Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila

Abstract Genomic enhancers are key transcriptional regulators which, upon the binding of sequence-specific transcription factors, activate their cognate target promoters. Although enhancers have been extensively studied in isolation, a substantial number of genes have more than one simultaneously active enhancer, and it remains unclear how these cooperate to regulate transcription. Using Drosophila melanogaster S2 cells as a model, we assay the activities of more than a thousand individual enhancers and a million enhancer pairs towards housekeeping and developmental core promoters with STARR-seq. We report that housekeeping and developmental enhancers show distinct modes of enhancer-enhancer cooperativity: while housekeeping enhancers are additive such that their combined activity mirrors the sum of their individual activities, developmental enhancers are synergistic and follow a multiplicative model of cooperativity. This developmental enhancer synergy is promiscuous and neither depends on the enhancers’ endogenous genomic contexts nor on specific transcription factor motif signatures, but it saturates for the highest levels of enhancer activity. These results have important implications for our understanding of gene-regulation in complex multi-enhancer loci and genomically clustered housekeeping genes, providing a rationale for strong and mild transcriptional effects of mutations within enhancer regions.