biostudies-literatureLoubiere VEuropean Molecular Biology Organization (EMBO)Human Frontier Science Program (HFSP)8584https://www.ebi.ac.uk/biostudies/studies/S-EPMC11450171biostudies-literatureUnknown15(1)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 about a million enhancer pairs toward 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 Nature communicationsDevelopmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila.PMC11450171790-2019LT000926/2020Loubiere Vde Almeida BPStark APagani MfalseDevelopmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila.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 about a million enhancer pairs toward 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 2024-01-01T00:00:00Z2024 Oct2025-04-18T13:06:27.487Z2025-04-06T22:37:51.258ZS-EPMC114501713936290210.1038/s41467-024-52921-2