset will form the foundation for our deep-learning approaches to determine the sequence constraints underlying enhancer synergy. Furthermore, we will map the 3D genome changes and examine the role of loop extrusion in synergistic gene activation. In addition, we will determine the activation kinetics at the promoter to reveal how multiple enhancers together control burst kinetics. Finally, we will examine how the addition of other regulatory elements, such as promoters or transposable elements, shape enhancer-promoter communication. We follow a bottom-up reductionist approach to study gene regulation: we will build gene regulatory landscapes and explore how enhancers navigate the genomic context to activate a target promoter. Ultimately, my mission is to unravel the mechanistic relationship among synergistic enhancers in activating distant target genes, complementing genomics and deep learning endeavours for a comprehensive understanding of gene regulation.