Enhancer cooperativity can compensate for loss of activity over large genomic distances

Enhancers are short DNA sequences that activate their target promoter from a distance; however, increasing the genomic distance between the enhancer and the promoter decreases expression levels. Many genes are controlled by combinations of multiple enhancers, yet the interaction and cooperation of individual enhancer elements are not well understood. Here, we developed a synthetic platform in mouse embryonic stem cells that allows building complex regulatory landscapes from the bottom up. We tested the system by integrating individual enhancers at different distances and confirmed that the strength of an enhancer contributes to how strongly it is affected by increased genomic distance. Furthermore, synergy between two enhancer elements depends on the distance at which the two elements are integrated: introducing a weak enhancer between a strong enhancer and the promoter strongly increases reporter gene expression, allowing enhancers to activate from increased genomic distances. [Display omitted] •Synthetic platform with multiple landing pads to build complex regulatory landscapes•Distance-dependent activation is specific to each enhancer•Position-dependent cooperation occurs between weak and strong enhancers•CTCF sites can lower enhancer-dependent activity but do not interfere with synergy Thomas, Feng, et al. introduce a synthetic platform that allows the building of complex regulatory landscapes. Integrating the same enhancer at different distances from a promoter uncovered that activation from a distance is an individual characteristic of each enhancer. Combining multiple enhancers revealed extensive cooperativity among individual elements.