Developmental 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, can activate their cognate promoter. 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 distinct elements cooperate to regulate transcription. In this work, we report that developmental enhancers – that regulate tissue-specific genes – and housekeeping enhancers rely on distinct modes of enhancer-enhancer cooperativity: while developmental enhancers are synergistic, housekeeping enhancers are additive (meaning that their combined activity mirrors the sum of their individual activities). Developmental enhancer synergy is promiscuous in our system and is not associated with specific combinations of transcription factors. However, developmental transcription factors globally contain higher fraction of intrinsically disordered domains, which might support such synergistic interactions. Overall design: The enhancer activity of three different pools of enhancer-enhancer pairs were measured using the STARR-Seq method in Drosophila S2 cells (with or without ecdysone) and OSC cells.